1
|
Schumacher AE, Kyu HH, Aali A, Abbafati C, Abbas J, Abbasgholizadeh R, Abbasi MA, Abbasian M, Abd ElHafeez S, Abdelmasseh M, Abd-Elsalam S, Abdelwahab A, Abdollahi M, Abdoun M, Abdullahi A, Abdurehman AM, Abebe M, Abedi A, Abedi A, Abegaz TM, Abeldaño Zuñiga RA, Abhilash ES, Abiodun OO, Aboagye RG, Abolhassani H, Abouzid M, Abreu LG, Abrha WA, Abrigo MRM, Abtahi D, Abu Rumeileh S, Abu-Rmeileh NME, Aburuz S, Abu-Zaid A, Acuna JM, Adair T, Addo IY, Adebayo OM, Adegboye OA, Adekanmbi V, Aden B, Adepoju AV, Adetunji CO, Adeyeoluwa TE, Adeyomoye OI, Adha R, Adibi A, Adikusuma W, Adnani QES, Adra S, Afework A, Afolabi AA, Afraz A, Afyouni S, Afzal S, Agasthi P, Aghamiri S, Agodi A, Agyemang-Duah W, Ahinkorah BO, Ahmad A, Ahmad D, Ahmad F, Ahmad MM, Ahmad T, Ahmadi K, Ahmadzade AM, Ahmadzade M, Ahmed A, Ahmed H, Ahmed LA, Ahmed MB, Ahmed SA, Ajami M, Aji B, Ajumobi O, Akalu GT, Akara EM, Akinosoglou K, Akkala S, Akyirem S, Al Hamad H, Al Hasan SM, Al Homsi A, Al Qadire M, Ala M, Aladelusi TO, AL-Ahdal TMA, Alalalmeh SO, Al-Aly Z, Alam K, Alam M, Alam Z, Al-amer RM, Alanezi FM, Alanzi TM, Albashtawy M, AlBataineh MT, Aldridge RW, Alemi S, Al-Eyadhy A, Al-Gheethi AAS, Alhabib KF, Alhalaiqa FAN, Al-Hanawi MK, Ali A, Ali A, Ali BA, Ali H, Ali MU, Ali R, Ali SSS, Ali Z, Alian Samakkhah S, Alicandro G, Alif SM, Aligol M, Alimi R, Aliyi AA, Al-Jumaily A, Aljunid SM, Almahmeed W, Al-Marwani S, Al-Maweri SAA, Almazan JU, Al-Mekhlafi HM, Almidani O, Alomari MA, Alonso N, Alqahtani JS, Alqutaibi AY, Al-Sabah SK, Altaf A, Al-Tawfiq JA, Altirkawi KA, Alvi FJ, Alwafi H, Al-Worafi YM, Aly H, Alzoubi KH, Amare AT, Ameyaw EK, Amhare AF, Amin TT, Amindarolzarbi A, Aminian Dehkordi J, Amiri S, Amu H, Amugsi DA, Amzat J, Ancuceanu R, Anderlini D, Andrade PP, Andrei CL, Andrei T, Angappan D, Anil A, Anjum A, Antony CM, Antriyandarti E, Anuoluwa IA, Anwar SL, Anyasodor AE, Appiah SCY, Aqeel M, Arabloo J, Arabzadeh Bahri R, Arab-Zozani M, Arafat M, Araújo AM, Aravkin AY, Aremu A, Ariffin H, Aripov T, Armocida B, Arooj M, Artamonov AA, Artanti KD, Arulappan J, Aruleba IT, Aruleba RT, Arumugam A, Asaad M, Asgary S, Ashemo MY, Ashraf M, Asika MO, Athari SS, Atout MMW, Atreya A, Attia S, Aujayeb A, Avan A, Awotidebe AW, Ayala Quintanilla BP, Ayanore MA, Ayele GM, Ayuso-Mateos JL, Ayyoubzadeh SM, Azadnajafabad S, Azhar GS, Aziz S, Azzam AY, Babashahi M, Babu AS, Badar M, Badawi A, Badiye AD, Baghdadi S, Bagheri N, Bagherieh S, Bah S, Bahadorikhalili S, Bai J, Bai R, Baker JL, Bakkannavar SM, Bako AT, Balakrishnan S, Balogun SA, Baltatu OC, Bam K, Banach M, Bandyopadhyay S, Banik B, Banik PC, Bansal H, Barati S, Barchitta M, Bardhan M, Barker-Collo SL, Barone-Adesi F, Barqawi HJ, Barr RD, Barrero LH, Basharat Z, Bashir AIJ, Bashiru HA, Baskaran P, Basnyat B, Bassat Q, Basso JD, Basu S, Batra K, Batra R, Baune BT, Bayati M, Bayileyegn NS, Beaney T, Bedi N, Begum T, Behboudi E, Behnoush AH, Beiranvand M, Bejarano Ramirez DF, Belgaumi UI, Bell ML, Bello AK, Bello MB, Bello OO, Belo L, Beloukas A, Bendak S, Bennett DA, Bensenor IM, Benzian H, Berezvai Z, Berman AE, Bermudez ANC, Bettencourt PJG, Beyene HB, Beyene KA, Bhagat DS, Bhagavathula AS, Bhala N, Bhalla A, Bhandari D, Bhardwaj N, Bhardwaj P, Bhardwaj PV, Bhargava A, Bhaskar S, Bhat V, Bhatti GK, Bhatti JS, Bhatti MS, Bhatti R, Bhutta ZA, Bikbov B, Binmadi N, Bintoro BS, Biondi A, Bisignano C, Bisulli F, Biswas A, Biswas RK, Bitaraf S, Bjørge T, Bleyer A, Boampong MS, Bodolica V, Bodunrin AO, Bolarinwa OA, Bonakdar Hashemi M, Bonny A, Bora K, Bora Basara B, Borodo SB, Borschmann R, Botero Carvajal A, Bouaoud S, Boudalia S, Boyko EJ, Bragazzi NL, Braithwaite D, Brenner H, Britton G, Browne AJ, Brunoni AR, Bulamu NB, Bulto LN, Buonsenso D, Burkart K, Burns RA, Burugina Nagaraja S, Busse R, Bustanji Y, Butt ZA, Caetano dos Santos FL, Cai T, Calina D, Cámera LA, Campos LA, Campos-Nonato IR, Cao C, Cardenas CA, Cárdenas R, Carr S, Carreras G, Carrero JJ, Carugno A, Carvalho F, Carvalho M, Castaldelli-Maia JM, Castañeda-Orjuela CA, Castelpietra G, Catalá-López F, Catapano AL, Cattaruzza MS, Caye A, Cederroth CR, Cembranel F, Cenderadewi M, Cercy KM, Cerin E, Cevik M, Chacón-Uscamaita PRU, Chahine Y, Chakraborty C, Chan JSK, Chang CK, Charalampous P, Charan J, Chattu VK, Chatzimavridou-Grigoriadou V, Chavula MP, Cheema HA, Chen AT, Chen H, Chen L, Chen MX, Chen S, Cherbuin N, Chew DS, Chi G, Chirinos-Caceres JL, Chitheer A, Cho SMJ, Cho WCS, Chong B, Chopra H, Choudhary R, Chowdhury R, Chu DT, Chukwu IS, Chung E, Chung E, Chung SC, Cini KI, Clark CCT, Coberly K, Columbus A, Comfort H, Conde J, Conti S, Cortesi PA, Costa VM, Cousin E, Cowden RG, Criqui MH, Cruz-Martins N, Culbreth GT, Cullen P, Cunningham M, da Silva e Silva D, Dadana S, Dadras O, Dai Z, Dalal K, Dalli LL, Damiani G, D'Amico E, Daneshvar S, Darwesh AM, Das JK, Das S, Dash NR, Dashti M, Dávila-Cervantes CA, Davis Weaver N, Davletov K, De Leo D, Debele AT, Degenhardt L, Dehbandi R, Deitesfeld L, Delgado-Enciso I, Delgado-Ortiz L, Demant D, Demessa BH, Demetriades AK, Deng X, Denova-Gutiérrez E, Deribe K, Dervenis N, Des Jarlais DC, Desai HD, Desai R, Deuba K, Devanbu VGC, Dey S, Dhali A, Dhama K, Dhimal ML, Dhimal M, Dhingra S, Dias da Silva D, Diaz D, Dima A, Ding DD, Dirac MA, Dixit A, Dixit SG, Do TC, Do THP, do Prado CB, Dodangeh M, Dokova KG, Dolecek C, Dorsey ER, dos Santos WM, Doshi R, Doshmangir L, Douiri A, Dowou RK, Driscoll TR, Dsouza HL, Dube J, Dumith SC, Dunachie SJ, Duncan BB, Duraes AR, Duraisamy S, Durojaiye OC, Dutta S, Dzianach PA, Dziedzic AM, Ebenezer O, Eboreime E, Ebrahimi A, Echieh CP, Ed-Dra A, Edinur HA, Edvardsson D, Edvardsson K, Efendi D, Efendi F, Eghdami S, Eikemo TA, Eini E, Ekholuenetale M, Ekpor E, Ekundayo TC, El Arab RA, El Morsi DAW, El Sayed Zaki M, El Tantawi M, Elbarazi I, Elemam NM, Elgar FJ, Elgendy IY, ElGohary GMT, Elhabashy HR, Elhadi M, Elmeligy OAA, Elshaer M, Elsohaby I, Emami Zeydi A, Emamverdi M, Emeto TI, Engelbert Bain L, Erkhembayar R, Eshetie TC, Eskandarieh S, Espinosa-Montero J, Estep K, Etaee F, Eze UA, Fabin N, Fadaka AO, Fagbamigbe AF, Fahimi S, Falzone L, Farinha CSES, Faris MEM, Farjoud Kouhanjani M, Faro A, Farrokhpour H, Fatehizadeh A, Fattahi H, Fauk NK, Fazeli P, Feigin VL, Fekadu G, Fereshtehnejad SM, Feroze AH, Ferrante D, Ferrara P, Ferreira N, Fetensa G, Filip I, Fischer F, Flavel J, Flaxman AD, Flor LS, Florin BT, Folayan MO, Foley KM, Fomenkov AA, Force LM, Fornari C, Foroutan B, Foschi M, Francis KL, Franklin RC, Freitas A, Friedman J, Friedman SD, Fukumoto T, Fuller JE, Gaal PA, Gadanya MA, Gaihre S, Gaipov A, Gakidou E, Galali Y, Galehdar N, Gallus S, Gan Q, Gandhi AP, Ganesan B, Garg J, Gau SY, Gautam P, Gautam RK, Gazzelloni F, Gebregergis MW, Gebrehiwot M, Gebremariam TB, Gerema U, Getachew ME, Getachew T, Gething PW, Ghafourifard M, Ghahramani S, Ghailan KY, Ghajar A, Ghanbarnia MJ, Ghasemi M, Ghasemzadeh A, Ghassemi F, Ghazy RM, Ghimire S, Gholamian A, Gholamrezanezhad A, Ghorbani Vajargah P, Ghozali G, Ghozy S, Ghuge AD, Gialluisi A, Gibson RM, Gil AU, Gill PS, Gill TK, Gillum RF, Ginindza TG, Girmay A, Glasbey JC, Gnedovskaya EV, Göbölös L, Goel A, Goldust M, Golechha M, Goleij P, Golestanfar A, Golinelli D, Gona PN, Goudarzi H, Goudarzian AH, Goyal A, Greenhalgh S, Grivna M, Guarducci G, Gubari MIM, Gudeta MD, Guha A, Guicciardi S, Gunawardane DA, Gunturu S, Guo C, Gupta AK, Gupta B, Gupta IR, Gupta RD, Gupta S, Gupta VB, Gupta VK, Gupta VK, Gutiérrez RA, Habibzadeh F, Habibzadeh P, Hachinski V, Haddadi M, Haddadi R, Haep N, Hajj Ali A, Halboub ES, Halim SA, Hall BJ, Haller S, Halwani R, Hamadeh RR, Hamagharib Abdullah K, Hamidi S, Hamiduzzaman M, Hammoud A, Hanifi N, Hankey GJ, Hannan MA, Haque MN, Harapan H, Haro JM, Hasaballah AI, Hasan F, Hasan I, Hasan MT, Hasani H, Hasanian M, Hasanpour- Dehkordi A, Hassan AM, Hassan A, Hassanian-Moghaddam H, Hassanipour S, Haubold J, Havmoeller RJ, Hay SI, Hbid Y, Hebert JJ, Hegazi OE, Heidari G, Heidari M, Heidari-Foroozan M, Heidari-Soureshjani R, Helfer B, Herteliu C, Hesami H, Hettiarachchi D, Heyi DZ, Hezam K, Hiraike Y, Hoffman HJ, Holla R, Horita N, Hossain MB, Hossain MM, Hossain S, Hosseini MS, Hosseinzadeh H, Hosseinzadeh M, Hostiuc M, Hostiuc S, Hsairi M, Hsieh VCR, Hu C, Huang J, Huda MN, Hugo FN, Hultström M, Hussain J, Hussain S, Hussein NR, Huy LD, Huynh HH, Hwang BF, Ibitoye SE, Idowu OO, Ijo D, Ikuta KS, Ilaghi M, Ilesanmi OS, Ilic IM, Ilic MD, Immurana M, Inbaraj LR, Iradukunda A, Iravanpour F, Iregbu KC, Islam MR, Islam MM, Islam SMS, Islami F, Ismail NE, Isola G, Iwagami M, Iwu CCD, Iwu-Jaja CJ, Iyer M, J LM, Jaafari J, Jacob L, Jacobsen KH, Jadidi-Niaragh F, Jafarinia M, Jaggi K, Jahankhani K, Jahanmehr N, Jahrami H, Jain A, Jain N, Jairoun AA, Jakovljevic M, Jalilzadeh Yengejeh R, Jamshidi E, Jani CT, Janko MM, Jatau AI, Jayapal SK, Jayaram S, Jeganathan J, Jema AT, Jemere DM, Jeong W, Jha AK, Jha RP, Ji JS, Jiang H, Jin Y, Jin Y, Johnson O, Jomehzadeh N, Jones DP, Joo T, Joseph A, Joseph N, Joshua CE, Jozwiak JJ, Jürisson M, Kaambwa B, Kabir A, Kabir H, Kabir Z, Kadashetti V, Kahe F, Kakodkar PV, Kalani R, Kalankesh LR, Kaliyadan F, Kalra S, Kamath A, Kamireddy A, Kanagasabai T, Kandel H, Kanmiki EW, Kanmodi KK, Kantar RS, Kapoor N, Karajizadeh M, Karami Matin B, Karanth SD, Karaye IM, Karim A, Karimi H, Karimi SE, Karimi Behnagh A, Karkhah S, Karna AK, Kashoo FZ, Kasraei H, Kassaw NA, Kassebaum NJ, Kassel MB, Katamreddy A, Katikireddi SV, Katoto PDMC, Kauppila JH, Kaur N, Kaydi N, Kayibanda JF, Kayode GA, Kazemi F, Kazemian S, Kazeminia S, Keikavoosi-Arani L, Keller C, Kempen JH, Kerr JA, Kesse-Guyot E, Keykhaei M, Khadembashiri MM, Khadembashiri MA, Khafaie MA, Khajuria H, Khalafi M, Khalaji A, Khalid N, Khalil IA, Khamesipour F, Khan A, Khan G, Khan I, Khan IA, Khan M, Khan MAB, Khan T, Khan suheb MZ, Khanmohammadi S, Khatab K, Khatami F, Khavandegar A, Khayat Kashani HR, Kheirallah KA, Khidri FF, Khodadoust E, Khormali M, Khosrowjerdi M, Khubchandani J, Khusun H, Kifle ZD, Kim G, Kim J, Kimokoti RW, Kinzel KE, Kiross GT, Kisa A, Kisa S, Kiss JB, Kivimäki M, Klu D, Knudsen AKS, Kolahi AA, Kompani F, Koren G, Kosen S, Kostev K, Kotnis AL, Koul PA, Koulmane Laxminarayana SL, Koyanagi A, Kravchenko MA, Krishan K, Krishna H, Krishnamoorthy V, Krishnamoorthy Y, Krohn KJ, Kuate Defo B, Kubeisy CM, Kucuk Bicer B, Kuddus MA, Kuddus M, Kuitunen I, Kujan O, Kulimbet M, Kulkarni V, Kumar A, Kumar H, Kumar N, Kumar R, Kumar S, Kumari M, Kurmanova A, Kurmi OP, Kusnali A, Kusuma D, Kutluk T, Kuttikkattu A, Kyei EF, Kyriopoulos I, La Vecchia C, Ladan MA, Laflamme L, Lahariya C, Lahmar A, Lai DTC, Laksono T, Lal DK, Lalloo R, Lallukka T, Lám J, Lamnisos D, Lan T, Lanfranchi F, Langguth B, Lansingh VC, Laplante-Lévesque A, Larijani B, Larsson AO, Lasrado S, Latief K, Latif M, Latifinaibin K, Lauriola P, Le LKD, Le NHH, Le TTT, Le TDT, Lee M, Lee PH, Lee SW, Lee SW, Lee WC, Lee YH, Legesse SM, Leigh J, Lenzi J, Leong E, Lerango TL, Li MC, Li W, Li X, Li Y, Li Z, Libra M, Ligade VS, Likaka ATM, Lim LL, Lin RT, Lin S, Lioutas VA, Listl S, Liu J, Liu S, Liu X, Livingstone KM, Llanaj E, Lo CH, Loreche AM, Lorenzovici L, Lotfi M, Lotfizadeh M, Lozano R, Lubinda J, Lucchetti G, Lugo A, Lunevicius R, Ma J, Ma S, Ma ZF, Mabrok M, Machairas N, Machoy M, Madsen C, Magaña Gómez JA, Maghazachi AA, Maharaj SB, Maharjan P, Mahjoub S, Mahmoud MA, Mahmoudi E, Mahmoudi M, Makram OM, Malagón-Rojas JN, Malakan Rad E, Malekzadeh R, Malhotra AK, Malhotra K, Malik AA, Malik I, Malinga LA, Malta DC, Mamun AA, Manla Y, Mannan F, Mansoori Y, Mansour A, Mansouri V, Mansournia MA, Mantovani LG, Marasini BP, Marateb HR, Maravilla JC, Marconi AM, Mardi P, Marino M, Marjani A, Marrugo Arnedo CA, Martinez-Guerra BA, Martinez-Piedra R, Martins CA, Martins-Melo FR, Martorell M, Marx W, Maryam S, Marzo RR, Mate KKV, Matei CN, Mathioudakis AG, Maude RJ, Maugeri A, May EA, Mayeli M, Mazaheri M, Mazidi M, Mazzotti A, McAlinden C, McGrath JJ, McKee M, McKowen ALW, McLaughlin SA, McPhail MA, McPhail SM, Mechili EA, Mediratta RP, Meena JK, Mehari M, Mehlman ML, Mehra R, Mehrabani-Zeinabad K, Mehrabi Nasab E, Mehrotra R, Mekonnen MM, Mendoza W, Menezes RG, Mengesha EW, Mensah GA, Mensah LG, Mentis AFA, Meo SA, Meretoja A, Meretoja TJ, Mersha AM, Mesfin BA, Mestrovic T, Mhlanga A, Mhlanga L, Mi T, Micha G, Michalek IM, Miller TR, Mindlin SN, Minelli G, Minh LHN, Mini GK, Minja NW, Mirdamadi N, Mirghafourvand M, Mirica A, Mirinezhad SK, Mirmosayyeb O, Mirutse MK, Mirza-Aghazadeh-Attari M, Mirzaei M, Misgana T, Misra S, Mitchell PB, Mithra P, Mittal C, Mittal M, Moazen B, Mohamed AI, Mohamed J, Mohamed MFH, Mohamed NS, Mohammad-Alizadeh-Charandabi S, Mohammadi S, Mohammadian-Hafshejani A, Mohammad-pour S, Mohammadshahi M, Mohammed M, Mohammed S, Mohammed S, Mojiri-forushani H, Mokdad AH, Mokhtarzadehazar P, Momenzadeh K, Momtazmanesh S, Monasta L, Moni MA, Montazeri F, Moodi Ghalibaf A, Moradi M, Moradi Y, Moradi-Lakeh M, Moradinazar M, Moradpour F, Moraga P, Morawska L, Moreira RS, Morovatdar N, Morrison SD, Morze J, Mosaddeghi Heris R, Mosser JF, Mossialos E, Mostafavi H, Mostofinejad A, Mougin V, Mouodi S, Mousavi P, Mousavi SE, Mousavi Khaneghah A, Mpundu-Kaambwa C, Mrejen M, Mubarik S, Muccioli L, Mueller UO, Mughal F, Mukherjee S, Mukoro GD, Mulita A, Mulita F, Muniyandi M, Munjal K, Musaigwa F, Musallam KM, Mustafa G, Muthu S, Muthupandian S, Myung W, Nabhan AF, Nafukho FM, Nagarajan AJ, Naghavi M, Naghavi P, Naik GR, Naik G, Naimzada MD, Nair S, Nair TS, Najmuldeen HHR, Naldi L, Nangia V, Nargus S, Nascimento BR, Nascimento GG, Naser AY, Nasiri MJ, Natto ZS, Nauman J, Naveed M, Nayak BP, Nayak VC, Nayyar AK, Nazri-Panjaki A, Negash H, Negero AK, Negoi I, Negoi RI, Negru SM, Nejadghaderi SA, Nejjari C, Nematollahi MH, Nena E, Nepal S, Nesbit OD, Newton CRJ, Ngunjiri JW, Nguyen DH, Nguyen PT, Nguyen PT, Nguyen TT, Nguyen