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Ali YM, Carnell GW, Fumagalli S, Mercurio D, Seminara S, Lynch NJ, Khatri P, Arachchilage CH, Mascheroni L, Kaminski C, George CL, Stewart H, Yabuki M, Demopulos G, Heeney JL, Schwaeble W. Inhibition of the Lectin Pathway of Complement Activation Reduces Acute Respiratory Distress Syndrome Severity in a Mouse Model of SARS-CoV-2 Infection. J Infect Dis 2024; 229:680-690. [PMID: 37878754 PMCID: PMC10938221 DOI: 10.1093/infdis/jiad462] [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: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Most patients with COVID-19 in the intensive care unit develop an acute respiratory distress syndrome characterized by severe hypoxemia, decreased lung compliance, and high vascular permeability. Activation of the complement system is a hallmark of moderate and severe COVID-19, with abundant deposition of complement proteins in inflamed tissue and on the endothelium during COVID-19. Using a transgenic mouse model of SARS-CoV-2 infection, we assessed the therapeutic utility of an inhibitory antibody (HG4) targeting MASP-2, a key enzyme in the lectin pathway. Treatment of infected mice with HG4 reduced the disease severity score and improved survival vs mice that received an isotype control antibody. Administration of HG4 significantly reduced the lung injury score, including alveolar inflammatory cell infiltration, alveolar edema, and alveolar hemorrhage. The ameliorating effect of MASP-2 inhibition on the severity of COVID-19 pathology is reflected by a significant reduction in the proinflammatory activation of brain microglia in HG4-treated mice.
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Affiliation(s)
- Youssif M Ali
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - George W Carnell
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Stefano Fumagalli
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Domenico Mercurio
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Serena Seminara
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Nicholas J Lynch
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Priyanka Khatri
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Chanuka H Arachchilage
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Charlotte L George
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | | | | | - Jonathan L Heeney
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Wilhelm Schwaeble
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
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2
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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [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: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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3
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Stewart H, Palmulli R, Johansen KH, McGovern N, Shehata OM, Carnell GW, Jackson HK, Lee JS, Brown JC, Burgoyne T, Heeney JL, Okkenhaug K, Firth AE, Peden AA, Edgar JR. Tetherin antagonism by SARS-CoV-2 ORF3a and spike protein enhances virus release. EMBO Rep 2023; 24:e57224. [PMID: 37818801 PMCID: PMC10702813 DOI: 10.15252/embr.202357224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 03/21/2023] [Revised: 08/23/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
The antiviral restriction factor, tetherin, blocks the release of several different families of enveloped viruses, including the Coronaviridae. Tetherin is an interferon-induced protein that forms parallel homodimers between the host cell and viral particles, linking viruses to the surface of infected cells and inhibiting their release. We demonstrate that SARS-CoV-2 infection causes tetherin downregulation and that tetherin depletion from cells enhances SARS-CoV-2 viral titres. We investigate the potential viral proteins involved in abrogating tetherin function and find that SARS-CoV-2 ORF3a reduces tetherin localisation within biosynthetic organelles where Coronaviruses bud, and increases tetherin localisation to late endocytic organelles via reduced retrograde recycling. We also find that expression of Spike protein causes a reduction in cellular tetherin levels. Our results confirm that tetherin acts as a host restriction factor for SARS-CoV-2 and highlight the multiple distinct mechanisms by which SARS-CoV-2 subverts tetherin function.
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Affiliation(s)
- Hazel Stewart
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Kristoffer H Johansen
- Department of PathologyUniversity of CambridgeCambridgeUK
- Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Naomi McGovern
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Ola M Shehata
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - George W Carnell
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | | | - Jin S Lee
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Thomas Burgoyne
- Royal Brompton HospitalGuy's and St Thomas' NHS Foundation TrustLondonUK
- UCL Institute of OphthalmologyUniversity College LondonLondonUK
| | | | | | - Andrew E Firth
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Andrew A Peden
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - James R Edgar
- Department of PathologyUniversity of CambridgeCambridgeUK
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4
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Stewart H, Lu Y, O’Keefe S, Valpadashi A, Cruz-Zaragoza LD, Michel HA, Nguyen SK, Carnell GW, Lukhovitskaya N, Milligan R, Adewusi Y, Jungreis I, Lulla V, Matthews DA, High S, Rehling P, Emmott E, Heeney JL, Davidson AD, Edgar JR, Smith GL, Firth AE. The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity. iScience 2023; 26:108080. [PMID: 37860693 PMCID: PMC10583119 DOI: 10.1016/j.isci.2023.108080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 08/06/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localizes to mitochondria, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signaling downstream of type I IFN stimulation. We find that ORF3c is inhibitory after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterized mechanism of innate immune evasion by this important human pathogen.
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Affiliation(s)
- Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sarah O’Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Anusha Valpadashi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | | | | | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rachel Milligan
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Yasmin Adewusi
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Valeria Lulla
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Stephen High
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - James R. Edgar
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
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5
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Raman B, McCracken C, Cassar MP, Moss AJ, Finnigan L, Samat AHA, Ogbole G, Tunnicliffe EM, Alfaro-Almagro F, Menke R, Xie C, Gleeson F, Lukaschuk E, Lamlum H, McGlynn K, Popescu IA, Sanders ZB, Saunders LC, Piechnik SK, Ferreira VM, Nikolaidou C, Rahman NM, Ho LP, Harris VC, Shikotra A, Singapuri A, Pfeffer P, Manisty C, Kon OM, Beggs M, O'Regan DP, Fuld J, Weir-McCall JR, Parekh D, Steeds R, Poinasamy K, Cuthbertson DJ, Kemp GJ, Semple MG, Horsley A, Miller CA, O'Brien C, Shah AM, Chiribiri A, Leavy OC, Richardson M, Elneima O, McAuley HJC, Sereno M, Saunders RM, Houchen-Wolloff L, Greening NJ, Bolton CE, Brown JS, Choudhury G, Diar Bakerly N, Easom N, Echevarria C, Marks M, Hurst JR, Jones MG, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Howard LS, Jacob J, Man WDC, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Singh SJ, Thomas DC, Toshner M, Lewis KE, Heaney LG, Harrison EM, Kerr S, Docherty AB, Lone NI, Quint J, Sheikh A, Zheng B, Jenkins RG, Cox E, Francis S, Halling-Brown M, Chalmers JD, Greenwood JP, Plein S, Hughes PJC, Thompson AAR, Rowland-Jones SL, Wild JM, Kelly M, Treibel TA, Bandula S, Aul R, Miller K, Jezzard P, Smith S, Nichols TE, McCann GP, Evans RA, Wain LV, Brightling CE, Neubauer S, Baillie JK, Shaw A, Hairsine B, Kurasz C, Henson H, Armstrong L, Shenton L, Dobson H, Dell A, Lucey A, Price A, Storrie A, Pennington C, Price C, Mallison G, Willis G, Nassa H, Haworth J, Hoare M, Hawkings N, Fairbairn S, Young S, Walker S, Jarrold I, Sanderson A, David C, Chong-James K, Zongo O, James WY, Martineau A, King B, Armour C, McAulay D, Major E, McGinness J, McGarvey L, Magee N, Stone R, Drain S, Craig T, Bolger A, Haggar A, Lloyd A, Subbe C, Menzies D, Southern D, McIvor E, Roberts K, Manley R, Whitehead V, Saxon W, Bularga A, Mills NL, El-Taweel H, Dawson J, Robinson L, Saralaya D, Regan K, Storton K, Brear L, Amoils S, Bermperi A, Elmer A, Ribeiro C, Cruz I, Taylor J, Worsley J, Dempsey K, Watson L, Jose S, Marciniak S, Parkes M, McQueen A, Oliver C, Williams J, Paradowski K, Broad L, Knibbs L, Haynes M, Sabit R, Milligan L, Sampson C, Hancock A, Evenden C, Lynch C, Hancock K, Roche L, Rees M, Stroud N, Thomas-Woods T, Heller S, Robertson E, Young B, Wassall H, Babores M, Holland M, Keenan N, Shashaa S, Price C, Beranova E, Ramos H, Weston H, Deery J, Austin L, Solly R, Turney S, Cosier T, Hazelton T, Ralser M, Wilson A, Pearce L, Pugmire S, Stoker W, McCormick W, Dewar A, Arbane G, Kaltsakas G, Kerslake H, Rossdale J, Bisnauthsing K, Aguilar Jimenez LA, Martinez LM, Ostermann M, Magtoto MM, Hart N, Marino P, Betts S, Solano TS, Arias AM, Prabhu A, Reed A, Wrey Brown C, Griffin D, Bevan E, Martin J, Owen J, Alvarez Corral M, Williams N, Payne S, Storrar W, Layton A, Lawson C, Mills C, Featherstone J, Stephenson L, Burdett T, Ellis Y, Richards A, Wright C, Sykes DL, Brindle K, Drury K, Holdsworth L, Crooks MG, Atkin P, Flockton R, Thackray-Nocera S, Mohamed A, Taylor A, Perkins E, Ross G, McGuinness H, Tench H, Phipps J, Loosley R, Wolf-Roberts R, Coetzee S, Omar Z, Ross A, Card B, Carr C, King C, Wood C, Copeland D, Calvelo E, Chilvers ER, Russell E, Gordon H, Nunag JL, Schronce J, March K, Samuel K, Burden L, Evison L, McLeavey L, Orriss-Dib L, Tarusan L, Mariveles M, Roy M, Mohamed N, Simpson N, Yasmin N, Cullinan P, Daly P, Haq S, Moriera S, Fayzan T, Munawar U, Nwanguma U, Lingford-Hughes