VT, Nigatu YT, Nikolouzakis TK, Nikoobar A, Nikpoor AR, Nizam MA, Nomura S, Noreen M, Noroozi N, Norouzian Baghani A, Norrving B, Noubiap JJ, Novotney A, Nri-Ezedi CA, Ntaios G, Ntsekhe M, Nuñez-Samudio V, Nurrika D, Oancea B, Obamiro KO, Odetokun IA, Ofakunrin AOD, Ogunsakin RE, Oguta JO, Oh IH, Okati-Aliabad H, Okeke SR, Okekunle AP, Okidi L, Okonji OC, Okwute PG, Olagunju AT, Olaiya MT, Olanipekun TO, Olatubi MI, Olivas-Martinez A, Oliveira GMM, Oliver S, Olorukooba AA, Olufadewa II, Olusanya BO, Olusanya JO, Oluwafemi YD, Oluwatunase GO, Omar HA, Omer GL, Ong S, Onwujekwe OE, Onyedibe KI, Opio JN, Ordak M, Orellana ER, Orisakwe OE, Orish VN, Orru H, Ortega-Altamirano DV, Ortiz A, Ortiz-Brizuela E, Ortiz-Prado E, Osuagwu UL, Otoiu A, Otstavnov N, Ouyahia A, Ouyang G, Owolabi MO, Oyeyemi IT, Oyeyemi OT, Ozten Y, P A MP, Padubidri JR, Pahlavikhah Varnosfaderani M, Pal PK, Palicz T, Palladino C, Palladino R, Palma-Alvarez RF, Pana A, Panahi P, Pandey A, Pandi-Perumal SR, Pando-Robles V, Pangaribuan HU, Panos GD, Pantazopoulos I, Papadopoulou P, Pardhan S, Parikh RR, Park S, Parthasarathi A, Pashaei A, Pasupula DK, Patel JR, Patel SK, Pathan AR, Patil A, Patil S, Patoulias D, Patthipati VS, Paudel U, Pawar S, Pazoki Toroudi H, Pease SA, Peden AE, Pedersini P, Peng M, Pensato U, Pepito VCF, Peprah EK, Pereira G, Pereira J, Pereira M, Peres MFP, Perianayagam A, Perico N, Petcu IR, Petermann-Rocha FE, Pezzani R, Pham HT, Phillips MR, Pierannunzio D, Pigeolet M, Pigott DM, Pilgrim T, Pinheiro M, Piradov MA, Plakkal N, Plotnikov E, Poddighe D, Pollner P, Poluru R, Pond CD, Postma MJ, Poudel GR, Poudel L, Pourali G, Pourtaheri N, Prada SI, Pradhan PMS, Prajapati VK, Prakash V, Prasad CP, Prasad M, Prashant A, Prates EJS, Purnobasuki H, Purohit BM, Puvvula J, Qaisar R, Qasim NH, Qattea I, Qian G, Quan NK, Radfar A, Radhakrishnan V, Raee P, Raeisi Shahraki H, Rafiei Alavi SN, Rafique I, Raggi A, Rahim F, Rahman MM, Rahman M, Rahman MA, Rahman T, Rahmani AM, Rahmani S, Rahnavard N, Rai P, Rajaa S, Rajabpour-Sanati A, Rajput P, Ram P, Ramadan H, Ramasamy SK, Ramazanu S, Rana J, Rana K, Ranabhat CL, Rancic N, Rani S, Ranjan S, Rao CR, Rao IR, Rao M, Rao SJ, Rasali DP, Rasella D, Rashedi S, Rashedi V, Rashid AM, Rasouli-Saravani A, Rastogi P, Rasul A, Ravangard R, Ravikumar N, Rawaf DL, Rawaf S, Rawassizadeh R, Razeghian-Jahromi I, Reddy MMRK, Redwan EMM, Rehman FU, Reiner Jr RC, Remuzzi G, Reshmi B, Resnikoff S, Reyes LF, Rezaee M, Rezaei N, Rezaei N, Rezaeian M, Riaz MA, Ribeiro AI, Ribeiro DC, Rickard J, Rios-Blancas MJ, Robinson-Oden HE, Rodrigues M, Rodriguez JAB, Roever L, Rohilla R, Rohloff P, Romadlon DS, Ronfani L, Roshandel G, Roshanzamir S, Rostamian M, Roy B, Roy P, Rubagotti E, Rumisha SF, Rwegerera GM, Rynkiewicz A, S M, S N C, S Sunnerhagen K, Saad AMA, Sabbatucci M, Saber K, Saber-Ayad MM, Sacco S, Saddik B, Saddler A, Sadee BA, Sadeghi E, Sadeghi M, Sadeghian S, Saeed U, Saeedi M, Safi S, Sagar R, Saghazadeh A, Saheb Sharif-Askari N, Sahoo SS, Sahraian MA, Sajedi SA, Sajid MR, Sakshaug JW, Salahi S, Salahi S, Salamati P, Salami AA, Salaroli LB, Saleh MA, Salehi S, Salem MR, Salem MZY, Salimi S, Samadi Kafil H, Samadzadeh S, Samara KA, Samargandy S, Samodra YL, Samuel VP, Samy AM, Sanabria J, Sanadgol N, Sanganyado E, Sanjeev RK, Sanmarchi F, Sanna F, Santri IN, Santric-Milicevic MM, Sarasmita MA, Saravanan A, Saravi B, Sarikhani Y, Sarkar C, Sarmiento-Suárez R, Sarode GS, Sarode SC, Sarveazad A, Sathian B, Sathish T, Sattin D, Saulam J, Sawyer SM, Saxena S, Saya GK, Sayadi Y, Sayeed A, Sayeed MA, Saylan M, Scarmeas N, Schaarschmidt BM, Schlee W, Schmidt MI, Schuermans A, Schwebel DC, Schwendicke F, Šekerija M, Selvaraj S, Semreen MH, Senapati S, Sengupta P, Senthilkumaran S, Sepanlou SG, Serban D, Sertsu A, Sethi Y, SeyedAlinaghi S, Seyedi SA, Shafaat A, Shafaat O, Shafie M, Shafiee A, Shah NS, Shah PA, Shahabi S, Shahbandi A, Shahid I, Shahid S, Shahid W, Shahwan MJ, Shaikh MA, Shakeri A, Shakil H, Sham S, Shamim MA, Shams-Beyranvand M, Shamshad H, Shamshirgaran MA, Shamsi MA, Shanawaz M, Shankar A, Sharfaei S, Sharifan A, Shariff M, Sharifi-Rad J, Sharma M, Sharma R, Sharma S, Sharma V, Shastry RP, Shavandi A, Shaw DH, Shayan AM, Shehabeldine AME, Sheikh A, Sheikhi RA, Shen J, Shenoy MM, Shetty BSK, Shetty RS, Shey RA, Shiani A, Shibuya K, Shiferaw D, Shigematsu M, Shin JI, Shin MJ, Shiri R, Shirkoohi R, Shittu A, Shiue I, Shivakumar KM, Shivarov V, Shool S, Shrestha S, Shuja KH, Shuval K, Si Y, Sibhat MM, Siddig EE, Sigfusdottir ID, Silva JP, Silva LMLR, Silva S, Simões JP, Simpson CR, Singal A, Singh A, Singh A, Singh A, Singh BB, Singh B, Singh M, Singh M, Singh NP, Singh P, Singh S, Siraj MS, Sitas F, Sivakumar S, Skryabin VY, Skryabina AA, Sleet DA, Slepak ELN, Sohrabi H, Soleimani H, Soliman SSM, Solmi M, Solomon Y, Song Y, Sorensen RJD, Soriano JB, Soyiri IN, Spartalis M, Sreeramareddy CT, Starnes JR, Starodubov VI, Starodubova AV, Stefan SC, Stein DJ, Steinbeis F, Steiropoulos P, Stockfelt L, Stokes MA, Stortecky S, Stranges S, Stroumpoulis K, Suleman M, Suliankatchi Abdulkader R, Sultana A, Sun J, Sunkersing D, Susanty S, Swain CK, Sykes BL, Szarpak L, Szeto MD, Szócska M, Tabaee Damavandi P, Tabatabaei Malazy O, Tabatabaeizadeh SA, Tabatabai S, Tabb KM, Tabish M, Taborda-Barata LM, Tabuchi T, Tadesse BT, Taheri A, Taheri Abkenar Y, Taheri Soodejani M, Taherkhani A, Taiba J, Tajbakhsh A, Talaat IM, Talukder A, Tamuzi JL, Tan KK, Tang H, Tang HK, Tat NY, Tat VY, Tavakoli Oliaee R, Tavangar SM, Taveira N, Tebeje TM, Tefera YM, Teimoori M, Temsah MH, Temsah RMH, Teramoto M, Tesfaye SH, Thangaraju P, Thankappan KR, Thapa R, Thapar R, Thomas N, Thrift AG, Thum CCC, Tian J, Tichopad A, Ticoalu JHV, Tiruye TY, Tohidast SA, Tonelli M, Touvier M, Tovani-Palone MR, Tram KH, Tran NM, Trico D, Trihandini I, Tromans SJ, Truong VT, Truyen TTTT, Tsermpini EE, Tumurkhuu M, Tung K, Tyrovolas S, Ubah CS, Udoakang AJ, Udoh A, Ulhaq I, Ullah S, Ullah S, Umair M, Umar TP, Umeokonkwo CD, Umesh A, Unim B, Unnikrishnan B, Upadhyay E, Urso D, Vacante M, Vahdani AM, Vaithinathan AG, Valadan Tahbaz S, Valizadeh R, Van den Eynde J, Varavikova E, Varga O, Varma SA, Vart P, Varthya SB, Vasankari TJ, Veerman LJ, Venketasubramanian N, Venugopal D, Verghese NA, Verma M, Verma P, Veroux M, Verras GI, Vervoort D, Vieira RJ, Villafañe JH, Villani L, Villanueva GI, Villeneuve PJ, Violante FS, Visontay R, Vlassov V, Vo B, Vollset SE, Volovat SR, Volovici V, Vongpradith A, Vos T, Vujcic IS, Vukovic R, Wado YD, Wafa HA, Waheed Y, Wamai RG, Wang C, Wang D, Wang F, Wang S, Wang S, Wang Y, Wang YP, Ward P, Watson S, Weaver MR, Weerakoon KG, Weiss DJ, Weldemariam AH, Wells KM, Wen YF, Werdecker A, Westerman R, Wickramasinghe DP, Wickramasinghe ND, Wijeratne T, Wilson S, Wojewodzic MW, Wool EE, Woolf AD, Wu D, Wulandari RD, Xiao H, Xu B, Xu X, Yadav L, Yaghoubi S, Yang L, Yano Y, Yao Y, Ye P, Yesera GE, Yesodharan R, Yesuf SA, Yiğit A, Yiğit V, Yip P, Yon DK, Yonemoto N, You Y, Younis MZ, Yu C, Zadey S, Zadnik V, Zafari N, Zahedi M, Zahid MN, Zahir M, Zakham F, Zaki N, Zakzuk J, Zamagni G, Zaman BA, Zaman SB, Zamora N, Zand R, Zandi M, Zandieh GGZ, Zanghì A, Zare I, Zastrozhin MS, Zeariya MGM, Zeng Y, Zhai C, Zhang C, Zhang H, Zhang H, Zhang Y, Zhang Z, Zhang Z, Zhao H, Zhao Y, Zhao Y, Zheng P, Zhong C, Zhou J, Zhu B, Zhu Z, Ziaeefar P, Zielińska M, Zou Z, Zumla A, Zweck E, Zyoud SH, Lim SS, Murray CJL. Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950-2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021. Lancet 2024; 403:1989-2056. [PMID: 38484753 DOI: 10.1016/s0140-6736(24)00476-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/08/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Estimates of demographic metrics are crucial to assess levels and trends of population health outcomes. The profound impact of the COVID-19 pandemic on populations worldwide has underscored the need for timely estimates to understand this unprecedented event within the context of long-term population health trends. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 provides new demographic estimates for 204 countries and territories and 811 additional subnational locations from 1950 to 2021, with a particular emphasis on changes in mortality and life expectancy that occurred during the 2020-21 COVID-19 pandemic period. METHODS 22 223 data sources from vital registration, sample registration, surveys, censuses, and other sources were used to estimate mortality, with a subset of these sources used exclusively to estimate excess mortality due to the COVID-19 pandemic. 2026 data sources were used for population estimation. Additional sources were used to estimate migration; the effects of the HIV epidemic; and demographic discontinuities due to conflicts, famines, natural disasters, and pandemics, which are used as inputs for estimating mortality and population. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate under-5 mortality rates, which synthesised 30 763 location-years of vital registration and sample registration data, 1365 surveys and censuses, and 80 other sources. ST-GPR was also used to estimate adult mortality (between ages 15 and 59 years) based on information from 31 642 location-years of vital registration and sample registration data, 355 surveys and censuses, and 24 other sources. Estimates of child and adult mortality rates were then used to generate life tables with a relational model life table system. For countries with large HIV epidemics, life tables were adjusted using independent estimates of HIV-specific mortality generated via an epidemiological analysis of HIV prevalence surveys, antenatal clinic serosurveillance, and other data sources. Excess mortality due to the COVID-19 pandemic in 2020 and 2021 was determined by subtracting observed all-cause mortality (adjusted for late registration and mortality anomalies) from the mortality expected in the absence of the pandemic. Expected mortality was calculated based on historical trends using an ensemble of models. In location-years where all-cause mortality data were unavailable, we estimated excess mortality rates using a regression model with covariates pertaining to the pandemic. Population size was computed using a Bayesian hierarchical cohort component model. Life expectancy was calculated using age-specific mortality rates and standard demographic methods. Uncertainty intervals (UIs) were calculated for every metric using the 25th and 975th ordered values from a 1000-draw posterior distribution. FINDINGS Global all-cause mortality followed two distinct patterns over the study period: age-standardised mortality rates declined between 1950 and 2019 (a 62·8% [95% UI 60·5-65·1] decline), and increased during the COVID-19 pandemic period (2020-21; 5·1% [0·9-9·6] increase). In contrast with the overall reverse in mortality trends during the pandemic period, child mortality continued to decline, with 4·66 million (3·98-5·50) global deaths in children younger than 5 years in 2021 compared with 5·21 million (4·50-6·01) in 2019. An estimated 131 million (126-137) people died globally from all causes in 2020 and 2021 combined, of which 15·9 million (14·7-17·2) were due to the COVID-19 pandemic (measured by excess mortality, which includes deaths directly due to SARS-CoV-2 infection and those indirectly due to other social, economic, or behavioural changes associated with the pandemic). Excess mortality rates exceeded 150 deaths per 100 000 population during at least one year of the pandemic in 80 countries and territories, whereas 20 nations had a negative excess mortality rate in 2020 or 2021, indicating that all-cause mortality in these countries was lower during the pandemic than expected based on historical trends. Between 1950 and 2021, global life expectancy at birth increased by 22·7 years (20·8-24·8), from 49·0 years (46·7-51·3) to 71·7 years (70·9-72·5). Global life expectancy at birth declined by 1·6 years (1·0-2·2) between 2019 and 2021, reversing historical trends. An increase in life expectancy was only observed in 32 (15·7%) of 204 countries and territories between 2019 and 2021. The global population reached 7·89 billion (7·67-8·13) people in 2021, by which time 56 of 204 countries and territories had peaked and subsequently populations have declined. The largest proportion of population growth between 2020 and 2021 was in sub-Saharan Africa (39·5% [28·4-52·7]) and south Asia (26·3% [9·0-44·7]). From 2000 to 2021, the ratio of the population aged 65 years and older to the population aged younger than 15 years increased in 188 (92·2%) of 204 nations. INTERPRETATION Global adult mortality rates markedly increased during the COVID-19 pandemic in 2020 and 2021, reversing past decreasing trends, while child mortality rates continued to decline, albeit more slowly than in earlier years. Although COVID-19 had a substantial impact on many demographic indicators during the first 2 years of the pandemic, overall global health progress over the 72 years evaluated has been profound, with considerable improvements in mortality and life expectancy. Additionally, we observed a deceleration of global population growth since 2017, despite steady or increasing growth in lower-income countries, combined with a continued global shift of population age structures towards older ages. These demographic changes will likely present future challenges to health systems, economies, and societies. The comprehensive demographic estimates reported here will enable researchers, policy makers, health practitioners, and other key stakeholders to better understand and address the profound changes that have occurred in the global health landscape following the first 2 years of the COVID-19 pandemic, and longer-term trends beyond the pandemic. FUNDING Bill & Melinda Gates Foundation.
Collapse
|
2
|
Goodyear CS, Patel A, Barnes E, Willicombe M, Siebert S, de Silva TI, Snowden JA, Lim SH, Bowden SJ, Billingham L, Richter A, Carroll M, Carr EJ, Beale R, Rea D, Parry H, Pirrie S, Lim Z, Satsangi J, Dunachie SJ, Cook G, Miller P, Basu N, Gilmour A, Hodgkins AM, Evans L, Hughes A, Longet S, Meacham G, Yong KL, A'Hearne MJ, Koh MBC, Burns SO, Orchard K, Paterson C, McIlroy G, Murray SM, Thomson T, Dimitriadis S, Goulston L, Miller S, Keillor V, Prendecki M, Thomas D, Kirkham A, McInnes IB, Kearns P. Immunogenicity of third dose COVID-19 vaccine strategies in patients who are immunocompromised with suboptimal immunity following two doses (OCTAVE-DUO): an open-label, multicentre, randomised, controlled, phase 3 trial. Lancet Rheumatol 2024:S2665-9913(24)00065-1. [PMID: 38734019 DOI: 10.1016/s2665-9913(24)00065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The humoral and T-cell responses to booster COVID-19 vaccine types in multidisease immunocompromised individuals who do not generate adequate antibody responses to two COVID-19 vaccine doses, is not fully understood. The OCTAVE DUO trial aimed to determine the value of third vaccinations in a wide range of patients with primary and secondary immunodeficiencies. METHODS OCTAVE-DUO was a prospective, open-label, multicentre, randomised, controlled, phase 3 trial investigating humoral and T-cell responses in patients who are immunocompromised following a third vaccine dose with BNT162b2 or mRNA-1273, and of NVX-CoV2373 for those with lymphoid malignancies. We recruited patients who were immunocompromised from 11 UK hospitals, aged at least 18 years, with previous sub-optimal responses to two doses of SARS-CoV-2 vaccine. Participants were randomly assigned 1:1 (1:1:1 for those with lymphoid malignancies), stratified by disease, previous vaccination type, and anti-spike antibody response following two doses. Individuals with lived experience of immune susceptibility were involved in the study design and implementation. The primary outcome was vaccine-specific immunity defined by anti-SARS-CoV-2 spike antibodies (Roche Diagnostics UK and Ireland, Burgess Hill, UK) and T-cell responses (Oxford Immunotec, Abingdon, UK) before and 21 days after the third vaccine dose analysed by a modified intention-to-treat analysis. The trial is registered with the ISRCTN registry, ISRCTN 15354495, and the EU Clinical Trials Register, EudraCT 2021-003632-87, and is complete. FINDINGS Between Aug 4, 2021 and Mar 31, 2022, 804 participants across nine disease cohorts were randomly assigned to receive BNT162b2 (n=377), mRNA-1273 (n=374), or NVX-CoV2373 (n=53). 356 (45%) of 789 participants were women, 433 (55%) were men, and 659 (85%) of 775 were White. Anti-SARS-CoV-2 spike antibodies measured 21 days after the third vaccine dose were significantly higher than baseline pre-third dose titres in the modified intention-to-treat analysis (median 1384 arbitrary units [AU]/mL [IQR 4·3-7990·0] compared with median 11·5 AU/mL [0·4-63·1]; p<0·001). Of participants who were baseline low responders, 380 (90%) of 423 increased their antibody concentrations to more than 400 AU/mL. Conversely, 166 (54%) of 308 baseline non-responders had no response after the third dose. Detectable T-cell responses following the third vaccine dose were seen in 494 (80%) of 616 participants. There were 24 serious adverse events (BNT612b2 eight [33%] of 24, mRNA-1273 12 [50%], NVX-CoV2373 four [17%]), two (8%) of which were categorised as vaccine-related. There were seven deaths (1%) during the trial, none of which were vaccine-related. INTERPRETATION A third vaccine dose improved the serological and T-cell response in the majority of patients who are immunocompromised. Individuals with chronic renal disease, lymphoid malignancy, on B-cell targeted therapies, or with no serological response after two vaccine doses are at higher risk of poor response to a third vaccine dose. FUNDING Medical Research Council, Blood Cancer UK.
Collapse
Affiliation(s)
- Carl S Goodyear
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Amit Patel
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Stefan Siebert
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Sheffield, UK
| | - John A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Sean H Lim
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Sarah J Bowden
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Lucinda Billingham
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alex Richter
- Clinical Immunology Service, University of Birmingham, Edgbaston, Birmingham, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Daniel Rea
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Helen Parry
- Department of Haematology, University Hospitals Birmingham NHS Foundations Trust, Birmingham, UK
| | - Sarah Pirrie
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Zixiang Lim
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Gordon Cook
- National Institute for Health Research Leeds MIC, University of Leeds, Leeds, UK
| | - Paul Miller
- British Society of Blood and Marrow Transplantation and Cellular Therapy, Guy's Hospital, London, UK
| | - Neil Basu
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Ashley Gilmour
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Anne-Marie Hodgkins
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Lili Evans
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ana Hughes
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Centre International de Recherche en Infectiologie, Team GIMAP (Saint-Etienne), Université Claude Bernard Lyon 1, Inserm, CNRS, Lyon, France
| | - Georgina Meacham
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kwee L Yong
- Cancer Institute, Department of Haematology, University College London, London, UK
| | | | - Mickey B C Koh
- Infection and Immunity Clinical Academic Group, St George's, University of London and Department of Haematology, St George's Hospital NHS Foundation Trust, London, UK
| | - Siobhan O Burns
- Clinical Immunology, Royal Free Hospital, Hampstead, London, UK; Institute of Immunity and Transplantation, University College London, Hampstead, London, UK
| | - Kim Orchard
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Caron Paterson
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Graham McIlroy
- Department of Haematology, University Hospitals Birmingham NHS Foundations Trust, Birmingham, UK
| | - Sam M Murray
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tina Thomson
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | | | - Lyndsey Goulston
- National Institute of Health Research, Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Samantha Miller
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Victoria Keillor
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Maria Prendecki
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - David Thomas
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Amanda Kirkham
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK
| | - Iain B McInnes
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Pamela Kearns
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Edgbaston, Birmingham, UK; National Institute for Health Research, Birmingham Biomedical Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| |
Collapse
|
3
|
Ali M, Longet S, Neale I, Rongkard P, Chowdhury FUH, Hill J, Brown A, Laidlaw S, Tipton T, Hoque A, Hassan N, Hackstein CP, Adele S, Akther HD, Abraham P, Paul S, Rahman MM, Alam MM, Parvin S, Hoque Mollah F, Hoque MM, Moore SC, Biswas SK, Turtle L, de Silva TI, Ogbe A, Frater J, Barnes E, Tomic A, Carroll MW, Klenerman P, Kronsteiner B, Chowdhury FR, Dunachie SJ. Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery. Clin Exp Immunol 2024:uxae030. [PMID: 38642547 DOI: 10.1093/cei/uxae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 04/22/2024] Open
Abstract
Obesity and type 2 diabetes (DM) are risk factors for severe COVID-19 outcomes, which disproportionately affect South Asian populations. This study aims to investigate the humoral and cellular immune responses to SARS-CoV-2 in adult COVID-19 survivors with obesity and DM in Bangladesh. In this cross-sectional study, SARS-CoV-2-specific antibody and T cell responses were investigated in 63 healthy and 75 PCR-confirmed COVID-19 recovered individuals in Bangladesh, during the pre-vaccination first wave of the COVID-19 pandemic in 2020. In COVID-19 survivors, SARS-CoV-2 infection induced robust antibody and T cell responses, which correlated with disease severity. After adjusting for age, sex, DM status, disease severity, and time since onset of symptoms, obesity was associated with decreased neutralising antibody titers, and increased SARS-CoV-2 spike-specific IFN-γ response along with increased proliferation and IL-2 production by CD8+ T cells. In contrast, DM was not associated with SARS-CoV-2-specific antibody and T cell responses after adjustment for obesity and other confounders. Obesity is associated with lower neutralising antibody levels and higher T cell responses to SARS-CoV-2 post COVID-19 recovery, while antibody or T cell responses remain unaltered in DM.
Collapse
Affiliation(s)
- Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Directorate General of Health Services, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Patpong Rongkard
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Jennifer Hill
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stephen Laidlaw
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Tipton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashraful Hoque
- Department of Transfusion Medicine, Sheikh Hasina National Burn & Plastics Surgery Institute, Dhaka, Bangladesh
| | - Nazia Hassan
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Hossain Delowar Akther
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Shrebash Paul
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Matiur Rahman
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Masum Alam
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shamima Parvin
- Department of Biochemistry and Molecular Biology, Mugda Medical College, Dhaka, Bangladesh
| | - Forhadul Hoque Mollah
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Mozammel Hoque
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shona C Moore
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Subrata K Biswas
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Lance Turtle
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, USA
- Department of Microbiology, Boston University School of Medicine, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Fazle Rabbi Chowdhury
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| |
Collapse
|
4
|
Naghavi M, Mestrovic T, Gray A, Gershberg Hayoon A, Swetschinski LR, Robles Aguilar G, Davis Weaver N, Ikuta KS, Chung E, Wool EE, Han C, Araki DT, Albertson SB, Bender R, Bertolacci G, Browne AJ, Cooper BS, Cunningham MW, Dolecek C, Doxey M, Dunachie SJ, Ghoba S, Haines-Woodhouse G, Hay SI, Hsu RL, Iregbu KC, Kyu HH, Ledesma JR, Ma J, Moore CE, Mosser JF, Mougin V, Naghavi P, Novotney A, Rosenthal VD, Sartorius B, Stergachis A, Troeger C, Vongpradith A, Walters MK, Wunrow HY, Murray CJL. Global burden associated with 85 pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet Infect Dis 2024:S1473-3099(24)00158-0. [PMID: 38640940 DOI: 10.1016/s1473-3099(24)00158-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Despite a global epidemiological transition towards increased burden of non-communicable diseases, communicable diseases continue to cause substantial morbidity and mortality worldwide. Understanding the burden of a wide range of infectious diseases, and its variation by geography and age, is pivotal to research priority setting and resource mobilisation globally. METHODS We estimated disability-adjusted life-years (DALYs) associated with 85 pathogens in 2019, globally, regionally, and for 204 countries and territories. The term pathogen included causative agents, pathogen groups, infectious conditions, and aggregate categories. We applied a novel methodological approach to account for underlying, immediate, and intermediate causes of death, which counted every death for which a pathogen had a role in the pathway to death. We refer to this measure as the burden associated with infection, which was estimated by combining different sources of information. To compare the burden among all pathogens, we used pathogen-specific ratios to incorporate the burden of immediate and intermediate causes of death for pathogens modelled previously by the GBD. We created the ratios by using multiple cause of death data, hospital discharge data, linkage data, and minimally invasive tissue sampling data to estimate the fraction of deaths coming from the pathway to death chain. We multiplied the pathogen-specific ratios by age-specific years of life lost (YLLs), calculated with GBD 2019 methods, and then added the adjusted YLLs to age-specific years lived with disability (YLDs) from GBD 2019 to produce adjusted DALYs to account for deaths in the chain. We used standard GBD methods to calculate 95% uncertainty intervals (UIs) for final estimates of DALYs by taking the 2·5th and 97·5th percentiles across 1000 posterior draws for each quantity of interest. We provided burden estimates pertaining to all ages and specifically to the under 5 years age group. FINDINGS Globally in 2019, an estimated 704 million (95% UI 610-820) DALYs were associated with 85 different pathogens, including 309 million (250-377; 43·9% of the burden) in children younger than 5 years. This burden accounted for 27·7% (and 65·5% in those younger than 5 years) of the previously reported total DALYs from all causes in 2019. Comparing super-regions, considerable differences were observed in the estimated pathogen-associated burdens in relation to DALYs from all causes, with the highest burden observed in sub-Saharan Africa (314 million [270-368] DALYs; 61·5% of total regional burden) and the lowest in the high-income super-region (31·8 million [25·4-40·1] DALYs; 9·8%). Three leading pathogens were responsible for more than 50 million DALYs each in 2019: tuberculosis (65·1 million [59·0-71·2]), malaria (53·6 million [27·0-91·3]), and HIV or AIDS (52·1 million [46·6-60·9]). Malaria was the leading pathogen for DALYs in children younger than 5 years (37·2 million [17·8-64·2]). We also observed substantial burden associated with previously less recognised pathogens, including Staphylococcus aureus and specific Gram-negative bacterial species (ie, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, and Helicobacter pylori). Conversely, some pathogens had a burden that was smaller than anticipated. INTERPRETATION Our detailed breakdown of DALYs associated with a comprehensive list of pathogens on a global, regional, and country level has revealed the magnitude of the problem and helps to indicate where research funding mismatch might exist. Given the disproportionate impact of infection on low-income and middle-income countries, an essential next step is for countries and relevant stakeholders to address these gaps by making targeted investments. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
Collapse
|
5
|
Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun 2024; 15:3284. [PMID: 38627386 PMCID: PMC11021415 DOI: 10.1038/s41467-024-47393-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
Collapse
Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Raksha Das
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Alexander J Mentzer
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
6
|
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun 2024; 15:2734. [PMID: 38548763 PMCID: PMC10978878 DOI: 10.1038/s41467-024-46982-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
Collapse
Affiliation(s)
- Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Muneeswaran Selvaraj
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, 10700, Thailand
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
7
|
Browne AJ, Chipeta MG, Fell FJ, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, Robles Aguilar G, McManigal B, Andrews JR, Ashley EA, Audi A, Baker S, Banda HC, Basnyat B, Bigogo G, Ngoun C, Chansamouth V, Chunga A, Clemens JD, Davong V, Dougan G, Dunachie SJ, Feasey NA, Garrett DO, Gordon MA, Hasan R, Haselbeck AH, Henry NJ, Heyderman RS, Holm M, Jeon HJ, Karkey A, Khanam F, Luby SP, Malik FR, Marks F, Mayxay M, Meiring JE, Moore CE, Munywoki PK, Musicha P, Newton PN, Pak G, Phommasone K, Pokharel S, Pollard AJ, Qadri F, Qamar FN, Rattanavong S, Reiner B, Roberts T, Saha S, Saha S, Shakoor S, Shakya M, Simpson AJ, Stanaway J, Turner C, Turner P, Verani JR, Vongsouvath M, Day NPJ, Naghavi M, Hay SI, Sartorius B, Dolecek C. Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study. Lancet Glob Health 2024; 12:e406-e418. [PMID: 38365414 PMCID: PMC10882211 DOI: 10.1016/s2214-109x(23)00585-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 11/19/2023] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Enteric fever, a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A, remains a major cause of morbidity and mortality in low-income and middle-income countries. Enteric fever is preventable through the provision of clean water and adequate sanitation and can be successfully treated with antibiotics. However, high levels of antimicrobial resistance (AMR) compromise the effectiveness of treatment. We provide estimates of the prevalence of AMR S Typhi and S Paratyphi A in 75 endemic countries, including 30 locations without data. METHODS We used a Bayesian spatiotemporal modelling framework to estimate the percentage of multidrug resistance (MDR), fluoroquinolone non-susceptibility (FQNS), and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections for 1403 administrative level one districts in 75 endemic countries from 1990 to 2019. We incorporated data from a comprehensive systematic review, public health surveillance networks, and large multicountry studies on enteric fever. Estimates of the prevalence of AMR and the number of AMR infections (based on enteric fever incidence estimates by the Global Burden of Diseases study) were produced at the country, super-region, and total endemic area level for each year of the study. FINDINGS We collated data from 601 sources, comprising 184 225 isolates of S Typhi and S Paratyphi A, covering 45 countries over 30 years. We identified a decline of MDR S Typhi in south Asia and southeast Asia, whereas in sub-Saharan Africa, the overall prevalence increased from 6·0% (95% uncertainty interval 4·3-8·0) in 1990 to 72·7% (67·7-77·3) in 2019. Starting from low levels in 1990, the prevalence of FQNS S Typhi increased rapidly, reaching 95·2% (91·4-97·7) in south Asia in 2019. This corresponded to 2·5 million (1·5-3·8) MDR S Typhi infections and 7·4 million (4·7-11·3) FQNS S Typhi infections in endemic countries in 2019. The prevalence of third-generation cephalosporin-resistant S Typhi remained low across the whole endemic area over the study period, except for Pakistan where prevalence of third-generation cephalosporin resistance in S Typhi reached 61·0% (58·0-63·8) in 2019. For S Paratyphi A, we estimated low prevalence of MDR and third-generation cephalosporin resistance in all endemic countries, but a drastic increase of FQNS, which reached 95·0% (93·7-96·1; 3·5 million [2·2-5·6] infections) in 2019. INTERPRETATION This study provides a comprehensive and detailed analysis of the prevalence of MDR, FQNS, and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections in endemic countries, spanning the last 30 years. Our analysis highlights the increasing levels of AMR in this preventable infection and serves as a resource to guide urgently needed public health interventions, such as improvements in water, sanitation, and hygiene and typhoid fever vaccination campaigns. FUNDING Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill and Melinda Gates Foundation.
Collapse
|
8
|
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.
Collapse
Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Willem J Wiersinga
- Division of Infectious Diseases, Center for Experimental Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| |
Collapse
|
9
|
Sartorius B, Gray AP, Davis Weaver N, Robles Aguilar G, Swetschinski LR, Ikuta KS, Mestrovic T, Chung E, Wool EE, Han C, Gershberg Hayoon A, Araki DT, Abd-Elsalam S, Aboagye RG, Adamu LH, Adepoju AV, Ahmed A, Akalu GT, Akande-Sholabi W, Amuasi JH, Amusa GA, Argaw AM, Aruleba RT, Awoke T, Ayalew MK, Azzam AY, Babin FX, Banerjee I, Basiru A, Bayileyegn NS, Belete MA, Berkley JA, Bielicki JA, Dekker D, Demeke D, Demsie DG, Dessie AM, Dunachie SJ, Ed-Dra A, Ekholuenetale M, Ekundayo TC, El Sayed I, Elhadi M, Elsohaby I, Eyre D, Fagbamigbe AF, Feasey NA, Fekadu G, Fell F, Forrest KM, Gebrehiwot M, Gezae KE, Ghazy RM, Hailegiyorgis TT, Haines-Woodhouse G, Hasaballah AI, Haselbeck AH, Hsia Y, Iradukunda A, Iregbu KC, Iwu CCD, Iwu-Jaja CJ, Iyasu AN, Jaiteh F, Jeon H, Joshua CE, Kassa GG, Katoto PDMC, Krumkamp R, Kumaran EAP, Kyu HH, Manilal A, Marks F, May J, McLaughlin SA, McManigal B, Melese A, Misgina KH, Mohamed NS, Mohammed M, Mohammed S, Mohammed S, Mokdad AH, Moore CE, Mougin V, Mturi N, Mulugeta T, Musaigwa F, Musicha P, Musila LA, Muthupandian S, Naghavi P, Negash H, Nuckchady DC, Obiero CW, Odetokun IA, Ogundijo OA, Okidi L, Okonji OC, Olagunju AT, Olufadewa II, Pak GD, Perovic O, Pollard A, Raad M, Rafaï C, Ramadan H, Redwan EMM, Roca A, Rosenthal VD, Saleh MA, Samy AM, Sharland M, Shittu A, Siddig EE, Sisay EA, Stergachis A, Tesfamariam WB, Tigoi C, Tincho MB, Tiruye TY, Umeokonkwo CD, Walsh T, Walson JL, Yusuf H, Zeru NG, Hay SI, Dolecek C, Murray CJL, Naghavi M. The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis. Lancet Glob Health 2024; 12:e201-e216. [PMID: 38134946 PMCID: PMC10805005 DOI: 10.1016/s2214-109x(23)00539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/18/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND A critical and persistent challenge to global health and modern health care is the threat of antimicrobial resistance (AMR). Previous studies have reported a disproportionate burden of AMR in low-income and middle-income countries, but there remains an urgent need for more in-depth analyses across Africa. This study presents one of the most comprehensive sets of regional and country-level estimates of bacterial AMR burden in the WHO African region to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen-drug combinations for countries in the WHO African region in 2019. Our methodological approach consisted of five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths attributable to AMR (considering an alternative scenario where infections with resistant pathogens are replaced with susceptible ones) and deaths associated with AMR (considering an alternative scenario where drug-resistant infections would not occur at all). We obtained data from research hospitals, surveillance networks, and infection databases maintained by private laboratories and medical technology companies. We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. FINDINGS In the WHO African region in 2019, there were an estimated 1·05 million deaths (95% UI 829 000-1 316 000) associated with bacterial AMR and 250 000 deaths (192 000-325 000) attributable to bacterial AMR. The largest fatal AMR burden was attributed to lower respiratory and thorax infections (119 000 deaths [92 000-151 000], or 48% of all estimated bacterial pathogen AMR deaths), bloodstream infections (56 000 deaths [37 000-82 000], or 22%), intra-abdominal infections (26 000 deaths [17 000-39 000], or 10%), and tuberculosis (18 000 deaths [3850-39 000], or 7%). Seven leading pathogens were collectively responsible for 821 000 deaths (636 000-1 051 000) associated with resistance in this region, with four pathogens exceeding 100 000 deaths each: Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. Third-generation cephalosporin-resistant K pneumoniae and meticillin-resistant S aureus were shown to be the leading pathogen-drug combinations in 25 and 16 countries, respectively (53% and 34% of the whole region, comprising 47 countries) for deaths attributable to AMR. INTERPRETATION This study reveals a high level of AMR burden for several bacterial pathogens and pathogen-drug combinations in the WHO African region. The high mortality rates associated with these pathogens demonstrate an urgent need to address the burden of AMR in Africa. These estimates also show that quality and access to health care and safe water and sanitation are correlated with AMR mortality, with a higher fatal burden found in lower resource settings. Our cross-country analyses within this region can help local governments to leverage domestic and global funding to create stewardship policies that target the leading pathogen-drug combinations. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
Collapse
|
10
|
Doran W, Tunnicliffe L, Muzambi R, Rentsch CT, Bhaskaran K, Smeeth L, Brayne C, Williams DM, Chaturvedi N, Eastwood SV, Dunachie SJ, Mathur R, Warren-Gash C. Incident dementia risk among patients with type 2 diabetes receiving metformin versus alternative oral glucose-lowering therapy: an observational cohort study using UK primary healthcare records. BMJ Open Diabetes Res Care 2024; 12:e003548. [PMID: 38272537 PMCID: PMC10823924 DOI: 10.1136/bmjdrc-2023-003548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION 4.2 million individuals in the UK have type 2 diabetes, a known risk factor for dementia and mild cognitive impairment (MCI). Diabetes treatment may modify this association, but existing evidence is conflicting. We therefore aimed to assess the association between metformin therapy and risk of incident all-cause dementia or MCI compared with other oral glucose-lowering therapies (GLTs). RESEARCH DESIGN AND METHODS We conducted an observational cohort study using the Clinical Practice Research Datalink among UK adults diagnosed with diabetes at ≥40 years between 1990 and 2019. We used an active comparator new user design to compare risks of dementia and MCI among individuals initially prescribed metformin versus an alternative oral GLT using Cox proportional hazards regression controlling for sociodemographic, lifestyle and clinical confounders. We assessed for interaction by age and sex. Sensitivity analyses included an as-treated analysis to mitigate potential exposure misclassification. RESULTS We included 211 396 individuals (median age 63 years; 42.8% female), of whom 179 333 (84.8%) initiated on metformin therapy. Over median follow-up of 5.4 years, metformin use was associated with a lower risk of dementia (adjusted HR (aHR) 0.86 (95% CI 0.79 to 0.94)) and MCI (aHR 0.92 (95% CI 0.86 to 0.99)). Metformin users aged under 80 years had a lower dementia risk (aHR 0.77 (95% CI 0.68 to 0.85)), which was not observed for those aged ≥80 years (aHR 0.95 (95% CI 0.87 to 1.05)). There was no interaction with sex. The as-treated analysis showed a reduced effect size compared with the main analysis (aHR 0.90 (95% CI 0.83 to 0.98)). CONCLUSIONS Metformin use was associated with lower risks of incident dementia and MCI compared with alternative GLT among UK adults with diabetes. While our findings are consistent with a neuroprotective effect of metformin against dementia, further research is needed to reduce risks of confounding by indication and assess causality.