A, Altmann D, Johnston D, Mitchell J, Valabhji J, Price L, Molyneaux PL, Thwaites RS, Walsh S, Frankel A, Lightstone L, Wilkins M, Willicombe M, McAdoo S, Touyz R, Guerdette AM, Warwick K, Hewitt M, Reddy R, White S, McMahon A, Hoare A, Knighton A, Ramos A, Te A, Jolley CJ, Speranza F, Assefa-Kebede H, Peralta I, Breeze J, Shevket K, Powell N, Adeyemi O, Dulawan P, Adrego R, Byrne S, Patale S, Hayday A, Malim M, Pariante C, Sharpe C, Whitney J, Bramham K, Ismail K, Wessely S, Nicholson T, Ashworth A, Humphries A, Tan AL, Whittam B, Coupland C, Favager C, Peckham D, Wade E, Saalmink G, Clarke J, Glossop J, Murira J, Rangeley J, Woods J, Hall L, Dalton M, Window N, Beirne P, Hardy T, Coakley G, Turtle L, Berridge A, Cross A, Key AL, Rowe A, Allt AM, Mears C, Malein F, Madzamba G, Hardwick HE, Earley J, Hawkes J, Pratt J, Wyles J, Tripp KA, Hainey K, Allerton L, Lavelle-Langham L, Melling L, Wajero LO, Poll L, Noonan MJ, French N, Lewis-Burke N, Williams-Howard SA, Cooper S, Kaprowska S, Dobson SL, Marsh S, Highett V, Shaw V, Beadsworth M, Defres S, Watson E, Tiongson GF, Papineni P, Gurram S, Diwanji SN, Quaid S, Briggs A, Hastie C, Rogers N, Stensel D, Bishop L, McIvor K, Rivera-Ortega P, Al-Sheklly B, Avram C, Faluyi D, Blaikely J, Piper Hanley K, Radhakrishnan K, Buch M, Hanley NA, Odell N, Osbourne R, Stockdale S, Felton T, Gorsuch T, Hussell T, Kausar Z, Kabir T, McAllister-Williams H, Paddick S, Burn D, Ayoub A, Greenhalgh A, Sayer A, Young A, Price D, Burns G, MacGowan G, Fisher H, Tedd H, Simpson J, Jiwa K, Witham M, Hogarth P, West S, Wright S, McMahon MJ, Neill P, Dougherty A, Morrow A, Anderson D, Grieve D, Bayes H, Fallon K, Mangion K, Gilmour L, Basu N, Sykes R, Berry C, McInnes IB, Donaldson A, Sage EK, Barrett F, Welsh B, Bell M, Quigley J, Leitch K, Macliver L, Patel M, Hamil R, Deans A, Furniss J, Clohisey S, Elliott A, Solstice AR, Deas C, Tee C, Connell D, Sutherland D, George J, Mohammed S, Bunker J, Holmes K, Dipper A, Morley A, Arnold D, Adamali H, Welch H, Morrison L, Stadon L, Maskell N, Barratt S, Dunn S, Waterson S, Jayaraman B, Light T, Selby N, Hosseini A, Shaw K, Almeida P, Needham R, Thomas AK, Matthews L, Gupta A, Nikolaidis A, Dupont C, Bonnington J, Chrystal M, Greenhaff PL, Linford S, Prosper S, Jang W, Alamoudi A, Bloss A, Megson C, Nicoll D, Fraser E, Pacpaco E, Conneh F, Ogg G, McShane H, Koychev I, Chen J, Pimm J, Ainsworth M, Pavlides M, Sharpe M, Havinden-Williams M, Petousi N, Talbot N, Carter P, Kurupati P, Dong T, Peng Y, Burns A, Kanellakis N, Korszun A, Connolly B, Busby J, Peto T, Patel B, Nolan CM, Cristiano D, Walsh JA, Liyanage K, Gummadi M, Dormand N, Polgar O, George P, Barker RE, Patel S, Price L, Gibbons M, Matila D, Jarvis H, Lim L, Olaosebikan O, Ahmad S, Brill S, Mandal S, Laing C, Michael A, Reddy A, Johnson C, Baxendale H, Parfrey H, Mackie J, Newman J, Pack J, Parmar J, Paques K, Garner L, Harvey A, Summersgill C, Holgate D, Hardy E, Oxton J, Pendlebury J, McMorrow L, Mairs N, Majeed N, Dark P, Ugwuoke R, Knight S, Whittaker S, Strong-Sheldrake S, Matimba-Mupaya W, Chowienczyk P, Pattenadk D, Hurditch E, Chan F, Carborn H, Foot H, Bagshaw J, Hockridge J, Sidebottom J, Lee JH, Birchall K, Turner K, Haslam L, Holt L, Milner L, Begum M, Marshall M, Steele N, Tinker N, Ravencroft P, Butcher R, Misra S, Walker S, Coburn Z, Fairman A, Ford A, Holbourn A, Howell A, Lawrie A, Lye A, Mbuyisa A, Zawia A, Holroyd-Hind B, Thamu B, Clark C, Jarman C, Norman C, Roddis C, Foote D, Lee E, Ilyas F, Stephens G, Newell H, Turton H, Macharia I, Wilson I, Cole J, McNeill J, Meiring J, Rodger J, Watson J, Chapman K, Harrington K, Chetham L, Hesselden L, Nwafor L, Dixon M, Plowright M, Wade P, Gregory R, Lenagh R, Stimpson R, Megson S, Newman T, Cheng Y, Goodwin C, Heeley C, Sissons D, Sowter D, Gregory H, Wynter I, Hutchinson J, Kirk J, Bennett K, Slack K, Allsop L, Holloway L, Flynn M, Gill M, Greatorex M, Holmes M, Buckley P, Shelton S, Turner S, Sewell TA, Whitworth V, Lovegrove W, Tomlinson J, Warburton L, Painter S, Vickers C, Redwood D, Tilley J, Palmer S, Wainwright T, Breen G, Hotopf M, Dunleavy A, Teixeira J, Ali M, Mencias M, Msimanga N, Siddique S, Samakomva T, Tavoukjian V, Forton D, Ahmed R, Cook A, Thaivalappil F, Connor L, Rees T, McNarry M, Williams N, McCormick J, McIntosh J, Vere J, Coulding M, Kilroy S, Turner V, Butt AT, Savill H, Fraile E, Ugoji J, Landers G, Lota H, Portukhay S, Nasseri M, Daniels A, Hormis A, Ingham J, Zeidan L, Osborne L, Chablani M, Banerjee A, David A, Pakzad A, Rangelov B, Williams B, Denneny E, Willoughby J, Xu M, Mehta P, Batterham R, Bell R, Aslani S, Lilaonitkul W, Checkley A, Bang D, Basire D, Lomas D, Wall E, Plant H, Roy K, Heightman M, Lipman M, Merida Morillas M, Ahwireng N, Chambers RC, Jastrub R, Logan S, Hillman T, Botkai A, Casey A, Neal A, Newton-Cox A, Cooper B, Atkin C, McGee C, Welch C, Wilson D, Sapey E, Qureshi H, Hazeldine J, Lord JM, Nyaboko J, Short J, Stockley J, Dasgin J, Draxlbauer K, Isaacs K, Mcgee K, Yip KP, Ratcliffe L, Bates M, Ventura M, Ahmad Haider N, Gautam N, Baggott R, Holden S, Madathil S, Walder S, Yasmin S, Hiwot T, Jackson T, Soulsby T, Kamwa V, Peterkin Z, Suleiman Z, Chaudhuri N, Wheeler H, Djukanovic R, Samuel R, Sass T, Wallis T, Marshall B, Childs C, Marouzet E, Harvey M, Fletcher S, Dickens C, Beckett P, Nanda U, Daynes E, Charalambou A, Yousuf AJ, Lea A, Prickett A, Gooptu B, Hargadon B, Bourne C, Christie C, Edwardson C, Lee D, Baldry E, Stringer E, Woodhead F, Mills G, Arnold H, Aung H, Qureshi IN, Finch J, Skeemer J, Hadley K, Khunti K, Carr L, Ingram L, Aljaroof M, Bakali M, Bakau M, Baldwin M, Bourne M, Pareek M, Soares M, Tobin M, Armstrong N, Brunskill N, Goodman N, Cairns P, Haldar P, McCourt P, Dowling R, Russell R, Diver S, Edwards S, Glover S, Parker S, Siddiqui S, Ward TJC, Mcnally T, Thornton T, Yates T, Ibrahim W, Monteiro W, Thickett D, Wilkinson D, Broome M, McArdle P, Upthegrove R, Wraith D, Langenberg C, Summers C, Bullmore E, Heeney JL, Schwaeble W, Sudlow CL, Adeloye D, Newby DE, Rudan I, Shankar-Hari M, Thorpe M, Pius R, Walmsley S, McGovern A, Ballard C, Allan L, Dennis J, Cavanagh J, Petrie J, O'Donnell K, Spears M, Sattar N, MacDonald S, Guthrie E, Henderson M, Guillen Guio B, Zhao B, Lawson C, Overton C, Taylor C, Tong C, Mukaetova-Ladinska E, Turner E, Pearl JE, Sargant J, Wormleighton J, Bingham M, Sharma M, Steiner M, Samani N, Novotny P, Free R, Allen RJ, Finney S, Terry S, Brugha T, Plekhanova T, McArdle A, Vinson B, Spencer LG, Reynolds W, Ashworth M, Deakin B, Chinoy H, Abel K, Harvie M, Stanel S, Rostron A, Coleman C, Baguley D, Hufton E, Khan F, Hall I, Stewart I, Fabbri L, Wright L, Kitterick P, Morriss R, Johnson S, Bates A, Antoniades C, Clark D, Bhui K, Channon KM, Motohashi K, Sigfrid L, Husain M, Webster M, Fu X, Li X, Kingham L, Klenerman P, Miiler K, Carson G, Simons G, Huneke N, Calder PC, Baldwin D, Bain S, Lasserson D, Daines L, Bright E, Stern M, Crisp P, Dharmagunawardena R, Reddington A, Wight A, Bailey L, Ashish A, Robinson E, Cooper J, Broadley A, Turnbull A, Brookes C, Sarginson C, Ionita D, Redfearn H, Elliott K, Barman L, Griffiths L, Guy Z, Gill R, Nathu R, Harris E, Moss P, Finnigan J, Saunders K, Saunders P, Kon S, Kon SS, O'Brien L, Shah K, Shah P, Richardson E, Brown V, Brown M, Brown J, Brown J, Brown A, Brown A, Brown M, Choudhury N, Jones S, Jones H, Jones L, Jones I, Jones G, Jones H, Jones D, Davies F, Davies E, Davies K, Davies G, Davies GA, Howard K, Porter J, Rowland J, Rowland A, Scott K, Singh S, Singh C, Thomas S, Thomas C, Lewis V, Lewis J, Lewis D, Harrison P, Francis C, Francis R, Hughes RA, Hughes J, Hughes AD, Thompson T, Kelly S, Smith D, Smith N, Smith A, Smith J, Smith L, Smith S, Evans T, Evans RI, Evans D, Evans R, Evans H, Evans J. Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med 2023; 11:1003-1019. [PMID: 37748493 PMCID: PMC7615263 DOI: 10.1016/s2213-2600(23)00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. METHODS In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. FINDINGS Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. INTERPRETATION After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification. FUNDING UK Research and Innovation and National Institute for Health Research.