Collapse
Affiliation(s)
- William Doran
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Louis Tunnicliffe
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Rutendo Muzambi
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Christopher T Rentsch
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Krishnan Bhaskaran
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Liam Smeeth
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Carol Brayne
- Cambridge Public Health, University of Cambridge, Cambridge, UK
| | - Dylan M Williams
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Nish Chaturvedi
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Sophie V Eastwood
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Susanna J Dunachie
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rohini Mathur
- Centre for Primary Care, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Charlotte Warren-Gash
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| |
Collapse
|
11
|
Ratcliffe H, Tiley KS, Longet S, Tonry C, Roarty C, Watson C, Amirthalingam G, Vichos I, Morey E, Douglas NL, Marinou S, Plested E, Aley PK, Galiza E, Faust SN, Hughes S, Murray C, Roderick MR, Shackley F, Oddie S, Lee TW, Turner DP, Raman M, Owens S, Turner PJ, Cockerill H, Lopez Bernal J, Ijaz S, Poh J, Shute J, Linley E, Borrow R, Hoschler K, Brown KE, Carroll MW, Klenerman P, Dunachie SJ, Ramsay M, Voysey M, Waterfield T, Snape MD. Serum HCoV-spike specific antibodies do not protect against subsequent SARS-CoV-2 infection in children and adolescents. iScience 2023; 26:108500. [PMID: 38089581 PMCID: PMC10711458 DOI: 10.1016/j.isci.2023.108500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/17/2023] [Accepted: 11/17/2023] [Indexed: 02/15/2024] Open
Abstract
SARS-CoV-2 infections in children are generally asymptomatic or mild and rarely progress to severe disease and hospitalization. Why this is so remains unclear. Here we explore the potential for protection due to pre-existing cross-reactive seasonal coronavirus antibodies and compare the rate of antibody decline for nucleocapsid and spike protein in serum and oral fluid against SARS-CoV-2 within the pediatric population. No differences in seasonal coronaviruses antibody concentrations were found at baseline between cases and controls, suggesting no protective effect from pre-existing immunity against seasonal coronaviruses. Antibodies against seasonal betacoronaviruses were boosted in response to SARS-CoV-2 infection. In serum, anti-nucleocapsid antibodies fell below the threshold of positivity more quickly than anti-spike protein antibodies. These findings add to our understanding of protection against infection with SARS-CoV-2 within the pediatric population, which is important when considering pediatric SARS-CoV-2 immunization policies.
Collapse
Affiliation(s)
- Helen Ratcliffe
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Karen S. Tiley
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire Tonry
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Cathal Roarty
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Chris Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | | | - Iason Vichos
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Ella Morey
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Naomi L. Douglas
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Spyridoula Marinou
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Emma Plested
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Parvinder K. Aley
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Eva Galiza
- St Georges Hospital NHS Foundation Trust
| | - Saul N. Faust
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust and Faculty of Medicine and Institute of Life Sciences, University of Southampton
- National Immunisation Schedule Evaluation Consortium
| | - Stephen Hughes
- Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Clare Murray
- Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | | | | | - Sam Oddie
- Bradford Teaching Hospitals NHS Foundation Trust
| | | | - David P.J. Turner
- School of Life Sciences, University of Nottingham
- Nottingham University Hospitals NHS Trust
| | | | - Stephen Owens
- The Newcastle Upon Tyne Hospitals NHS Foundation Trust
| | - Paul J. Turner
- National Heart & Lung Institute, Imperial College London
| | | | | | | | | | | | | | | | | | | | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford BRC
| | - Susanna J. Dunachie
- National Institute for Health Research (NIHR) Oxford BRC
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Merryn Voysey
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Thomas Waterfield
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Matthew D. Snape
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
- National Immunisation Schedule Evaluation Consortium
- West Suffolk NHS Foundation Trust
| |
Collapse
|
12
|
Wagner GE, Stanjek TFP, Albrecht D, Lipp M, Dunachie SJ, Föderl-Höbenreich E, Riedel K, Kohler A, Steinmetz I, Kohler C. Deciphering the human antibody response against Burkholderia pseudomallei during melioidosis using a comprehensive immunoproteome approach. Front Immunol 2023; 14:1294113. [PMID: 38146371 PMCID: PMC10749318 DOI: 10.3389/fimmu.2023.1294113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 12/27/2023] Open
Abstract
Introduction The environmental bacterium Burkholderia pseudomallei causes the often fatal and massively underreported infectious disease melioidosis. Antigens inducing protective immunity in experimental models have recently been identified and serodiagnostic tools have been improved. However, further elucidation of the antigenic repertoire of B. pseudomallei during human infection for diagnostic and vaccine purposes is required. The adaptation of B. pseudomallei to very different habitats is reflected by a huge genome and a selective transcriptional response to a variety of conditions. We, therefore, hypothesized that exposure of B. pseudomallei to culture conditions mimicking habitats encountered in the human host might unravel novel antigens that are recognized by melioidosis patients. Methods and results In this study, B. pseudomallei was exposed to various stress and growth conditions, including anaerobiosis, acid stress, oxidative stress, iron starvation and osmotic stress. Immunogenic proteins were identified by probing two-dimensional Western blots of B. pseudomallei intracellular and extracellular protein extracts with sera from melioidosis patients and controls and subsequent MALDI-TOF MS. Among B. pseudomallei specific immunogenic signals, 90 % (55/61) of extracellular immunogenic proteins were identified by acid, osmotic or oxidative stress. A total of 84 % (44/52) of intracellular antigens originated from the stationary growth phase, acidic, oxidative and anaerobic conditions. The majority of the extracellular and intracellular protein antigens were identified in only one of the various stress conditions. Sixty-three immunoreactive proteins and an additional 38 candidates from a literature screening were heterologously expressed and subjected to dot blot analysis using melioidosis sera and controls. Our experiments confirmed melioidosis-specific signals in 58 of our immunoproteome candidates. These include 15 antigens with average signal ratios (melioidosis:controls) greater than 10 and another 26 with average ratios greater than 5, including new promising serodiagnostic candidates with a very high signal-to-noise ratio. Conclusion Our study shows that a comprehensive B. pseudomallei immunoproteomics approach, using conditions which are likely to be encountered during infection, can identify novel antibody targets previously unrecognized in human melioidosis.
Collapse
Affiliation(s)
- Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Michaela Lipp
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Susanna J. Dunachie
- Nuffield Department of Medicine (NDM) Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Esther Föderl-Höbenreich
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Diagnostic & Research Institute of Pathology, Medical University Graz, Graz, Austria
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Anne Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
| |
Collapse
|
13
|
Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ Med 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
Collapse
Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
14
|
Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P, Gallis M, Supasa P, Selvaraj M, Abraham P, Neale I, Ali M, Barratt NA, Nell JM, Gustafsson L, Strickland S, Grouneva I, Rostron T, Moore SC, Hering LM, Dobson SL, Bibi S, Mongkolsapaya J, Lambe T, Wootton D, Hall V, Hopkins S, Dong T, Barnes E, Screaton G, Richter A, Turtle L, Rowland-Jones SL, Carroll M, Duncan CJA, Klenerman P, Dunachie SJ, Payne RP, de Silva TI. Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history. Nat Commun 2023; 14:5065. [PMID: 37604803 PMCID: PMC10442364 DOI: 10.1038/s41467-023-40592-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
Pronounced immune escape by the SARS-CoV-2 Omicron variant has resulted in many individuals possessing hybrid immunity, generated through a combination of vaccination and infection. Concerns have been raised that omicron breakthrough infections in triple-vaccinated individuals result in poor induction of omicron-specific immunity, and that prior SARS-CoV-2 infection is associated with immune dampening. Taking a broad and comprehensive approach, we characterize mucosal and blood immunity to spike and non-spike antigens following BA.1/BA.2 infections in triple mRNA-vaccinated individuals, with and without prior SARS-CoV-2 infection. We find that most individuals increase BA.1/BA.2/BA.5-specific neutralizing antibodies following infection, but confirm that the magnitude of increase and post-omicron titres are higher in the infection-naive. In contrast, significant increases in nasal responses, including neutralizing activity against BA.5 spike, are seen regardless of infection history. Spike-specific T cells increase only in infection-naive vaccinees; however, post-omicron T cell responses are significantly higher in the previously-infected, who display a maximally induced response with a highly cytotoxic CD8+ phenotype following their 3rd mRNA vaccine dose. Responses to non-spike antigens increase significantly regardless of prior infection status. These findings suggest that hybrid immunity induced by omicron breakthrough infections is characterized by significant immune enhancement that can help protect against future omicron variants.
Collapse
Affiliation(s)
- Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Alexander R Nicols
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Stephanie Longet
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Adrienn Angyal
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jessica K Tyerman
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Tom Tipton
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peijun Zhang
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Marta Gallis
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Natalie A Barratt
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Jeremy M Nell
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lotta Gustafsson
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Scarlett Strickland
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Irina Grouneva
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Timothy Rostron
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Luisa M Hering
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susan L Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Dan Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Victoria Hall
- UK Health Security Agency, London, UK
- Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK
| | - Susan Hopkins
- UK Health Security Agency, London, UK
- Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alex Richter
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | - Sarah L Rowland-Jones
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Miles Carroll
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK.
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK.
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
| |
Collapse
|
15
|
Preechanukul A, Kronsteiner B, Saiprom N, Rochaikun K, Moonmueangsan B, Phunpang R, Ottiwet O, Kongphrai Y, Wapee S, Chotivanich K, Morakot C, Janon R, Dunachie SJ, Chantratita N. Identification and function of a novel human memory-like NK cell population expressing CD160 in melioidosis. iScience 2023; 26:107234. [PMID: 37520720 PMCID: PMC10372747 DOI: 10.1016/j.isci.2023.107234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
NK cells are endowed with immunological memory to a range of pathogens but the development of NK cell memory in bacterial infections remains elusive. Here, we establish an assay inducing memory-like NK cell response to Burkholderia pseudomallei, the causative agent of the severe bacterial disease called melioidosis, and explore NK cell memory in a melioidosis patient cohort. We show that NK cells require bacteria-primed monocytes to acquire memory-like properties, demonstrated by bacteria-specific responses, features that strongly associate with CD160 expression. Induction of this memory-like NK cell is partly dependent on CD160 and IL-12R. Importantly, CD160 expression identifies memory-like NK cells in a cohort of recovered melioidosis patients with heightened responses maintained at least 3 months post hospital admission and reduced numbers of this cell population independently correlate with recurrent melioidosis. These newly identified memory-like NK cells are a promising target for future vaccine design and for monitoring protection against infection.
Collapse
Affiliation(s)
- Anucha Preechanukul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kitilak Rochaikun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Boonthanom Moonmueangsan
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orawan Ottiwet
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Yuphin Kongphrai
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Soonthon Wapee
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Chumpol Morakot
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | - Rachan Janon
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | - Susanna J. Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| |
Collapse
|
16
|
Barnes E, Goodyear CS, Willicombe M, Gaskell C, Siebert S, I de Silva T, Murray SM, Rea D, Snowden JA, Carroll M, Pirrie S, Bowden SJ, Dunachie SJ, Richter A, Lim Z, Satsangi J, Cook G, Pope A, Hughes A, Harrison M, Lim SH, Miller P, Klenerman P, Basu N, Gilmour A, Irwin S, Meacham G, Marjot T, Dimitriadis S, Kelleher P, Prendecki M, Clarke C, Mortimer P, McIntyre S, Selby R, Meardon N, Nguyen D, Tipton T, Longet S, Laidlaw S, Orchard K, Ireland G, Thomas D, Kearns P, Kirkham A, McInnes IB. SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease. Nat Med 2023; 29:1760-1774. [PMID: 37414897 PMCID: PMC10353927 DOI: 10.1038/s41591-023-02414-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 05/23/2023] [Indexed: 07/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune responses and infection outcomes were evaluated in 2,686 patients with varying immune-suppressive disease states after administration of two Coronavirus Disease 2019 (COVID-19) vaccines. Overall, 255 of 2,204 (12%) patients failed to develop anti-spike antibodies, with an additional 600 of 2,204 (27%) patients generating low levels (<380 AU ml-1). Vaccine failure rates were highest in ANCA-associated vasculitis on rituximab (21/29, 72%), hemodialysis on immunosuppressive therapy (6/30, 20%) and solid organ transplant recipients (20/81, 25% and 141/458, 31%). SARS-CoV-2-specific T cell responses were detected in 513 of 580 (88%) patients, with lower T cell magnitude or proportion in hemodialysis, allogeneic hematopoietic stem cell transplantation and liver transplant recipients (versus healthy controls). Humoral responses against Omicron (BA.1) were reduced, although cross-reactive T cell responses were sustained in all participants for whom these data were available. BNT162b2 was associated with higher antibody but lower cellular responses compared to ChAdOx1 nCoV-19 vaccination. We report 474 SARS-CoV-2 infection episodes, including 48 individuals with hospitalization or death from COVID-19. Decreased magnitude of both the serological and the T cell response was associated with severe COVID-19. Overall, we identified clinical phenotypes that may benefit from targeted COVID-19 therapeutic strategies.
Collapse
Affiliation(s)
- Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Carl S Goodyear
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Charlotte Gaskell
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Stefan Siebert
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Sheffield, UK
| | - Sam M Murray
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Rea
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - John A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Pirrie
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Sarah J Bowden
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alex Richter
- Clinical Immunology Service, University of Birmingham, Edgbaston, Birmingham, UK
| | - Zixiang Lim
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon Cook
- National Institute for Health Research, Leeds MIC, University of Leeds, Leeds, UK
| | - Ann Pope
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Ana Hughes
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Molly Harrison
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Sean H Lim
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Paul Miller
- British Society of Blood and Marrow Transplantation and Cellular Therapy, Guy's Hospital, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Neil Basu
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Ashley Gilmour
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophie Irwin
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Georgina Meacham
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Marjot
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Peter Kelleher
- Department of Infectious Diseases, Imperial College London, School of Medicine Chelsea and Westminster Hospital, London, UK
| | - Maria Prendecki
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Candice Clarke
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Paige Mortimer
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Stacey McIntyre
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Rachael Selby
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Naomi Meardon
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Sheffield, UK
| | - Dung Nguyen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tom Tipton
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Laidlaw
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kim Orchard
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Georgina Ireland
- UK Health Security Agency (UKHSA), Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK
| | - David Thomas
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Pamela Kearns
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
- National Institute for Health Research Birmingham Biomedical Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Amanda Kirkham
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Iain B McInnes
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
17
|
Ragonnet-Cronin M, Nutalai R, Huo J, Dijokaite-Guraliuc A, Das R, Tuekprakhon A, Supasa P, Liu C, Selvaraj M, Groves N, Hartman H, Ellaby N, Mark Sutton J, Bahar MW, Zhou D, Fry E, Ren J, Brown C, Klenerman P, Dunachie SJ, Mongkolsapaya J, Hopkins S, Chand M, Stuart DI, Screaton GR, Rokadiya S. Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy. Nat Commun 2023; 14:3334. [PMID: 37286554 PMCID: PMC10246534 DOI: 10.1038/s41467-023-37826-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/03/2023] [Indexed: 06/09/2023] Open
Abstract
COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.
Collapse
Affiliation(s)
- Manon Ragonnet-Cronin
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
- Centre for Global Infectious Disease Analysis, Imperial College London, London, England.
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie Groves
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Hassan Hartman
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Nicholas Ellaby
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - J Mark Sutton
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Mohammad W Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Elizabeth Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Colin Brown
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Meera Chand
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Sakib Rokadiya
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
| |
Collapse
|
18
|
Johnson SA, Phillips E, Adele S, Longet S, Malone T, Mason C, Stafford L, Jamsen A, Gardiner S, Deeks A, Neo J, Blurton EJ, White J, Ali M, Kronsteiner B, Wilson JD, Skelly DT, Jeffery K, Conlon CP, Goulder P, Consortium PITCH, Carroll M, Barnes E, Klenerman P, Dunachie SJ. Evaluation of QuantiFERON SARS-CoV-2 interferon-γ release assay following SARS-CoV-2 infection and vaccination. Clin Exp Immunol 2023; 212:249-261. [PMID: 36807499 PMCID: PMC10243914 DOI: 10.1093/cei/uxad027] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/18/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
T cells are important in preventing severe disease from SARS-CoV-2, but scalable and field-adaptable alternatives to expert T-cell assays are needed. The interferon-gamma release assay QuantiFERON platform was developed to detect T-cell responses to SARS-CoV-2 from whole blood with relatively basic equipment and flexibility of processing timelines. Forty-eight participants with different infection and vaccination backgrounds were recruited. Whole blood samples were analysed using the QuantiFERON SARS-CoV-2 assay in parallel with the well-established 'Protective Immunity from T Cells in Healthcare workers' (PITCH) ELISpot, which can evaluate spike-specific T-cell responses. The primary aims of this cross-sectional observational cohort study were to establish if the QuantiFERON SARS-Co-V-2 assay could discern differences between specified groups and to assess the sensitivity of the assay compared with the PITCH ELISpot. The QuantiFERON SARS-CoV-2 distinguished acutely infected individuals (12-21 days post positive PCR) from naïve individuals (P < 0.0001) with 100% sensitivity and specificity for SARS-CoV-2 T cells, whilst the PITCH ELISpot had reduced sensitivity (62.5%) for the acute infection group. Sensitivity with QuantiFERON for previous infection was 12.5% (172-444 days post positive test) and was inferior to the PITCH ELISpot (75%). Although the QuantiFERON assay could discern differences between unvaccinated and vaccinated individuals (55-166 days since second vaccination), the latter also had reduced sensitivity (44.4%) compared to the PITCH ELISpot (66.6%). The QuantiFERON SARS-CoV-2 assay showed potential as a T- cell evaluation tool soon after SARS-CoV-2 infection but has lower sensitivity for use in reliable evaluation of vaccination or more distant infection.
Collapse
Affiliation(s)
- Síle A Johnson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- University of Oxford Medical School, University of Oxford, Oxford, UK
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Eloise Phillips
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Malone
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Chris Mason
- University of Oxford Medical School, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anni Jamsen
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Siobhan Gardiner
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Alexandra Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Janice Neo
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Emily J Blurton
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Jemima White
- University of Oxford Medical School, University of Oxford, Oxford, UK
| | - Muhammed Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Joseph D Wilson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- King’s College Hospital NHS Foundation Trust, London, UK
| | - Dónal T Skelly
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher P Conlon
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | - PITCH Consortium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| |
Collapse
|
19
|
Yazicioglu YF, Marin E, Sandhu C, Galiani S, Raza IGA, Ali M, Kronsteiner B, Compeer EB, Attar M, Dunachie SJ, Dustin ML, Clarke AJ. Dynamic mitochondrial transcription and translation in B cells control germinal center entry and lymphomagenesis. Nat Immunol 2023; 24:991-1006. [PMID: 37095377 PMCID: PMC10232359 DOI: 10.1038/s41590-023-01484-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/09/2023] [Indexed: 04/26/2023]
Abstract
Germinal center (GC) B cells undergo proliferation at very high rates in a hypoxic microenvironment but the cellular processes driving this are incompletely understood. Here we show that the mitochondria of GC B cells are highly dynamic, with significantly upregulated transcription and translation rates associated with the activity of transcription factor A, mitochondrial (TFAM). TFAM, while also necessary for normal B cell development, is required for entry of activated GC precursor B cells into the germinal center reaction; deletion of Tfam significantly impairs GC formation, function and output. Loss of TFAM in B cells compromises the actin cytoskeleton and impairs cellular motility of GC B cells in response to chemokine signaling, leading to their spatial disorganization. We show that B cell lymphoma substantially increases mitochondrial translation and that deletion of Tfam in B cells is protective against the development of lymphoma in a c-Myc transgenic mouse model. Finally, we show that pharmacological inhibition of mitochondrial transcription and translation inhibits growth of GC-derived human lymphoma cells and induces similar defects in the actin cytoskeleton.
Collapse
Affiliation(s)
| | - Eros Marin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ciaran Sandhu
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Silvia Galiani
- Medical Research Centre Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iwan G A Raza
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Mohammad Ali
- Nuffield Department of Medicine Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Barbara Kronsteiner
- Nuffield Department of Medicine Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- National Institute for Health and Care Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | |
Collapse
|
20
|
van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED. Accelerated waning of the humoral response to COVID-19 vaccines in obesity. Nat Med 2023; 29:1146-1154. [PMID: 37169862 PMCID: PMC10202802 DOI: 10.1038/s41591-023-02343-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023]
Abstract
Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m2) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m2). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.
Collapse
Affiliation(s)
- Agatha A van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Utkarsh Agrawal
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Sarah Spencer
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Bensi Vergese
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Isobel D Ramsay
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack A Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Iain M Hay
- Babraham Institute, Babraham Research Campus, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sam Thompson
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Lucy H Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Chris Robertson
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Colin McCowan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Steven Kerr
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Maria A Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Alex Ferreira
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Soraya Ebrahimi
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacopo Scotucci
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Adrian J Park
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Francesco Rubino
- Department of Diabetes, King's College London and King's College Hospital NHS Foundation Trust, London, UK
| | - Abigail A Lamikanra
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lise Estcourt
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - David J Roberts
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rainer Doffinger
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Aziz Sheikh
- Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | | |
Collapse
|
21
|
Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep 2023; 42:112271. [PMID: 36995936 PMCID: PMC9988707 DOI: 10.1016/j.celrep.2023.112271] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
Collapse
Key Words
- CP: Immunology
- CP: Microbiology
- SARS-CoV-2, BA.2, variant, mutation, RBD, antibodies, binding site, breakthrough, neutralizing, structure, COVID-19
Collapse
Affiliation(s)
- Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Neil G Paterson
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
22
|
Inthawong M, Sunyakumthorn P, Wongwairot S, Anantatat T, Dunachie SJ, Im-Erbsin R, Jones JW, Mason CJ, Lugo LA, Blacksell SD, Day NPJ, Sonthayanon P, Richards AL, Paris DH. Correction: A time-course comparative clinical and immune response evaluation study between the human pathogenic Orientia tsutsugamushi strains: Karp and Gilliam in a rhesus macaque (Macaca mulatta) model. PLoS Negl Trop Dis 2023; 17:e0011277. [PMID: 37043432 PMCID: PMC10096177 DOI: 10.1371/journal.pntd.0011277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pntd.0010611.].
Collapse
|
23
|
Inthawong M, Pinthong N, Thaiprakhong A, Wangrangsimakul T, Sunyakumthorn P, Hill J, Sonthayanon P, Paris DH, Dunachie SJ, Kronsteiner B. A whole blood intracellular cytokine assay optimised for field site studies demonstrates polyfunctionality of CD4+ T cells in acute scrub typhus. PLoS Negl Trop Dis 2023; 17:e0010905. [PMID: 36961865 PMCID: PMC10075457 DOI: 10.1371/journal.pntd.0010905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/05/2023] [Accepted: 02/25/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Assessment of cellular immune responses by combining intracellular cytokine staining and immunophenotyping using flow cytometry enables the simultaneous measurement of T cell phenotype and effector function in response to pathogens and vaccines. The use of whole blood samples rather than peripheral blood mononuclear cells avoids both the need for immediate processing and loss of functional antigen presenting cells due to processing and cryopreservation. Using whole blood provides the possibility to stimulate peripheral T cells in situ, and is more suitable for studies where sample volume is limited, such as those involving children, the elderly and critically ill patients. The aim of this study was to provide a robust tool for the assessment of antigen-specific T cell responses in a field site setting with limited resources. METHODOLOGY/PRINCIPLE FINDINGS We optimised a flow cytometry-based whole blood intracellular cytokine assay (WBA) with respect to duration of antigen stimulation and intracellular protein retention time. We demonstrate the ability of the WBA to capture polyfunctional T cell responses in the context of acute scrub typhus infection, by measuring IFN-γ, TNF and IL-2 in CD4+ and CD8+ T cells in response to the causative agent O. tsutsugamushi (OT). Using an optimised OT antigen preparation, we demonstrate the presence of polyfunctional antigen-specific memory CD4+ T cells in the blood of scrub typhus patients. CONCLUSIONS/SIGNIFICANCE In conclusion, this flow cytometry-based WBA is well-suited for use at field study sites, and enables the assessment of polyfunctional T cell responses to infectious agents and vaccines through delineation of antigen-specific cytokine secretion at the single cell level.
Collapse
Affiliation(s)
- Manutsanun Inthawong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Nattapon Pinthong
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Areerat Thaiprakhong
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tri Wangrangsimakul
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Center for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Piyanate Sunyakumthorn
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Jennifer Hill
- NDM Center for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Piengchan Sonthayanon
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Daniel H. Paris
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Medicine, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Center for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Barbara Kronsteiner
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Center for Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
24
|
Huo J, Dijokaite-Guraliuc A, Liu C, Zhou D, Ginn HM, Das R, Supasa P, Selvaraj M, Nutalai R, Tuekprakhon A, Duyvesteyn HME, Mentzer AJ, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Paterson NG, Williams MA, Hall DR, Plowright M, Newman TAH, Hornsby H, de Silva TI, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Pollard AJ, Lambe T, Goulder P, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75. Cell Rep 2023; 42:111903. [PMID: 36586406 PMCID: PMC9747698 DOI: 10.1016/j.celrep.2022.111903] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused successive global waves of infection. These variants, with multiple mutations in the spike protein, are thought to facilitate escape from natural and vaccine-induced immunity and often increase in affinity for ACE2. The latest variant to cause concern is BA.2.75, identified in India where it is now the dominant strain, with evidence of wider dissemination. BA.2.75 is derived from BA.2 and contains four additional mutations in the receptor-binding domain (RBD). Here, we perform an antigenic and biophysical characterization of BA.2.75, revealing an interesting balance between humoral evasion and ACE2 receptor affinity. ACE2 affinity for BA.2.75 is increased 9-fold compared with BA.2; there is also evidence of escape of BA.2.75 from immune serum, particularly that induced by Delta infection, which may explain the rapid spread in India, where where there is a high background of Delta infection. ACE2 affinity appears to be prioritized over greater escape.
Collapse
Affiliation(s)
- Jiandong Huo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Guangzhou Laboratory, Bio-island, Guangzhou 510320, China.
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sandra Adele
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Neil G Paterson
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
25
|
Dijokaite-Guraliuc A, Das R, Nutalai R, Zhou D, Mentzer AJ, Liu C, Supasa P, Dunachie SJ, Lambe T, Fry EE, Mongkolsapaya J, Ren J, Huo J, Stuart DI, Screaton GR. Antigenic characterization of SARS-CoV-2 Omicron subvariant BA.4.6. Cell Discov 2022; 8:127. [PMID: 36443292 PMCID: PMC9705283 DOI: 10.1038/s41421-022-00493-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jiandong Huo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
26
|
Inthawong M, Sunyakumthorn P, Wongwairot S, Anantatat T, Dunachie SJ, Im-Erbsin R, Jones JW, Mason CJ, Lugo LA, Blacksell SD, Day NPJ, Sonthayanon P, Richards AL, Paris DH. A time-course comparative clinical and immune response evaluation study between the human pathogenic Orientia tsutsugamushi strains: Karp and Gilliam in a rhesus macaque (Macaca mulatta) model. PLoS Negl Trop Dis 2022; 16:e0010611. [PMID: 35925895 PMCID: PMC9352090 DOI: 10.1371/journal.pntd.0010611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Scrub typhus is a vector-borne febrile illness caused by Orientia tsutsugamushi transmitted by the bite of Trombiculid mites. O. tsutsugamushi has a high genetic diversity and is increasingly recognized to have a wider global distribution than previously assumed. METHODOLOGY/PRINCIPLE FINDINGS We evaluated the clinical outcomes and host immune responses of the two most relevant human pathogenic strains of O. tsutsugamushi; Karp (n = 4) and Gilliam (n = 4) in a time-course study over 80 days post infection (dpi) in a standardized scrub typhus non-human primate rhesus macaque model. We observed distinct features in clinical progression and immune response between the two strains; Gilliam-infected macaques developed more pronounced systemic infection characterized by an earlier onset of bacteremia, lymph node enlargement, eschar lesions and higher inflammatory markers during the acute phase of infection, when compared to the Karp strain. C-reactive protein (CRP) plasma levels, interferon gamma (IFN-γ, interleukin-1 receptor antagonist (IL-1ra), IL-15 serum concentrations, CRP/IL10- and IFN-γ/IL-10 ratios correlated positively with bacterial load in blood, implying activation of the innate immune response and preferential development of a T helper-type 1 immune response. The O. tsutsugamushi-specific immune memory responses in cells isolated from skin and lymph nodes at 80 dpi were more markedly elevated in the Gilliam-infected macaques than in the Karp-infected group. The comparative cytokine response dynamics of both strains revealed significant up-regulation of IFN-γ, tumor necrosis factor (TNF), IL-15, IL-6, IL-18, regulatory IL-1ra, IL-10, IL-8 and granulocyte-colony-stimulating factor (G-CSF). These data suggest that the clinical outcomes and host immune responses to scrub typhus could be associated with counter balancing effects of pro- and anti-inflammatory cytokine-mediated responses. Currently, no data on characterized time-course comparisons of O. tsutsugamushi strains regarding measures of disease severity and immune response is available. Our study provides evidence for the strain-specificity of host responses in scrub typhus, which supports our understanding of processes at the initial inoculation site (eschar), systemic disease progression, protective and/or pathogenic host immune mechanisms and cellular immune memory function. CONCLUSIONS/SIGNIFICANCE This study characterised an improved intradermal rhesus macaque challenge model for scrub typhus, whereby the Gilliam strain infection associated with higher disease severity in the rhesus macaque model than the previous Karp strain infection. Difficulties associated with inoculum quantitation for obligate-intracellular bacteria were overcome by using functional inoculum titrations in outbred mice. The Gilliam-based rhesus macaque model provides improved endpoint measurements and contributes towards the identification of correlates of protection for future vaccine development.
Collapse
Affiliation(s)
- Manutsanun Inthawong
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyanate Sunyakumthorn
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sirima Wongwairot
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippawan Anantatat
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Rawiwan Im-Erbsin
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - James W. Jones
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Carl J. Mason
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Luis A. Lugo
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Stuart D. Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Piengchan Sonthayanon
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Allen L. Richards
- Viral & Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Daniel H. Paris
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Department of Medicine, Swiss Tropical and Public Health Institute, Faculty of Medicine, University of Basel, Switzerland
- Department of Clinical Research, Faculty of Medicine, University of Basel, Switzerland
| |
Collapse
|
27
|
Pérez-Hernández CA, Moreno-Altamirano MMB, López-Villegas EO, Butkeviciute E, Ali M, Kronsteiner B, Dunachie SJ, Dockrell HM, Smith SG, Sánchez-García FJ. Mitochondrial Ultrastructure and Activity Are Differentially Regulated by Glycolysis-, Krebs Cycle-, and Microbiota-Derived Metabolites in Monocytes. Biology (Basel) 2022; 11:biology11081132. [PMID: 36009759 PMCID: PMC9404980 DOI: 10.3390/biology11081132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022]
Abstract
Several intermediate metabolites harbour cell-signalling properties, thus, it is likely that specific metabolites enable the communication between neighbouring cells, as well as between host cells with the microbiota, pathogens, and tumour cells. Mitochondria, a source of intermediate metabolites, participate in a wide array of biological processes beyond that of ATP production, such as intracellular calcium homeostasis, cell signalling, apoptosis, regulation of immune responses, and host cell-microbiota crosstalk. In this regard, mitochondria's plasticity allows them to adapt their bioenergetics status to intra- and extra-cellular cues, and the mechanisms driving such plasticity are currently a matter of intensive research. Here, we addressed whether mitochondrial ultrastructure and activity are differentially shaped when human monocytes are exposed to an exogenous source of lactate (derived from glycolysis), succinate, and fumarate (Krebs cycle metabolic intermediates), or butyrate and acetate (short-chain fatty acids produced by intestinal microbiota). It has previously been shown that fumarate induces mitochondrial fusion, increases the mitochondrial membrane potential (Δψm), and reshapes the mitochondrial cristae ultrastructure. Here, we provide evidence that, in contrast to fumarate, lactate, succinate, and butyrate induce mitochondrial fission, while acetate induces mitochondrial swelling. These traits, along with mitochondrial calcium influx kinetics and glycolytic vs. mitochondrial ATP-production rates, suggest that these metabolites differentially shape mitochondrial function, paving the way for the understanding of metabolite-induced metabolic reprogramming of monocytes and its possible use for immune-response intervention.
Collapse
Affiliation(s)
- C. Angélica Pérez-Hernández
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (C.A.P.-H.); (M.M.B.M.-A.)
| | - M. Maximina Bertha Moreno-Altamirano
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (C.A.P.-H.); (M.M.B.M.-A.)
| | - Edgar O. López-Villegas
- Unidad de Microscopía, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Egle Butkeviciute
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.B.); (H.M.D.)
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 3SY, UK; (M.A.); (B.K.); (S.J.D.)
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 3SY, UK; (M.A.); (B.K.); (S.J.D.)
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Susanna J. Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 3SY, UK; (M.A.); (B.K.); (S.J.D.)
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Hazel M. Dockrell
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.B.); (H.M.D.)
| | - Steven G. Smith
- Division of Biosciences, Brunel University London, London UB8 3PH, UK;
| | - F. Javier Sánchez-García
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (C.A.P.-H.); (M.M.B.M.-A.)
- Correspondence:
| |
Collapse
|
28
|
Phillips E, Adele S, Malone T, Deeks A, Stafford L, Dobson SL, Amini A, Skelly D, Eyre D, Jeffery K, Conlon CP, Dold C, Otter A, D’Arcangelo S, Turtle L, Klenerman P, Barnes E, Dunachie SJ. Comparison of two T-cell assays to evaluate T-cell responses to SARS-CoV-2 following vaccination in naïve and convalescent healthcare workers. Clin Exp Immunol 2022; 209:90-98. [PMID: 35522978 PMCID: PMC9129206 DOI: 10.1093/cei/uxac042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
T-cell responses to SARS-CoV-2 following infection and vaccination are less characterized than antibody responses, due to a more complex experimental pathway. We measured T-cell responses in 108 healthcare workers (HCWs) using the commercialized Oxford Immunotec T-SPOT Discovery SARS-CoV-2 assay service (OI T-SPOT) and the PITCH ELISpot protocol established for academic research settings. Both assays detected T-cell responses to SARS-CoV-2 spike, membrane, and nucleocapsid proteins. Responses were significantly lower when reported by OI T-SPOT than by PITCH ELISpot. Four weeks after two doses of either Pfizer/BioNTech BNT162b or ChAdOx1 nCoV-19 AZD1222 vaccine, the responder rate was 63% for OI T-SPOT Panels 1 + 2 (peptides representing SARS-CoV-2 spike protein excluding regions present in seasonal coronaviruses), 69% for OI T-SPOT Panel 14 (peptides representing the entire SARS-CoV-2 spike), and 94% for the PITCH ELISpot total spike. The two OI T-SPOT panels correlated strongly with each other showing that either readout quantifies spike-specific T-cell responses, although the correlation between the OI T-SPOT panels and the PITCH ELISpot total spike was moderate. The standardization, relative scalability, and longer interval between blood acquisition and processing are advantages of the commercial OI T-SPOT assay. However, the OI T-SPOT assay measures T-cell responses at a significantly lower magnitude compared to the PITCH ELISpot assay, detecting T-cell responses in a lower proportion of vaccinees. This has implications for the reporting of low-level T-cell responses that may be observed in patient populations and for the assessment of T-cell durability after vaccination.