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Aguinam ET, Nadesalingam A, Chan A, Smith P, Paloniemi M, Cantoni D, Gronlund J, Gronlund H, Carnell GW, Castillo-Olivares J, Temperton N, Blacklaws B, Heeney JL, Baxendale H. Differential T-cell and Antibody Responses induced by mRNA versus adenoviral vectored COVID-19 vaccines in Patients with Immunodeficiencies. J Allergy Clin Immunol Glob 2023; 2:100091. [PMID: 37038555 PMCID: PMC10015741 DOI: 10.1016/j.jacig.2023.100091] [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] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/18/2023] [Accepted: 02/02/2023] [Indexed: 03/17/2023]
Abstract
Background Immunodeficient patients (IDPs) are at higher risk of contracting severe COVID-19 disease. Targeted vaccination strategies have been implemented to enhance vaccine-induced protection. In this population however, clinical effectiveness is variable and duration of protection unknown. Objective To understand the cellular and humoral immune responses to mRNA and adenoviral vectored COVID-19 vaccines in patients with immunodeficiency. Methods Immune responses to SARS-COV-2 spike were assessed after two doses of homologous ChAdOx1-nCoV-19 or BNT162b2 vaccines in 112 infection-naïve IDPs and 131 healthy health care workers (HCWs) as controls. Predictors of vaccine responsiveness were investigated. Results Immune responses to vaccination were low, and viral neutralisation by antibody not detected despite high titre binding responses in many IDPs. In those responding, the frequency of specific T-cell responses in IDPs was similar to controls whilst antibody responses were lower. Sustained vaccine specific differences were identified: T-cell responses were greater in ChAdOx1-nCoV-19 compared with BNT162b2 immunised IDPs and antibody binding and neutralisation was greater in all cohorts immunised with BNT162b2. The positive correlation between T-cell and antibody responses was weak and increased with subsequent vaccination. Conclusion Immunodeficient patients have impaired immune responses to mRNA and viral vector COVID-19 vaccines that appear influenced by vaccine formulation. Understanding the relative roles of T-cell and antibody mediated protection and potential of heterologous prime and boost immunization protocols is needed to optimise the vaccination approach in these high-risk groups.
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Key Words
- covid-19
- sars-cov-2
- vaccine
- chadox1-ncov-19
- bnt162b2
- immunodeficiency
- antibodies
- t-cells
- immunoglobulins
- healthcare workers
- ceft, peptides pool from human cytomegalovirus, epstein barr virus, influenza a virus and clostridium tetani
- covid-19, coronavirus disease 2019
- hcws, health care workers
- hcws-npi, health care workers with no prior covid-19 infection
- hcws-pi, health care workers with prior covid-19 infection
- hicc, humoral immune correlates of covid-19
- idps, immunodeficient patients
- iga, immunoglobulin a
- igg, immunoglobulin g
- iggrx, immunoglobulin replacement therapy
- pbmc, peripheral blood mononuclear cells
- pmn, pseudovirus micro neutralisation
- pv1, post first vaccine dose
- pv2, post second vaccine dose
- rbd, receptor binding domain
- rph, royal papworth hospital
- rx, treatment
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
- sid, secondary immunodeficiency
- vocs, variants of concern
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Affiliation(s)
- Ernest T Aguinam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Angalee Nadesalingam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Andrew Chan
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Peter Smith
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Minna Paloniemi
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | | | | | - George W Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - Barbara Blacklaws
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, UK
| | - Helen Baxendale
- Royal Papworth Hospital, Cambridgeshire, UK,Correspondence to: Helen Baxendale, Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge Biomedical Campus,CB2 0AY, +44 (0)1223 639508
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7
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Nadesalingam A, Cantoni D, Aguinam ET, Chan AC, Paloniemi M, Ohlendorf L, George C, Carnell G, Lyall J, Ferrari M, Temperton N, Wagner R, Castillo-Olivares J, Baxendale H, Heeney JL. Vaccination and protective immunity to SARS-CoV-2 omicron variants in people with immunodeficiencies. Lancet Microbe 2023; 4:e58-e59. [PMID: 36332646 PMCID: PMC9625114 DOI: 10.1016/s2666-5247(22)00297-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/16/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Angalee Nadesalingam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway, UK
| | - Ernest T Aguinam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Andrew Cy Chan
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Minna Paloniemi
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Luis Ohlendorf
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Charlotte George
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Jon Lyall
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Matteo Ferrari
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway, UK
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK
| | - Helen Baxendale
- Clinical Immunology Department, Royal Papworth NHS Foundation Trust, Cambridge, UK
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK.
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Carnell GW, Billmeier M, Vishwanath S, Suau Sans M, Wein H, George CL, Neckermann P, Del Rosario JMM, Sampson AT, Einhauser S, Aguinam ET, Ferrari M, Tonks P, Nadesalingam A, Schütz A, Huang CQ, Wells DA, Paloniemi M, Jordan I, Cantoni D, Peterhoff D, Asbach B, Sandig V, Temperton N, Kinsley R, Wagner R, Heeney JL. Glycan masking of a non-neutralising epitope enhances neutralising antibodies targeting the RBD of SARS-CoV-2 and its variants. Front Immunol 2023; 14:1118523. [PMID: 36911730 PMCID: PMC9995963 DOI: 10.3389/fimmu.2023.1118523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/07/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
The accelerated development of the first generation COVID-19 vaccines has saved millions of lives, and potentially more from the long-term sequelae of SARS-CoV-2 infection. The most successful vaccine candidates have used the full-length SARS-CoV-2 spike protein as an immunogen. As expected of RNA viruses, new variants have evolved and quickly replaced the original wild-type SARS-CoV-2, leading to escape from natural infection or vaccine induced immunity provided by the original SARS-CoV-2 spike sequence. Next generation vaccines that confer specific and targeted immunity to broadly neutralising epitopes on the SARS-CoV-2 spike protein against different variants of concern (VOC) offer an advance on current booster shots of previously used vaccines. Here, we present a targeted approach to elicit antibodies that neutralise both the ancestral SARS-CoV-2, and the VOCs, by introducing a specific glycosylation site on a non-neutralising epitope of the RBD. The addition of a specific glycosylation site in the RBD based vaccine candidate focused the immune response towards other broadly neutralising epitopes on the RBD. We further observed enhanced cross-neutralisation and cross-binding using a DNA-MVA CR19 prime-boost regime, thus demonstrating the superiority of the glycan engineered RBD vaccine candidate across two platforms and a promising candidate as a broad variant booster vaccine.
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Affiliation(s)
- George W Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martina Billmeier
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Sneha Vishwanath
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Maria Suau Sans
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Wein
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Charlotte L George
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Neckermann
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | | | - Alexander T Sampson
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian Einhauser
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Ernest T Aguinam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Paul Tonks
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Anja Schütz
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Chloe Qingzhou Huang
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Minna Paloniemi
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ingo Jordan
- Applied Science & Technologies, ProBioGen AG, Berlin, Germany
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - David Peterhoff
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt Asbach
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Volker Sandig
- Applied Science & Technologies, ProBioGen AG, Berlin, Germany
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Rebecca Kinsley
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, Ltd., Cambridge, United Kingdom
| | - Ralf Wagner
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonathan L Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, Ltd., Cambridge, United Kingdom
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Stewart H, Palmulli R, Johansen KH, McGovern N, Shehata OM, Carnell GW, Jackson HK, Lee JS, Brown JC, Burgoyne T, Heeney JL, Okkenhaug K, Firth AE, Peden AA, Edgar JR. Tetherin antagonism by SARS-CoV-2 enhances virus release: multiple mechanisms including ORF3a-mediated defective retrograde traffic. bioRxiv 2022:2021.01.06.425396. [PMID: 33442692 PMCID: PMC7805449 DOI: 10.1101/2021.01.06.425396] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The antiviral restriction factor, tetherin, blocks the release of several different families of enveloped viruses, including the Coronaviridae. Tetherin is an interferon-induced protein that forms parallel homodimers between the host cell and viral particles, linking viruses to the surface of infected cells and inhibiting their release. We demonstrated that SARS-CoV-2 infection causes tetherin downregulation, and that tetherin depletion from cells enhances SARS-CoV-2 viral titres. We investigated the potential viral proteins involved in abrogating tetherin function and found that SARS-CoV-2 ORF3a reduces tetherin localisation within biosynthetic organelles via reduced retrograde recycling and increases tetherin localisation to late endocytic organelles. By removing tetherin from the Coronavirus budding compartments, ORF3a enhances virus release. We also found expression of Spike protein caused a reduction in cellular tetherin levels. Our results confirm that tetherin acts as a host restriction factor for SARS-CoV-2 and highlight the multiple distinct mechanisms by which SARS-CoV-2 subverts tetherin function.
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Affiliation(s)
- Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Roberta Palmulli
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Kristoffer H. Johansen
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
- Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Naomi McGovern
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Ola M. Shehata
- Department of Biomedical Science, University of Sheffield, Firth Court, Sheffield. S10 2TN. UK
| | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge. CB3 0ES. UK
| | - Hannah K. Jackson
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Jin S. Lee
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, London. W2 1PG. UK
| | - Thomas Burgoyne
- Royal Brompton Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London. SW3 6NP. UK
- UCL Institute of Ophthalmology, University College London, London. EC1V 9EL. UK
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge. CB3 0ES. UK
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
| | - Andrew A. Peden
- Department of Biomedical Science, University of Sheffield, Firth Court, Sheffield. S10 2TN. UK
| | - James R. Edgar
- Department of Pathology, University of Cambridge, Cambridge. CB2 1QP. UK
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10
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Atti A, Insalata F, Carr EJ, Otter AD, Castillo-Olivares J, Wu M, Harvey R, Howell M, Chan A, Lyall J, Temperton N, Cantoni D, da Costa K, Nadesalingam A, Taylor-Kerr A, Hettiarachchi N, Tranquillini C, Hewson J, Cole MJ, Foulkes S, Munro K, Monk EJM, Milligan ID, Linley E, Chand MA, Brown CS, Islam J, Semper A, Charlett A, Heeney JL, Beale R, Zambon M, Hopkins S, Brooks T, Hall V. Antibody correlates of protection from SARS-CoV-2 reinfection prior to vaccination: A nested case-control within the SIREN study. J Infect 2022; 85:545-556. [PMID: 36089104 PMCID: PMC9458758 DOI: 10.1016/j.jinf.2022.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES To investigate serological differences between SARS-CoV-2 reinfection cases and contemporary controls, to identify antibody correlates of protection against reinfection. METHODS We performed a case-control study, comparing reinfection cases with singly infected individuals pre-vaccination, matched by gender, age, region and timing of first infection. Serum samples were tested for anti-SARS-CoV-2 spike (anti-S), anti-SARS-CoV-2 nucleocapsid (anti-N), live virus microneutralisation (LV-N) and pseudovirus microneutralisation (PV-N). Results were analysed using fixed effect linear regression and fitted into conditional logistic regression models. RESULTS We identified 23 cases and 92 controls. First infections occurred before November 2020; reinfections occurred before February 2021, pre-vaccination. Anti-S levels, LV-N and PV-N titres were significantly lower among cases; no difference was found for anti-N levels. Increasing anti-S levels were associated with reduced risk of reinfection (OR 0·63, CI 0·47-0·85), but no association for anti-N levels (OR 0·88, CI 0·73-1·05). Titres >40 were correlated with protection against reinfection for LV-N Wuhan (OR 0·02, CI 0·001-0·31) and LV-N Alpha (OR 0·07, CI 0·009-0·62). For PV-N, titres >100 were associated with protection against Wuhan (OR 0·14, CI 0·03-0·64) and Alpha (0·06, CI 0·008-0·40). CONCLUSIONS Before vaccination, protection against SARS-CoV-2 reinfection was directly correlated with anti-S levels, PV-N and LV-N titres, but not with anti-N levels. Detectable LV-N titres were sufficient for protection, whilst PV-N titres >100 were required for a protective effect. TRIAL REGISTRATION NUMBER ISRCTN11041050.