Collapse
Affiliation(s)
- Eloise Phillips
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Tom Malone
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Alexandra Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Lizzie Stafford
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Susan L Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University ofLiverpool, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Nuffield Department of Clinical Neuroscience, University ofOxford, UK
| | - David Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher P Conlon
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University ofLiverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, member of Liverpool Health Partners, Liverpool, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| |
Collapse
|
29
|
Tuekprakhon A, Nutalai R, Dijokaite-Guraliuc A, Zhou D, Ginn HM, Selvaraj M, Liu C, Mentzer AJ, Supasa P, Duyvesteyn HME, Das R, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Fry EE, Huo J, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell 2022; 185:2422-2433.e13. [PMID: 35772405 PMCID: PMC9181312 DOI: 10.1016/j.cell.2022.06.005] [Citation(s) in RCA: 419] [Impact Index Per Article: 209.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022]
Abstract
The Omicron lineage of SARS-CoV-2, which was first described in November 2021, spread rapidly to become globally dominant and has split into a number of sublineages. BA.1 dominated the initial wave but has been replaced by BA.2 in many countries. Recent sequencing from South Africa's Gauteng region uncovered two new sublineages, BA.4 and BA.5, which are taking over locally, driving a new wave. BA.4 and BA.5 contain identical spike sequences, and although closely related to BA.2, they contain further mutations in the receptor-binding domain of their spikes. Here, we study the neutralization of BA.4/5 using a range of vaccine and naturally immune serum and panels of monoclonal antibodies. BA.4/5 shows reduced neutralization by the serum from individuals vaccinated with triple doses of AstraZeneca or Pfizer vaccine compared with BA.1 and BA.2. Furthermore, using the serum from BA.1 vaccine breakthrough infections, there are, likewise, significant reductions in the neutralization of BA.4/5, raising the possibility of repeat Omicron infections.
Collapse
Affiliation(s)
- Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sandra Adele
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
30
|
Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR. Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell 2022; 185:2116-2131.e18. [PMID: 35662412 PMCID: PMC9120130 DOI: 10.1016/j.cell.2022.05.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 05/14/2022] [Indexed: 11/28/2022]
Abstract
Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
Collapse
Affiliation(s)
- Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sandra Adele
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
31
|
Shankar S, Beckett J, Tipton T, Ogbe A, Kasanyinga M, Dold C, Lumley S, Dengu F, Rompianesi G, Elgilani F, Longet S, Deeks A, Payne RP, Duncan CJ, Richter A, de Silva TI, Turtle L, Bull K, Barnardo M, Friend PJ, Dunachie SJ, Hester J, Issa F, Barnes E, Carroll MW, Klenerman P. SARS-CoV-2-Specific T Cell Responses Are Not Associated with Protection against Reinfection in Hemodialysis Patients. J Am Soc Nephrol 2022; 33:883-887. [PMID: 35361708 PMCID: PMC9063898 DOI: 10.1681/asn.2021121587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Significance Statement
Patients on hemodialysis (HD) are vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mount poor neutralizing antibody responses after two-dose vaccination. Although serological responses have been associated with reduced rates of reinfection, the relationship between cellular immunogenicity and protection has not been established. We report, for the first time, high incidence of reinfection in patients on HD who are vaccine naive (25%), which identifies that T cell responses do not predict protection against reinfection. Instead, patients on HD who went on to become reinfected had mounted highly variable and sometimes robust proliferative T cell responses to a broad array of SARS-CoV-2 peptide pools during the primary infection. The understanding that SARS-CoV-2–specific T cell responses are not predictive of protection against future infection will be a critical issue when measuring clinical efficacy of vaccination in these vulnerable cohorts, particularly when facing rapidly emerging variants of concern.
Collapse
Affiliation(s)
- Sushma Shankar
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Joseph Beckett
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Tom Tipton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Mwila Kasanyinga
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Christina Dold
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Sheila Lumley
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Fungai Dengu
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Gianluca Rompianesi
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Faysal Elgilani
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Stephanie Longet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alexandra Deeks
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Rebecca P. Payne
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher J.A. Duncan
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Alex Richter
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Lance Turtle
- National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Trust, Liverpool, United Kingdom
| | - Katherine Bull
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Martin Barnardo
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Peter J. Friend
- Oxford Transplant Centre, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Susanna J. Dunachie
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Joanna Hester
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Fadi Issa
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Miles W. Carroll
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
32
|
Tomic A, Skelly DT, Ogbe A, O'Connor D, Pace M, Adland E, Alexander F, Ali M, Allott K, Azim Ansari M, Belij-Rammerstorfer S, Bibi S, Blackwell L, Brown A, Brown H, Cavell B, Clutterbuck EA, de Silva T, Eyre D, Lumley S, Flaxman A, Grist J, Hackstein CP, Halkerston R, Harding AC, Hill J, James T, Jay C, Johnson SA, Kronsteiner B, Lie Y, Linder A, Longet S, Marinou S, Matthews PC, Mellors J, Petropoulos C, Rongkard P, Sedik C, Silva-Reyes L, Smith H, Stockdale L, Taylor S, Thomas S, Tipoe T, Turtle L, Vieira VA, Wrin T, Pollard AJ, Lambe T, Conlon CP, Jeffery K, Travis S, Goulder P, Frater J, Mentzer AJ, Stafford L, Carroll MW, James WS, Klenerman P, Barnes E, Dold C, Dunachie SJ. Divergent trajectories of antiviral memory after SARS-CoV-2 infection. Nat Commun 2022; 13:1251. [PMID: 35273178 PMCID: PMC8913789 DOI: 10.1038/s41467-022-28898-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/17/2022] [Indexed: 12/17/2022] Open
Abstract
The trajectories of acquired immunity to severe acute respiratory syndrome coronavirus 2 infection are not fully understood. We present a detailed longitudinal cohort study of UK healthcare workers prior to vaccination, presenting April-June 2020 with asymptomatic or symptomatic infection. Here we show a highly variable range of responses, some of which (T cell interferon-gamma ELISpot, N-specific antibody) wane over time, while others (spike-specific antibody, B cell memory ELISpot) are stable. We use integrative analysis and a machine-learning approach (SIMON - Sequential Iterative Modeling OverNight) to explore this heterogeneity. We identify a subgroup of participants with higher antibody responses and interferon-gamma ELISpot T cell responses, and a robust trajectory for longer term immunity associates with higher levels of neutralising antibodies against the infecting (Victoria) strain and also against variants B.1.1.7 (alpha) and B.1.351 (beta). These variable trajectories following early priming may define subsequent protection from severe disease from novel variants.
Collapse
Affiliation(s)
- Adriana Tomic
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Donal T Skelly
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Dept of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Matthew Pace
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Emily Adland
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Frances Alexander
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kirk Allott
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Luke Blackwell
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Helen Brown
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Breeze Cavell
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | | | - Thushan de Silva
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - David Eyre
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Big Data Institute, Nuffield Dept. of Population Health, University of Oxford, Oxford, UK
| | - Sheila Lumley
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, University of Oxford, Oxford, UK
| | - James Grist
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Rachel Halkerston
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | - Adam C Harding
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Tim James
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Cecilia Jay
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Síle A Johnson
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford University Medical School, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yolanda Lie
- Monogram Biosciences LabCorp, San Francisco, CA, USA
| | - Aline Linder
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Stephanie Longet
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Spyridoula Marinou
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Philippa C Matthews
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jack Mellors
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | | | - Patpong Rongkard
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Cynthia Sedik
- Monogram Biosciences LabCorp, San Francisco, CA, USA
| | - Laura Silva-Reyes
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Holly Smith
- Jenner Institute, University of Oxford, Oxford, UK
| | - Lisa Stockdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Stephen Taylor
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | - Stephen Thomas
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
| | - Timothy Tipoe
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Lance Turtle
- HPRU in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (a member of Liverpool Health Partners), Liverpool, UK
| | - Vinicius Adriano Vieira
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Terri Wrin
- Monogram Biosciences LabCorp, San Francisco, CA, USA
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, University of Oxford, Oxford, UK
| | - Chris P Conlon
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Travis
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alex J Mentzer
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Miles W Carroll
- United Kingdom Health Security Agency, Porton Down, Wiltshire, England
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William S James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| |
Collapse
|
33
|
Ahern DJ, Ai Z, Ainsworth M, Allan C, Allcock A, Angus B, Ansari MA, Arancibia-Cárcamo CV, Aschenbrenner D, Attar M, Baillie JK, Barnes E, Bashford-Rogers R, Bashyal A, Beer S, Berridge G, Beveridge A, Bibi S, Bicanic T, Blackwell L, Bowness P, Brent A, Brown A, Broxholme J, Buck D, Burnham KL, Byrne H, Camara S, Candido Ferreira I, Charles P, Chen W, Chen YL, Chong A, Clutterbuck EA, Coles M, Conlon CP, Cornall R, Cribbs AP, Curion F, Davenport EE, Davidson N, Davis S, Dendrou CA, Dequaire J, Dib L, Docker J, Dold C, Dong T, Downes D, Drakesmith H, Dunachie SJ, Duncan DA, Eijsbouts C, Esnouf R, Espinosa A, Etherington R, Fairfax B, Fairhead R, Fang H, Fassih S, Felle S, Fernandez Mendoza M, Ferreira R, Fischer R, Foord T, Forrow A, Frater J, Fries A, Gallardo Sanchez V, Garner LC, Geeves C, Georgiou D, Godfrey L, Golubchik T, Gomez Vazquez M, Green A, Harper H, Harrington HA, Heilig R, Hester S, Hill J, Hinds C, Hird C, Ho LP, Hoekzema R, Hollis B, Hughes J, Hutton P, Jackson-Wood MA, Jainarayanan A, James-Bott A, Jansen K, Jeffery K, Jones E, Jostins L, Kerr G, Kim D, Klenerman P, Knight JC, Kumar V, Kumar Sharma P, Kurupati P, Kwok A, Lee A, Linder A, Lockett T, Lonie L, Lopopolo M, Lukoseviciute M, Luo J, Marinou S, Marsden B, Martinez J, Matthews PC, Mazurczyk M, McGowan S, McKechnie S, Mead A, Mentzer AJ, Mi Y, Monaco C, Montadon R, Napolitani G, Nassiri I, Novak A, O'Brien DP, O'Connor D, O'Donnell D, Ogg G, Overend L, Park I, Pavord I, Peng Y, Penkava F, Pereira Pinho M, Perez E, Pollard AJ, Powrie F, Psaila B, Quan TP, Repapi E, Revale S, Silva-Reyes L, Richard JB, Rich-Griffin C, Ritter T, Rollier CS, Rowland M, Ruehle F, Salio M, Sansom SN, Sanches Peres R, Santos Delgado A, Sauka-Spengler T, Schwessinger R, Scozzafava G, Screaton G, Seigal A, Semple MG, Sergeant M, Simoglou Karali C, Sims D, Skelly D, Slawinski H, Sobrinodiaz A, Sousos N, Stafford L, Stockdale L, Strickland M, Sumray O, Sun B, Taylor C, Taylor S, Taylor A, Thongjuea S, Thraves H, Todd JA, Tomic A, Tong O, Trebes A, Trzupek D, Tucci FA, Turtle L, Udalova I, Uhlig H, van Grinsven E, Vendrell I, Verheul M, Voda A, Wang G, Wang L, Wang D, Watkinson P, Watson R, Weinberger M, Whalley J, Witty L, Wray K, Xue L, Yeung HY, Yin Z, Young RK, Youngs J, Zhang P, Zurke YX. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell 2022; 185:916-938.e58. [PMID: 35216673 PMCID: PMC8776501 DOI: 10.1016/j.cell.2022.01.012] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19.
Collapse
|
34
|
Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, Han C, Bisignano C, Rao P, Wool E, Johnson SC, Browne AJ, Chipeta MG, Fell F, Hackett S, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, McManigal B, Achalapong S, Agarwal R, Akech S, Albertson S, Amuasi J, Andrews J, Aravkin A, Ashley E, Babin FX, Bailey F, Baker S, Basnyat B, Bekker A, Bender R, Berkley JA, Bethou A, Bielicki J, Boonkasidecha S, Bukosia J, Carvalheiro C, Castañeda-Orjuela C, Chansamouth V, Chaurasia S, Chiurchiù S, Chowdhury F, Clotaire Donatien R, Cook AJ, Cooper B, Cressey TR, Criollo-Mora E, Cunningham M, Darboe S, Day NPJ, De Luca M, Dokova K, Dramowski A, Dunachie SJ, Duong Bich T, Eckmanns T, Eibach D, Emami A, Feasey N, Fisher-Pearson N, Forrest K, Garcia C, Garrett D, Gastmeier P, Giref AZ, Greer RC, Gupta V, Haller S, Haselbeck A, Hay SI, Holm M, Hopkins S, Hsia Y, Iregbu KC, Jacobs J, Jarovsky D, Javanmardi F, Jenney AWJ, Khorana M, Khusuwan S, Kissoon N, Kobeissi E, Kostyanev T, Krapp F, Krumkamp R, Kumar A, Kyu HH, Lim C, Lim K, Limmathurotsakul D, Loftus MJ, Lunn M, Ma J, Manoharan A, Marks F, May J, Mayxay M, Mturi N, Munera-Huertas T, Musicha P, Musila LA, Mussi-Pinhata MM, Naidu RN, Nakamura T, Nanavati R, Nangia S, Newton P, Ngoun C, Novotney A, Nwakanma D, Obiero CW, Ochoa TJ, Olivas-Martinez A, Olliaro P, Ooko E, Ortiz-Brizuela E, Ounchanum P, Pak GD, Paredes JL, Peleg AY, Perrone C, Phe T, Phommasone K, Plakkal N, Ponce-de-Leon A, Raad M, Ramdin T, Rattanavong S, Riddell A, Roberts T, Robotham JV, Roca A, Rosenthal VD, Rudd KE, Russell N, Sader HS, Saengchan W, Schnall J, Scott JAG, Seekaew S, Sharland M, Shivamallappa M, Sifuentes-Osornio J, Simpson AJ, Steenkeste N, Stewardson AJ, Stoeva T, Tasak N, Thaiprakong A, Thwaites G, Tigoi C, Turner C, Turner P, van Doorn HR, Velaphi S, Vongpradith A, Vongsouvath M, Vu H, Walsh T, Walson JL, Waner S, Wangrangsimakul T, Wannapinij P, Wozniak T, Young Sharma TEMW, Yu KC, Zheng P, Sartorius B, Lopez AD, Stergachis A, Moore C, Dolecek C, Naghavi M. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399:629-655. [PMID: 35065702 PMCID: PMC8841637 DOI: 10.1016/s0140-6736(21)02724-0] [Citation(s) in RCA: 3979] [Impact Index Per Article: 1989.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. FINDINGS On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911-1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in Australasia, at 6·5 deaths (4·3-9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to AMR and 3·57 million (2·62-4·78) deaths associated with AMR in 2019. One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. INTERPRETATION To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
Collapse
|
35
|
Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 2022; 185:467-484.e15. [PMID: 35081335 PMCID: PMC8723827 DOI: 10.1016/j.cell.2021.12.046] [Citation(s) in RCA: 605] [Impact Index Per Article: 302.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022]
Abstract
On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.
Collapse
Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nicola Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kuan-Ying A Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital and Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
36
|
Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HM, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter T, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Clemens SAC, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Ditse Z, Da Silva K, Madhi S, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. bioRxiv 2021:2021.12.03.471045. [PMID: 34981049 PMCID: PMC8722586 DOI: 10.1101/2021.12.03.471045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
Collapse
Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M.E. Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M. Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
- Department of Respiratory Sciences, University of Leicester
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Nikki Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios- IOC/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Kuan-Ying A. Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J. Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Neil G. Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A. Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R. Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
- corresponding authors: , , , ,
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- corresponding authors: , , , ,
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- corresponding authors: , , , ,
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
- corresponding authors: , , , ,
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- corresponding authors: , , , ,
| |
Collapse
|
37
|
Tomás-Cortázar J, Bossi L, Quinn C, Reynolds CJ, Butler DK, Corcoran N, Murchú MÓ, McMahon E, Singh M, Rongkard P, Anguita J, Blanco A, Dunachie SJ, Altmann D, Boyton RJ, Arnold J, Giltaire S, McClean S. BpOmpW Antigen Stimulates the Necessary Protective T-Cell Responses Against Melioidosis. Front Immunol 2021; 12:767359. [PMID: 34966388 PMCID: PMC8710444 DOI: 10.3389/fimmu.2021.767359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022] Open
Abstract
Melioidosis is a potentially fatal bacterial disease caused by Burkholderia pseudomallei and is estimated to cause 89,000 deaths per year in endemic areas of Southeast Asia and Northern Australia. People with diabetes mellitus are most at risk of melioidosis, with a 12-fold increased susceptibility for severe disease. Interferon gamma (IFN-γ) responses from CD4 and CD8 T cells, but also from natural killer (NK) and natural killer T (NKT) cells, are necessary to eliminate the pathogen. We previously reported that immunization with B. pseudomallei OmpW (BpOmpW antigen) protected mice from lethal B. pseudomallei challenge for up to 81 days. Elucidating the immune correlates of protection of the protective BpOmpW vaccine is an essential step prior to clinical trials. Thus, we immunized either non-insulin-resistant C57BL/6J mice or an insulin-resistant C57BL/6J mouse model of type 2 diabetes (T2D) with a single dose of BpOmpW. BpOmpW induced strong antibody responses, stimulated effector CD4+ and CD8+ T cells and CD4+ CD25+ Foxp3+ regulatory T cells, and produced higher IFN-γ responses in CD4+, CD8+, NK, and NKT cells in non-insulin-resistant mice. The T-cell responses of insulin-resistant mice to BpOmpW were comparable to those of non-insulin-resistant mice. In addition, as a precursor to its evaluation in human studies, humanized HLA-DR and HLA-DQ (human leukocyte antigen DR and DQ isotypes, respectively) transgenic mice elicited IFN-γ recall responses in an enzyme-linked immune absorbent spot (ELISpot)-based study. Moreover, human donor peripheral blood mononuclear cells (PBMCs) exposed to BpOmpW for 7 days showed T-cell proliferation. Finally, plasma from melioidosis survivors with diabetes recognized our BpOmpW vaccine antigen. Overall, the range of approaches used strongly indicated that BpOmpW elicits the necessary immune responses to combat melioidosis and bring this vaccine closer to clinical trials.
Collapse
MESH Headings
- Animals
- Antigens, Bacterial/immunology
- Bacterial Outer Membrane Proteins/immunology
- Bacterial Vaccines/administration & dosage
- Bacterial Vaccines/immunology
- Burkholderia pseudomallei/immunology
- Burkholderia pseudomallei/metabolism
- Burkholderia pseudomallei/physiology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD4-Positive T-Lymphocytes/microbiology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/microbiology
- Cells, Cultured
- Diabetes Mellitus, Type 2/immunology
- Humans
- Interferon-gamma/immunology
- Interferon-gamma/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Killer Cells, Natural/microbiology
- Male
- Melioidosis/immunology
- Melioidosis/microbiology
- Melioidosis/prevention & control
- Mice, Inbred C57BL
- Mice, Transgenic
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/microbiology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/microbiology
- Mice
Collapse
Affiliation(s)
- Julen Tomás-Cortázar
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Lorenzo Bossi
- Immunxperts SA, a Nexelis Company, Gosselies, Belgium
| | - Conor Quinn
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Catherine J. Reynolds
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - David K. Butler
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Niamh Corcoran
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Maitiú Ó Murchú
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Eve McMahon
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Mahavir Singh
- LIONEX Diagnostics and Therapeutics GmbH, Brunswick, Germany
| | - Patpong Rongkard
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Oxford Centre for Global Health Research, University of Oxford, Oxford, United Kingdom
| | - Juan Anguita
- Inflammation and Macrophage Plasticity Lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Alfonso Blanco
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Oxford Centre for Global Health Research, University of Oxford, Oxford, United Kingdom
| | - Daniel Altmann
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Rosemary J. Boyton
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Johan Arnold
- Immunxperts SA, a Nexelis Company, Gosselies, Belgium
| | | | - Siobhán McClean
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
38
|
Skelly DT, Harding AC, Gilbert-Jaramillo J, Knight ML, Longet S, Brown A, Adele S, Adland E, Brown H, Tipton T, Stafford L, Mentzer AJ, Johnson SA, Amini A, Tan TK, Schimanski L, Huang KYA, Rijal P, Frater J, Goulder P, Conlon CP, Jeffery K, Dold C, Pollard AJ, Sigal A, de Oliveira T, Townsend AR, Klenerman P, Dunachie SJ, Barnes E, Carroll MW, James WS. Two doses of SARS-CoV-2 vaccination induce robust immune responses to emerging SARS-CoV-2 variants of concern. Nat Commun 2021; 12:5061. [PMID: 34404775 PMCID: PMC8371089 DOI: 10.1038/s41467-021-25167-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
The extent to which immune responses to natural infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and immunization with vaccines protect against variants of concern (VOC) is of increasing importance. Accordingly, here we analyse antibodies and T cells of a recently vaccinated, UK cohort, alongside those recovering from natural infection in early 2020. We show that neutralization of the VOC compared to a reference isolate of the original circulating lineage, B, is reduced: more profoundly against B.1.351 than for B.1.1.7, and in responses to infection or a single dose of vaccine than to a second dose of vaccine. Importantly, high magnitude T cell responses are generated after two vaccine doses, with the majority of the T cell response directed against epitopes that are conserved between the prototype isolate B and the VOC. Vaccination is required to generate high potency immune responses to protect against these and other emergent variants.