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Affiliation(s)
- Ana Atti
- UK Health Security Agency, Smith Square, London SW1P, UK.
| | | | - Edward J Carr
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Ashley D Otter
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Mary Wu
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Ruth Harvey
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Michael Howell
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Andrew Chan
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Jonathan Lyall
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Greenwich and Kent at Medway, Central Ave, Gillingham, Chatham ME4 4BF, UK
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Greenwich and Kent at Medway, Central Ave, Gillingham, Chatham ME4 4BF, UK
| | - Kelly da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Greenwich and Kent at Medway, Central Ave, Gillingham, Chatham ME4 4BF, UK
| | - Angalee Nadesalingam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | | | | | | | | | | | - Sarah Foulkes
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Katie Munro
- UK Health Security Agency, Smith Square, London SW1P, UK
| | | | | | - Ezra Linley
- Manchester Royal Infirmary, UK Health Security Agency, Oxford Road, Manchester M139WL, UK
| | - Meera A Chand
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Colin S Brown
- UK Health Security Agency, Smith Square, London SW1P, UK; The National Institute for Health Research Health Protection Research (NIHR) Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Jasmin Islam
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Amanda Semper
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Andre Charlett
- UK Health Security Agency, Smith Square, London SW1P, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol in partnership with Public Health England, Queens Road, Bristol BS8 1QU, UK; NIHR Health Protection Research Unit in Immunisation at the London School of Hygiene and Tropical Medicine in partnership with Public Health England, Keppel St, London WC1E 7HT, UK
| | | | - Rupert Beale
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Maria Zambon
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Susan Hopkins
- UK Health Security Agency, Smith Square, London SW1P, UK; The National Institute for Health Research Health Protection Research (NIHR) Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Tim Brooks
- UK Health Security Agency, Smith Square, London SW1P, UK
| | - Victoria Hall
- UK Health Security Agency, Smith Square, London SW1P, UK; The National Institute for Health Research Health Protection Research (NIHR) Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
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Happi AN, Olumade TJ, Ogunsanya OA, Sijuwola AE, Ogunleye SC, Oguzie JU, Nwofoke C, Ugwu CA, Okoro SJ, Otuh PI, Ngele LN, Ojo OO, Adelabu A, Adeleye RF, Oyejide NE, Njaka CS, Heeney JL, Happi CT. Increased Prevalence of Lassa Fever Virus-Positive Rodents and Diversity of Infected Species Found during Human Lassa Fever Epidemics in Nigeria. Microbiol Spectr 2022; 10:e0036622. [PMID: 35913205 PMCID: PMC9430508 DOI: 10.1128/spectrum.00366-22] [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: 02/01/2022] [Accepted: 06/07/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamics of Lassa virus (LASV) infections in rodent reservoirs and their endemic human caseloads remain poorly understood. During the endemic period, human infections are believed to be associated with the seasonal migration of Mastomys natalensis, thought to be the primary reservoir that triggers multiple spillovers of LASV to humans. It has become imperative to improve LASV diagnosis in rodents while updating their prevalence in two regions of Lassa fever endemicity in Nigeria. Rodents (total, 942) were trapped in Ondo (531) and Ebonyi (411) states between October 2018 and April 2020 for detection of LASV using various tissues. Overall, the LASV prevalence was 53.6%. The outbreak area sampled in Ondo had three and two times higher capture success and LASV prevalence, respectively, than Ebonyi State. This correlated with the higher number of annual cases of Lassa fever (LF) in Ondo State versus Ebonyi State. All rodent genera (Mastomys, Rattus, Crocidura, Mus, and Tatera) captured in both states showed slightly variable LASV positivity, with Rattus spp. being the most predominantly infected (77.3%) rodents in Ondo State versus Mastomys spp. (41.6%) in Ebonyi State. The tissues with the highest LASV positivity were the kidneys, spleen, and testes. The finding of a relatively high LASV prevalence in all of the rodent genera captured highlights the complex interspecies transmission dynamics of LASV infections in the reservoirs and their potential association with increased environmental contact, as well as the risk of zoonotic spillover in these communities, which have the highest prevalence of Lassa fever in Nigeria. IMPORTANCE Our findings show the highest LASV positivity in small rodents ever recorded and the first direct detection of LASV in Tatera spp. Our findings also indicate the abundance of LASV-infected small rodents in houses, with probable interspecies transmission through vertical and horizontal coitus routes. Consequently, we suggest that the abundance of different reservoir species for LASV may fuel the epizootic outbreaks of LF in affected human communities. The high prevalence of LASV with the diversity of affected rodents has direct implications for our understanding of the transmission risk, mitigation, and ultimately, the prevention of LF in humans. Optimal tissues for LASV detection in rodents are also presented.