Collapse
Affiliation(s)
- Donal T Skelly
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Clinial Neurosciences, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adam C Harding
- James and Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Javier Gilbert-Jaramillo
- James and Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Michael L Knight
- James and Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Public Health England, Porton Down, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emily Adland
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Helen Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Tipton
- Public Health England, Porton Down, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Síle A Johnson
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Ali Amini
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lisa Schimanski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford, UK
| | - Kuan-Ying A Huang
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and Taipei Medical University, Taipei, Taiwan
| | - Pramila Rijal
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Miles W Carroll
- Public Health England, Porton Down, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William S James
- James and Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
39
|
Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang B, Tuekprakhon A, Nutalai R, Zhou D, Mentzer AJ, Zhao Y, Duyvesteyn HME, López-Camacho C, Slon-Campos J, Walter TS, Skelly D, Johnson SA, Ritter TG, Mason C, Costa Clemens SA, Gomes Naveca F, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Dold C, Temperton N, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert SC, Malik T, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Baillie V, Serafin N, Ditse Z, Da Silva K, Paterson NG, Williams MA, Hall DR, Madhi S, Nunes MC, Goulder P, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell 2021; 184:4220-4236.e13. [PMID: 34242578 PMCID: PMC8218332 DOI: 10.1016/j.cell.2021.06.020] [Citation(s) in RCA: 501] [Impact Index Per Article: 167.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.
Collapse
Affiliation(s)
- Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas S Walter
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Clutterbuck
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sagida Bibi
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mustapha Bittaye
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - David I Stuart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK; Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
40
|
Chaichana P, Jenjaroen K, Chumseng S, Sumonwiriya M, Rongkard P, Kronsteiner B, Teparrukkul P, Limmathurotsakul D, Day NPJ, Chantratita N, Dunachie SJ. Role of Burkholderia pseudomallei-Specific IgG2 in Adults with Acute Melioidosis, Thailand. Emerg Infect Dis 2021; 27:463-470. [PMID: 33496230 PMCID: PMC7853568 DOI: 10.3201/eid2702.200213] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Melioidosis is a life-threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei. An effective vaccine is needed, but data on protective immune responses in human melioidosis are lacking. We used ELISA and an antibody-dependent cellular phagocytosis assay to identify the major features of protective antibodies in patients with acute melioidosis in Thailand. We found that high levels of B. pseudomallei–specific IgG2 are associated with protection against death in a multivariable logistic regression analysis adjusting for age, diabetes, renal disease, and neutrophil count. Serum from melioidosis survivors enhanced bacteria uptake into human monocytes expressing FcγRIIa-H/R131, an intermediate-affinity IgG2-receptor, compared with serum from nonsurvivors. We did not find this enhancement when using monocytes carrying the low IgG2–affinity FcγRIIa-R131 allele. The findings indicate the importance of IgG2 in protection against death in human melioidosis, a crucial finding for antibody-based therapeutics and vaccine development.
Collapse
|
41
|
Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, Zhao Y, Duyvesteyn HME, Tuekprakhon A, Nutalai R, Wang B, López-Camacho C, Slon-Campos J, Walter TS, Skelly D, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Dold C, Levin R, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert SC, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Hulswit RJG, Bowden TA, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell 2021; 184:2939-2954.e9. [PMID: 33852911 PMCID: PMC8008340 DOI: 10.1016/j.cell.2021.03.055] [Citation(s) in RCA: 402] [Impact Index Per Article: 134.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations, including P.1 from Brazil, B.1.351 from South Africa, and B.1.1.7 from the UK (12, 10, and 9 changes in the spike, respectively). All have mutations in the ACE2 binding site, with P.1 and B.1.351 having a virtually identical triplet (E484K, K417N/T, and N501Y), which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine-induced antibody responses than B.1.351, suggesting that changes outside the receptor-binding domain (RBD) impact neutralization. Monoclonal antibody (mAb) 222 neutralizes all three variants despite interacting with two of the ACE2-binding site mutations. We explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.
Collapse
Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Yuguang Zhao
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas S Walter
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil
| | | | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Alex Pauvolid-Correa
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Clutterbuck
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sagida Bibi
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mustapha Bittaye
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Ruben J G Hulswit
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas A Bowden
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
42
|
Zhou D, Dejnirattisai W, Supasa P, Liu C, Mentzer AJ, Ginn HM, Zhao Y, Duyvesteyn HME, Tuekprakhon A, Nutalai R, Wang B, Paesen GC, Lopez-Camacho C, Slon-Campos J, Hallis B, Coombes N, Bewley K, Charlton S, Walter TS, Skelly D, Lumley SF, Dold C, Levin R, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert S, James W, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cell 2021; 184:2348-2361.e6. [PMID: 33730597 PMCID: PMC7901269 DOI: 10.1016/j.cell.2021.02.037] [Citation(s) in RCA: 714] [Impact Index Per Article: 238.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
The race to produce vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began when the first sequence was published, and this forms the basis for vaccines currently deployed globally. Independent lineages of SARS-CoV-2 have recently been reported: UK, B.1.1.7; South Africa, B.1.351; and Brazil, P.1. These variants have multiple changes in the immunodominant spike protein that facilitates viral cell entry via the angiotensin-converting enzyme-2 (ACE2) receptor. Mutations in the receptor recognition site on the spike are of great concern for their potential for immune escape. Here, we describe a structure-function analysis of B.1.351 using a large cohort of convalescent and vaccinee serum samples. The receptor-binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K, although K417N and N501Y act together against some important antibody classes. In a number of cases, it would appear that convalescent and some vaccine serum offers limited protection against this variant.
Collapse
Affiliation(s)
- Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen M Ginn
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guido C Paesen
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Cesar Lopez-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bassam Hallis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Naomi Coombes
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Kevin Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Sue Charlton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Thomas S Walter
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sheila F Lumley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Tao Dong
- Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Clutterbuck
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sagida Bibi
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mustapha Bittaye
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - William James
- Sir William Dunn School of Pathology University of Oxford, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
43
|
Supasa P, Zhou D, Dejnirattisai W, Liu C, Mentzer AJ, Ginn HM, Zhao Y, Duyvesteyn HME, Nutalai R, Tuekprakhon A, Wang B, Paesen GC, Slon-Campos J, López-Camacho C, Hallis B, Coombes N, Bewley KR, Charlton S, Walter TS, Barnes E, Dunachie SJ, Skelly D, Lumley SF, Baker N, Shaik I, Humphries HE, Godwin K, Gent N, Sienkiewicz A, Dold C, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert S, Hall DR, Williams MA, Paterson NG, James W, Carroll MW, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell 2021; 184:2201-2211.e7. [PMID: 33743891 PMCID: PMC7891044 DOI: 10.1016/j.cell.2021.02.033] [Citation(s) in RCA: 347] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/06/2021] [Accepted: 02/13/2021] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.
Collapse
Affiliation(s)
- Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Yuguang Zhao
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guido C Paesen
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jose Slon-Campos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bassam Hallis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Naomi Coombes
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Kevin R Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Sue Charlton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Thomas S Walter
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sheila F Lumley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie Baker
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Imam Shaik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Holly E Humphries
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Kerry Godwin
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Nick Gent
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Alex Sienkiewicz
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Clutterbuck
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sagida Bibi
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mustapha Bittaye
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - William James
- Sir William Dunn School of Pathology University of Oxford, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| |
Collapse
|
44
|
Rongkard P, Kronsteiner B, Hantrakun V, Jenjaroen K, Sumonwiriya M, Chaichana P, Chumseng S, Chantratita N, Wuthiekanun V, Fletcher HA, Teparrukkul P, Limmathurotsakul D, Day NPJ, Dunachie SJ. Human Immune Responses to Melioidosis and Cross-Reactivity to Low-Virulence Burkholderia Species, Thailand 1. Emerg Infect Dis 2021; 26:463-471. [PMID: 32091359 PMCID: PMC7045851 DOI: 10.3201/eid2603.190206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Melioidosis is a neglected tropical disease with an estimated annual mortality rate of 89,000 in 45 countries across tropical regions. The causative agent is Burkholderia pseudomallei, a gram-negative soil-dwelling bacterium. In Thailand, B. pseudomallei can be found across multiple regions, along with the low-virulence B. thailandensis and the recently discovered B. thailandensis variant (BTCV), which expresses B. pseudomallei-like capsular polysaccharide. Comprehensive studies of human immune responses to B. thailandensis variants and cross-reactivity to B. pseudomallei are not complete. We evaluated human immune responses to B. pseudomallei, B. thailandensis, and BTCV in melioidosis patients and healthy persons in B. pseudomallei-endemic areas using a range of humoral and cellular immune assays. We found immune cross-reactivity to be strong for both humoral and cellular immunity among B. pseudomallei, B. thailandensis, and BTCV. Our findings suggest that environmental exposure to low-virulence strains may build cellular immunity to B. pseudomallei.
Collapse
|
45
|
Frost JN, Tan TK, Abbas M, Wideman SK, Bonadonna M, Stoffel NU, Wray K, Kronsteiner B, Smits G, Campagna DR, Duarte TL, Lopes JM, Shah A, Armitage AE, Arezes J, Lim PJ, Preston AE, Ahern D, Teh M, Naylor C, Salio M, Gileadi U, Andrews SC, Dunachie SJ, Zimmermann MB, van der Klis FR, Cerundolo V, Bannard O, Draper SJ, Townsend AR, Galy B, Fleming MD, Lewis MC, Drakesmith H. Hepcidin-Mediated Hypoferremia Disrupts Immune Responses to Vaccination and Infection. Med 2021; 2:164-179.e12. [PMID: 33665641 PMCID: PMC7895906 DOI: 10.1016/j.medj.2020.10.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/26/2020] [Accepted: 10/16/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND How specific nutrients influence adaptive immunity is of broad interest. Iron deficiency is the most common micronutrient deficiency worldwide and imparts a significant burden of global disease; however, its effects on immunity remain unclear. METHODS We used a hepcidin mimetic and several genetic models to examine the effect of low iron availability on T cells in vitro and on immune responses to vaccines and viral infection in mice. We examined humoral immunity in human patients with raised hepcidin and low serum iron caused by mutant TMPRSS6. We tested the effect of iron supplementation on vaccination-induced humoral immunity in piglets, a natural model of iron deficiency. FINDINGS We show that low serum iron (hypoferremia), caused by increased hepcidin, severely impairs effector and memory responses to immunizations. The intensified metabolism of activated lymphocytes requires the support of enhanced iron acquisition, which is facilitated by IRP1/2 and TFRC. Accordingly, providing extra iron improved the response to vaccination in hypoferremic mice and piglets, while conversely, hypoferremic humans with chronically increased hepcidin have reduced concentrations of antibodies specific for certain pathogens. Imposing hypoferremia blunted the T cell, B cell, and neutralizing antibody responses to influenza virus infection in mice, allowing the virus to persist and exacerbating lung inflammation and morbidity. CONCLUSIONS Hypoferremia, a well-conserved physiological innate response to infection, can counteract the development of adaptive immunity. This nutrient trade-off is relevant for understanding and improving immune responses to infections and vaccines in the globally common contexts of iron deficiency and inflammatory disorders. FUNDING Medical Research Council, UK.
Collapse
Affiliation(s)
- Joe N. Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Munawar Abbas
- Food and Nutritional Sciences, School of Chemistry, Food, and Pharmacy, University of Reading, Reading, UK
| | - Sarah K. Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Michael Bonadonna
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Nicole U. Stoffel
- ETH Zurich, Human Nutrition Laboratory, Institute of Food, Nutrition, and Health, Zurich, Switzerland
| | - Katherine Wray
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Barbara Kronsteiner
- Centre for Tropical Medicine and Global Health, and Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Gaby Smits
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Dean R. Campagna
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tiago L. Duarte
- Instituto de Biologia Molecular e Celular & Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - José M. Lopes
- Faculty of Medicine (FMUP) and Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, Porto, Portugal
| | - Akshay Shah
- Radcliffe Department of Medicine, University of Oxford and John Radcliffe Hospital, Oxford, UK
| | - Andrew E. Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - João Arezes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Pei Jin Lim
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alexandra E. Preston
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Ahern
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Megan Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Caitlin Naylor
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Simon C. Andrews
- School of Biological Sciences, University of Reading, Reading, UK
| | - Susanna J. Dunachie
- Centre for Tropical Medicine and Global Health, and Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Michael B. Zimmermann
- ETH Zurich, Human Nutrition Laboratory, Institute of Food, Nutrition, and Health, Zurich, Switzerland
| | - Fiona R.M. van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Oliver Bannard
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Alain R.M. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Bruno Galy
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mark D. Fleming
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Marie C. Lewis
- Food and Nutritional Sciences, School of Chemistry, Food, and Pharmacy, University of Reading, Reading, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Haematology Theme, Oxford Biomedical Research Centre, Oxford, UK
| |
Collapse
|
46
|
Ainsworth M, Andersson M, Auckland K, Baillie JK, Barnes E, Beer S, Beveridge A, Bibi S, Blackwell L, Borak M, Bown A, Brooks T, Burgess-Brown NA, Camara S, Catton M, Chau KK, Christott T, Clutterbuck E, Coker J, Cornall RJ, Cox S, Crawford-Jones D, Crook DW, D'Arcangelo S, Dejnirattsai W, Dequaire JMM, Dimitriadis S, Dingle KE, Doherty G, Dold C, Dong T, Dunachie SJ, Ebner D, Emmenegger M, Espinosa A, Eyre DW, Fairhead R, Fassih S, Feehily C, Felle S, Fernandez-Cid A, Fernandez Mendoza M, Foord TH, Fordwoh T, Fox McKee D, Frater J, Gallardo Sanchez V, Gent N, Georgiou D, Groves CJ, Hallis B, Hammond PM, Hatch SB, Harvala HJ, Hill J, Hoosdally SJ, Horsington B, Howarth A, James T, Jeffery K, Jones E, Justice A, Karpe F, Kavanagh J, Kim DS, Kirton R, Klenerman P, Knight JC, Koukouflis L, Kwok A, Leuschner U, Levin R, Linder A, Lockett T, Lumley SF, Marinou S, Marsden BD, Martinez J, Martins Ferreira L, Mason L, Matthews PC, Mentzer AJ, Mobbs A, Mongkolsapaya J, Morrow J, Mukhopadhyay SMM, Neville MJ, Oakley S, Oliveira M, Otter A, Paddon K, Pascoe J, Peng Y, Perez E, Perumal PK, Peto TEA, Pickford H, Ploeg RJ, Pollard AJ, Richardson A, Ritter TG, Roberts DJ, Rodger G, Rollier CS, Rowe C, Rudkin JK, Screaton G, Semple MG, Sienkiewicz A, Silva-Reyes L, Skelly DT, Sobrino Diaz A, Stafford L, Stockdale L, Stoesser N, Street T, Stuart DI, Sweed A, Taylor A, Thraves H, Tsang HP, Verheul MK, Vipond R, Walker TM, Wareing S, Warren Y, Wells C, Wilson C, Withycombe K, Young RK. Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison. Lancet Infect Dis 2020; 20:1390-1400. [PMID: 32979318 PMCID: PMC7511171 DOI: 10.1016/s1473-3099(20)30634-4] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in 2020. Testing is crucial for mitigating public health and economic effects. Serology is considered key to population-level surveillance and potentially individual-level risk assessment. However, immunoassay performance has not been compared on large, identical sample sets. We aimed to investigate the performance of four high-throughput commercial SARS-CoV-2 antibody immunoassays and a novel 384-well ELISA. METHODS We did a head-to-head assessment of SARS-CoV-2 IgG assay (Abbott, Chicago, IL, USA), LIAISON SARS-CoV-2 S1/S2 IgG assay (DiaSorin, Saluggia, Italy), Elecsys Anti-SARS-CoV-2 assay (Roche, Basel, Switzerland), SARS-CoV-2 Total assay (Siemens, Munich, Germany), and a novel 384-well ELISA (the Oxford immunoassay). We derived sensitivity and specificity from 976 pre-pandemic blood samples (collected between Sept 4, 2014, and Oct 4, 2016) and 536 blood samples from patients with laboratory-confirmed SARS-CoV-2 infection, collected at least 20 days post symptom onset (collected between Feb 1, 2020, and May 31, 2020). Receiver operating characteristic (ROC) curves were used to assess assay thresholds. FINDINGS At the manufacturers' thresholds, for the Abbott assay sensitivity was 92·7% (95% CI 90·2-94·8) and specificity was 99·9% (99·4-100%); for the DiaSorin assay sensitivity was 96·2% (94·2-97·7) and specificity was 98·9% (98·0-99·4); for the Oxford immunoassay sensitivity was 99·1% (97·8-99·7) and specificity was 99·0% (98·1-99·5); for the Roche assay sensitivity was 97·2% (95·4-98·4) and specificity was 99·8% (99·3-100); and for the Siemens assay sensitivity was 98·1% (96·6-99·1) and specificity was 99·9% (99·4-100%). All assays achieved a sensitivity of at least 98% with thresholds optimised to achieve a specificity of at least 98% on samples taken 30 days or more post symptom onset. INTERPRETATION Four commercial, widely available assays and a scalable 384-well ELISA can be used for SARS-CoV-2 serological testing to achieve sensitivity and specificity of at least 98%. The Siemens assay and Oxford immunoassay achieved these metrics without further optimisation. This benchmark study in immunoassay assessment should enable refinements of testing strategies and the best use of serological testing resource to benefit individuals and population health. FUNDING Public Health England and UK National Institute for Health Research.
Collapse
|
47
|
Dunachie SJ, Day NP, Dolecek C. The challenges of estimating the human global burden of disease of antimicrobial resistant bacteria. Curr Opin Microbiol 2020; 57:95-101. [PMID: 33147565 PMCID: PMC7763986 DOI: 10.1016/j.mib.2020.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/29/2022]
Abstract
Estimating the contribution of antimicrobial resistance (AMR) to global mortality and healthcare costs enables evaluation of interventions, informs policy decisions on resource allocation, and drives research priorities. However assembling the high quality, patient-level data required for global estimates is challenging. Capacity for accurate microbiology culture and antimicrobial susceptibility testing is woefully neglected in low and middle-income countries, and further surveillance and research on community antimicrobial usage, bias in blood culture sampling, and the contribution of co-morbidities such as diabetes is essential. International collaboration between governments, policy makers, academics, microbiologists, front-line clinicians, veterinarians, the food and agriculture industry and the public is critical to understand and tackle AMR.
Collapse
Affiliation(s)
- Susanna J Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Nicholas Pj Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
48
|
Chaichana P, Kronsteiner B, Rongkard P, Teparrukkul P, Limmathurotsakul D, Chantratita N, Day NPJ, Fletcher HA, Dunachie SJ. Serum From Melioidosis Survivors Diminished Intracellular Burkholderia pseudomallei Growth in Macrophages: A Brief Research Report. Front Cell Infect Microbiol 2020; 10:442. [PMID: 32984070 PMCID: PMC7479196 DOI: 10.3389/fcimb.2020.00442] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/20/2020] [Indexed: 11/18/2022] Open
Abstract
Melioidosis is a neglected tropical disease with high mortality rate. It is caused by the Gram-negative, CDC category B select agent Burkholderia pseudomallei (B. ps) that is intrinsically resistant to first-line antibiotics. An antibody-based vaccine is likely to be the most effective control measure. Previous studies have demonstrated significant mechanistic roles of antibodies in protection against death in animal models, but data from human melioidosis is scarce. Herein, we used in-vitro antibody-dependent cellular phagocytosis and growth inhibition assays to assess the mechanism of protective antibodies in patients with acute melioidosis. We found that serum from patients who survived the disease enable more live B. ps to be engulfed by THP-1 derived macrophages (median 1.7 × 103 CFU/ml, IQR 1.1 × 103-2.5 × 103 CFU/ml) than serum from patients who did not survive (median 1.2 × 103 CFU/ml, IQR 0.7 × 103-1.8 × 103, p = 0.02). In addition, the intracellular growth rate of B. ps pre-opsonized with serum from survivors (median 7.89, IQR 5.58–10.85) was diminished when compared with those with serum from non-survivors (median 10.88, IQR 5.42–14.88, p = 0.04). However, the difference of intracellular bacterial growth rate failed to reach statistical significance when using purified IgG antibodies (p = 0.09). These results provide new insights into a mechanistic role of serum in protection against death in human melioidosis for antibody-based vaccine development.
Collapse
Affiliation(s)
- Panjaporn Chaichana
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.,Center for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Patpong Rongkard
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Prapit Teparrukkul
- Medical Department, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Center for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Department of Tropical Hygiene, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Center for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Helen A Fletcher
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.,Center for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
49
|
Wagner GE, Föderl-Höbenreich E, Assig K, Lipp M, Berner A, Kohler C, Lichtenegger S, Stiehler J, Karoonboonyanan W, Thanapattarapairoj N, Promkong C, Koosakulnirand S, Chaichana P, Ehricht R, Gad AM, Söffing HH, Dunachie SJ, Chantratita N, Steinmetz I. Melioidosis DS rapid test: A standardized serological dipstick assay with increased sensitivity and reliability due to multiplex detection. PLoS Negl Trop Dis 2020; 14:e0008452. [PMID: 32658917 PMCID: PMC7416965 DOI: 10.1371/journal.pntd.0008452] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/10/2020] [Accepted: 06/04/2020] [Indexed: 11/30/2022] Open
Abstract
Background Melioidosis, caused by Burkholderia pseudomallei, is a severe infectious disease with high mortality rates, but is under-recognized worldwide. In endemic areas, there is a great need for simple, low-cost and rapid diagnostic tools. In a previous study we showed, that a protein multiplex array with 20 B. pseudomallei-specific antigens detects antibodies in melioidosis patients with high sensitivity and specificity. In a subsequent study the high potential of anti-B. pseudomallei antibody detection was confirmed using a rapid Hcp1 single protein-based assay. Our protein array also showed that the antibody profile varies between patients, possibly due to a combination of host factors but also antigen variations in the infecting B. pseudomallei strains. The aim of this study was to develop a rapid test, combining Hcp1 and the best performing antigens BPSL2096, BPSL2697 and BPSS0477 from our previous study, to take advantage of simultaneous antibody detection. Methods and principal findings The 4-plex dipstick was validated with sera from 75 patients on admission plus control groups, achieving 92% sensitivity and 97–100% specificity. We then re-evaluated melioidosis sera with the 4-plex assay that were previously misclassified by the monoplex Hcp1 rapid test. 12 out of 55 (21.8%) false-negative samples were positive in our new dipstick assay. Among those, 4 sera (7.3%) were Hcp1 positive, whereas 8 (14.5%) sera remained Hcp1 negative but gave a positive reaction with our additional antigens. Conclusions Our dipstick rapid test represents an inexpensive, standardized and simple diagnostic tool with an improved serodiagnostic performance due to multiplex detection. Each additional band on the test strip makes a false-positive result more unlikely, contributing to its reliability. Future prospective studies will seek to validate the gain in sensitivity and specificity of our multiplex rapid test approach in different melioidosis patient cohorts. The Gram-negative environmental pathogen Burkholderia pseudomallei, causes the severe disease melioidosis. It is highly endemic in southeast Asia and northern Australia, but recent studies suggest that it is also present in many other parts of the world where it is severely underreported. The latter results from the extremely variable and non-specific clinical manifestations of the disease, lack of clinical recognition, and the global scarcity of good quality laboratories to allow diagnosis from microbiological culture. This is even more unfortunate, as early diagnosis of the disease is indispensable for an effective therapy, since B. pseudomallei is intrinsically resistant to many antibiotics used for empirical treatment in endemic areas. Therefore, the development of new, standardized and sensitive tools is of high importance for both diagnostics and epidemiology. We focused on the development of a dipstick assay, which is based on the detection of serum antibodies against four B. pseudomallei specific protein antigens. Here we present a cost effective, simple and rapid melioidosis assay with improved sensitivity that does not depend on sophisticated laboratory equipment and therefore addresses most of the before mentioned obstacles and is easy to manufacture in large scales.
Collapse
Affiliation(s)
- Gabriel E. Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Esther Föderl-Höbenreich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Karoline Assig
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Michaela Lipp
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Berner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Kohler
- Friedrich Loeffler Institute for Medical Microbiology, Greifswald, Germany
| | - Sabine Lichtenegger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Julia Stiehler
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | | | - Chidchanok Promkong
- Department of Medical Laboratory, Nakhon Phanom Hospital, Nakhon Phanom, Thailand
| | - Sirikamon Koosakulnirand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Panjaporn Chaichana
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Anne-Marie Gad
- Senova Gesellschaft für Biowissenschaft und Technik mbH, Weimar, Germany
| | - Hans H. Söffing
- Senova Gesellschaft für Biowissenschaft und Technik mbH, Weimar, Germany
| | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ivo Steinmetz
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| |
Collapse
|
50
|
Reiner RC, Wiens KE, Deshpande A, Baumann MM, Lindstedt PA, Blacker BF, Troeger CE, Earl L, Munro SB, Abate D, Abbastabar H, Abd-Allah F, Abdelalim A, Abdollahpour I, Abdulkader RS, Abebe G, Abegaz KH, Abreu LG, Abrigo MRM, Accrombessi MMK, Acharya D, Adabi M, Adebayo OM, Adedoyin RA, Adekanmbi V, Adetokunboh OO, Adhena BM, Afarideh M, Ahmadi K, Ahmadi M, Ahmed AE, Ahmed MB, Ahmed R, Ajumobi O, Akal CG, Akalu TY, Akanda AS, Alamene GM, Alanzi TM, Albright JR, Alcalde Rabanal JE, Alemnew BT, Alemu ZA, Ali BA, Ali M, Alijanzadeh M, Alipour V, Aljunid SM, Almasi A, Almasi-Hashiani A, Al-Mekhlafi HM, Altirkawi K, Alvis-Guzman N, Alvis-Zakzuk NJ, Amare AT, Amini S, Amit AML, Andrei CL, Anegago MT, Anjomshoa M, Ansari F, Antonio CAT, Antriyandarti E, Appiah SCY, Arabloo J, Aremu O, Armoon B, Aryal KK, Arzani A, Asadi-Lari M, Ashagre AF, Atalay HT, Atique S, Atre SR, Ausloos M, Avila-Burgos L, Awasthi A, Awoke N, Ayala Quintanilla BP, Ayano G, Ayanore MA, Ayele AA, Aynalem YAA, Azari S, Babaee E, Badawi A, Bakkannavar SM, Balakrishnan S, Bali AG, Banach M, Barac A, Bärnighausen TW, Basaleem H, Bassat Q, Bayati M, Bedi N, Behzadifar M, Behzadifar M, Bekele YA, Bell ML, Bennett DA, Berbada DA, Beyranvand T, Bhat AG, Bhattacharyya K, Bhattarai S, Bhaumik S, Bijani A, Bikbov B, Biswas RK, Bogale KA, Bohlouli S, Brady OJ, Bragazzi NL, Briko NI, Briko AN, Burugina Nagaraja S, Butt ZA, Campos-Nonato IR, Campuzano Rincon JC, Cárdenas R, Carvalho F, Castro F, Chansa C, Chatterjee P, Chattu VK, Chauhan BG, Chin KL, Christopher DJ, Chu DT, Claro RM, Cormier NM, Costa VM, Damiani G, Daoud F, Dandona L, Dandona R, Darwish AH, Daryani A, Das JK, Das Gupta R, Dasa TT, Davila CA, Davis Weaver N, Davitoiu DV, De Neve JW, Demeke FM, Demis AB, Demoz GT, Denova-Gutiérrez E, Deribe K, Desalew A, Dessie GA, Dharmaratne SD, Dhillon P, Dhimal M, Dhungana GP, Diaz D, Ding EL, Diro HD, Djalalinia S, Do HP, Doku DT, Dolecek C, Dubey M, Dubljanin E, Duko Adema B, Dunachie SJ, Durães AR, Duraisamy S, Effiong A, Eftekhari A, El Sayed I, El Sayed Zaki M, El Tantawi M, Elemineh DA, El-Jaafary SI, Elkout H, Elsharkawy A, Enany S, Endalamfaw A, Endalew DA, Eskandarieh S, Esteghamati A, Etemadi A, Farag TH, Faraon EJA, Fareed M, Faridnia R, Farioli A, Faro A, Farzam H, Fazaeli AA, Fazlzadeh M, Fentahun N, Fereshtehnejad SM, Fernandes E, Filip I, Fischer F, Foroutan M, Francis JM, Franklin RC, Frostad JJ, Fukumoto T, Gayesa RT, Gebremariam KT, Gebremedhin KBB, Gebremeskel GG, Gedefaw GA, Geramo YCD, Geta B, Gezae KE, Ghashghaee A, Ghassemi F, Gill PS, Ginawi IA, Goli S, Gomes NGM, Gopalani SV, Goulart BNG, Grada A, Gugnani HC, Guido D, Guimares RA, Guo Y, Gupta R, Gupta R, Hafezi-Nejad N, Haile MT, Hailu GB, Haj-Mirzaian A, Haj-Mirzaian A, Hall BJ, Handiso DW, Haririan H, Hariyani N, Hasaballah AI, Hasan MM, Hasanzadeh A, Hassankhani H, Hassen HY, Hayelom DH, Heidari B, Henry NJ, Herteliu C, Heydarpour F, Hidru HDD, Hoang CL, Hoogar P, Hoseini-Ghahfarokhi M, Hossain N, Hosseini M, Hosseinzadeh M, Househ M, Hu G, Humayun A, Hussain SA, Ibitoye SE, Ilesanmi OS, Ilic MD, Inbaraj LR, Irvani SSN, Islam SMS, Iwu CJ, Jaca A, Jafari Balalami N, Jahanmehr N, Jakovljevic M, Jalali A, Jayatilleke AU, Jenabi E, Jha RP, Jha V, Ji JS, Jia P, Johnson KB, Jonas JB, Jozwiak JJ, Kabir A, Kabir Z, Kahsay A, Kalani H, Kanchan T, Karami Matin B, Karch A, Karki S, Kasaeian A, Kasahun GG, Kayode GA, Kazemi Karyani A, Keiyoro PN, Ketema DB, Khader YS, Khafaie MA, Khalid N, Khalil AT, Khalil I, Khalilov R, Khan MN, Khan EA, Khan G, Khan J, Khatab K, Khater A, Khater MM, Khatony A, Khayamzadeh M, Khazaei M, Khazaei S, Khodamoradi E, Khosravi MH, Khubchandani J, Kiadaliri AA, Kim YJ, Kimokoti RW, Kisa S, Kisa A, Kissoon N, Kondlahalli SKMKMM, Kosek MN, Koyanagi A, Kraemer MUG, Krishan K, Kugbey N, Kumar GA, Kumar M, Kumar P, Kusuma D, La Vecchia C, Lacey B, Lal A, Lal DK, Lami FH, Lansingh VC, Lasrado S, Lee PH, Leili M, Lenjebo TTLL, Levine AJ, Lewycka S, Li S, Linn S, Lodha R, Longbottom J, Lopukhov PD, Magdeldin S, Mahasha PW, Mahotra NB, Malta DC, Mamun AA, Manafi N, Manafi F, Manda AL, Mansournia MA, Mapoma CC, Marami D, Marczak LB, Martins-Melo FR, März W, Masaka A, Mathur MR, Maulik PK, Mayala BK, McAlinden C, Mehndiratta MM, Mehrotra R, Mehta KM, Meles GG, Melese A, Memish ZA, Mena AT, Menezes RG, Mengesha MM, Mengistu DT, Mengistu G, Meretoja TJ, Miazgowski B, Mihretie KMM, Miller-Petrie MK, Mills EJ, Mir SM, Mirabi P, Mirrakhimov EM, Mohamadi-Bolbanabad A, Mohammad KA, Mohammad Y, Mohammad DK, Mohammad Darwesh A, Mohammad Gholi Mezerji N, Mohammadifard N, Mohammed AS, Mohammed S, Mohammed JA, Mohebi F, Mokdad AH, Monasta L, Moodley Y, Moradi M, Moradi G, Moradi-Joo M, Moradi-Lakeh M, Moraga P, Mosapour A, Mouodi S, Mousavi SM, Mozaffor MMM, Muluneh AG, Muriithi MK, Murray CJL, Murthy GVS, Musa KI, Mustafa G, Muthupandian S, Naderi M, Nagarajan AJ, Naghavi M, Najafi F, Nangia V, Nazari J, Ndwandwe DE, Negoi I, Ngunjiri JW, Nguyen QP, Nguyen TH, Nguyen CT, Nigatu D, Ningrum DNA, Nnaji CA, Nojomi M, Noubiap JJ, Oh IH, Okpala O, Olagunju AT, Omar Bali A, Onwujekwe OE, Ortega-Altamirano DDV, Osarenotor O, Osei FB, Owolabi MO, P A M, Padubidri JR, Pana A, Pashaei T, Pati S, Patle A, Patton GC, Paulos K, Pepito VCF, Pereira A, Perico N, Pesudovs K, Pigott DM, Piroozi B, Platts-Mills JA, Poljak M, Postma MJ, Pourjafar H, Pourmalek F, Pourshams A, Poustchi H, Prada SI, Preotescu L, Quintana H, Rabiee N, Rabiee M, Radfar A, Rafiei A, Rahim F, Rahimi-Movaghar V, Rahman MA, Rajati F, Ramezanzadeh K, Rana SM, Ranabhat CL, Rasella D, Rawaf S, Rawaf DL, Rawal L, Remuzzi G, Renjith V, Renzaho AMN, Reta MA, Rezaei S, Ribeiro AI, Rickard J, Rios González CM, Rios-Blancas MJ, Roever L, Ronfani L, Roro EM, Rostami A, Rothenbacher D, Rubagotti E, Rubino S, Saad AM, Sabour S, Sadeghi E, Safari S, Safdarian M, Sagar R, Sahraian MA, Sajadi SM, Salahshoor MR, Salam N, Salehi F, Salehi Zahabi S, Salem MRR, Salem H, Salimi Y, Salimzadeh H, Sambala EZ, Samy AM, Sanabria J, Santos IS, Saraswathy SYI, Sarker AR, Sartorius B, Sathian B, Satpathy M, Sbarra AN, Schaeffer LE, Schwebel DC, Senbeta AM, Senthilkumaran S, Shabaninejad H, Shaheen AA, Shaikh MA, Shalash AS, Shallo SA, Shams-Beyranvand M, Shamsi M, Shamsizadeh M, Sharif M, Shey MS, Shibuya K, Shiferaw WSS, Shigematsu M, Shil A, Shin JI, Shiri R, Shirkoohi R, Si S, Siabani S, Singh JA, Singh NP, Sinha DN, Sisay MM, Skiadaresi E, Smith DL, Sobhiyeh MR, Sokhan A, Soofi M, Soriano JB, Sorrie MB, Soyiri IN, Sreeramareddy CT, Sudaryanto A, Sufiyan MB, Suleria HAR, Sykes BL, Tamirat KS, Tassew AA, Taveira N, Taye B, Tehrani-Banihashemi A, Temsah MH, Tesfay BE, Tesfay FH, Tessema ZT, Thankappan KR, Thirunavukkarasu S, Thomas N, Tlaye KG, Tlou B, Tovani-Palone MR, Traini E, Tran KB, Trihandini I, Ullah I, Unnikrishnan B, Valadan Tahbaz S, Valdez PR, Varughese S, Veisani Y, Violante FS, Vollmer S, Vos T, Wada FW, Waheed Y, Wang Y, Wang YP, Weldesamuel GT, Welgan CA, Westerman R, Wiangkham T, Wijeratne T, Wiysonge CSS, Wolde HF, Wondafrash DZ, Wonde TE, Wu AM, Xu G, Yadollahpour A, Yahyazadeh Jabbari SH, Yamada T, Yaseri M, Yenesew MA, Yeshaneh A, Yilma MT, Yimer EM, Yip P, Yirsaw BD, Yisma E, Yonemoto N, Younis MZ, Yousof HASA, Yu C, Yusefzadeh H, Zamani M, Zambrana-Torrelio C, Zandian H, Zeleke AJ, Zepro NB, Zewale TA, Zhang D, Zhang Y, Zhao XJ, Ziapour A, Zodpey S, Hay SI. Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000-17: analysis for the Global Burden of Disease Study 2017. Lancet 2020; 395:1779-1801. [PMID: 32513411 PMCID: PMC7314599 DOI: 10.1016/s0140-6736(20)30114-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/24/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Across low-income and middle-income countries (LMICs), one in ten deaths in children younger than 5 years is attributable to diarrhoea. The substantial between-country variation in both diarrhoea incidence and mortality is attributable to interventions that protect children, prevent infection, and treat disease. Identifying subnational regions with the highest burden and mapping associated risk factors can aid in reducing preventable childhood diarrhoea. METHODS We used Bayesian model-based geostatistics and a geolocated dataset comprising 15 072 746 children younger than 5 years from 466 surveys in 94 LMICs, in combination with findings of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, to estimate posterior distributions of diarrhoea prevalence, incidence, and mortality from 2000 to 2017. From these data, we estimated the burden of diarrhoea at varying subnational levels (termed units) by spatially aggregating draws, and we investigated the drivers of subnational patterns by creating aggregated risk factor estimates. FINDINGS The greatest declines in diarrhoeal mortality were seen in south and southeast Asia and South America, where 54·0% (95% uncertainty interval [UI] 38·1-65·8), 17·4% (7·7-28·4), and 59·5% (34·2-86·9) of units, respectively, recorded decreases in deaths from diarrhoea greater than 10%. Although children in much of Africa remain at high risk of death due to diarrhoea, regions with the most deaths were outside Africa, with the highest mortality units located in Pakistan. Indonesia showed the greatest within-country geographical inequality; some regions had mortality rates nearly four times the average country rate. Reductions in mortality were correlated to improvements in water, sanitation, and hygiene (WASH) or reductions in child growth failure (CGF). Similarly, most high-risk areas had poor WASH, high CGF, or low oral rehydration therapy coverage. INTERPRETATION By co-analysing geospatial trends in diarrhoeal burden and its key risk factors, we could assess candidate drivers of subnational death reduction. Further, by doing a counterfactual analysis of the remaining disease burden using key risk factors, we identified potential intervention strategies for vulnerable populations. In view of the demands for limited resources in LMICs, accurately quantifying the burden of diarrhoea and its drivers is important for precision public health. FUNDING Bill & Melinda Gates Foundation.
Collapse
|