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Affiliation(s)
- Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
| | - Testimony J. Olumade
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
| | - Cecilia Nwofoke
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi, Nigeria
| | - Chinedu A. Ugwu
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
| | - Samuel J. Okoro
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi, Nigeria
| | - Patricia I. Otuh
- Michael Okpara University of Agriculture, Umudike, Abia, Nigeria
| | - Louis N. Ngele
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi, Nigeria
| | | | | | | | - Nicholas E. Oyejide
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
| | | | - Jonathan L. Heeney
- Lab of Viral Zoonotics, University of Cambridge, Cambridge, United Kingdom
| | - Christian T. Happi
- African Centre of Excellence for Genomics of Infectious Disease, Redeemer’s University, Ede, Osun, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Perdiguero B, Asbach B, Gómez CE, Köstler J, Barnett SW, Koutsoukos M, Weiss DE, Cristillo AD, Foulds KE, Roederer M, Montefiori DC, Yates NL, Ferrari G, Shen X, Sawant S, Tomaras GD, Sato A, Fulp WJ, Gottardo R, Ding S, Heeney JL, Pantaleo G, Esteban M, Wagner R. Early and Long-Term HIV-1 Immunogenicity Induced in Macaques by the Combined Administration of DNA, NYVAC and Env Protein-Based Vaccine Candidates: The AUP512 Study. Front Immunol 2022; 13:939627. [PMID: 35935978 PMCID: PMC9354927 DOI: 10.3389/fimmu.2022.939627] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
To control HIV infection there is a need for vaccines to induce broad, potent and long-term B and T cell immune responses. With the objective to accelerate and maintain the induction of substantial levels of HIV-1 Env-specific antibodies and, at the same time, to enhance balanced CD4 and CD8 T cell responses, we evaluated the effect of concurrent administration of MF59-adjuvanted Env protein together with DNA or NYVAC vectors at priming to establish if early administration of Env leads to early induction of antibody responses. The primary goal was to assess the immunogenicity endpoint at week 26. Secondary endpoints were (i) to determine the quality of responses with regard to RV144 correlates of protection and (ii) to explore a potential impact of two late boosts. In this study, five different prime/boost vaccination regimens were tested in rhesus macaques. Animals received priming immunizations with either NYVAC or DNA alone or in combination with Env protein, followed by NYVAC + protein or DNA + protein boosts. All regimens induced broad, polyfunctional and well-balanced CD4 and CD8 T cell responses, with DNA-primed regimens eliciting higher response rates and magnitudes than NYVAC-primed regimens. Very high plasma binding IgG titers including V1/V2 specific antibodies, modest antibody-dependent cellular cytotoxicity (ADCC) and moderate neutralization activity were observed. Of note, early administration of the MF59-adjuvanted Env protein in parallel with DNA priming leads to more rapid elicitation of humoral responses, without negatively affecting the cellular responses, while responses were rapidly boosted after repeated immunizations, indicating the induction of a robust memory response. In conclusion, our findings support the use of the Env protein component during priming in the context of an heterologous immunization regimen with a DNA and/or NYVAC vector as an optimized immunization protocol against HIV infection.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII ), Madrid, Spain
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Carmen E. Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII ), Madrid, Spain
| | - Josef Köstler
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | | | - Marguerite Koutsoukos
- Department of Product Development, GlaxoSmithKline (GSK) Vaccines, Rixensart, Belgium
| | - Deborah E. Weiss
- Department of Immunobiology, Advanced BioScience Laboratories (ABL) Inc., Rockville, MD, United States
| | - Anthony D. Cristillo
- Department of Immunobiology, Advanced BioScience Laboratories (ABL) Inc., Rockville, MD, United States
| | - Kathryn E. Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David C. Montefiori
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Nicole L. Yates
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Guido Ferrari
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Xiaoying Shen
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Sheetal Sawant
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Alicia Sato
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - William J. Fulp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Biomedical Data Sciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Song Ding
- EuroVacc Foundation EuroVacc Programme Coordinator, Lausanne, Switzerland
| | - Jonathan L. Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Giuseppe Pantaleo
- Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII ), Madrid, Spain
- *Correspondence: Mariano Esteban, ; Ralf Wagner,
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- *Correspondence: Mariano Esteban, ; Ralf Wagner,
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14
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Wells DA, Cantoni D, Mayora-Neto M, Di Genova C, Sampson A, Ferrari M, Carnell G, Nadesalingam A, Smith P, Chan A, Raddi G, Castillo-Olivares J, Baxendale H, Temperton N, Heeney JL. Human seasonal coronavirus neutralisation and COVID-19 severity. J Med Virol 2022; 94:4820-4829. [PMID: 35705514 PMCID: PMC9349487 DOI: 10.1002/jmv.27937] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022]
Abstract
The virus severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), responsible for the global coronavirus disease‐2019 (COVID‐19) pandemic, spread rapidly around the world causing high morbidity and mortality. However, there are four known, endemic seasonal coronaviruses in humans (HCoVs), and whether antibodies for these HCoVs play a role in severity of COVID‐19 disease has generated a lot of interest. Of these seasonal viruses NL63 is of particular interest as it uses the same cell entry receptor as SARS‐CoV‐2. We use functional, neutralizing assays to investigate cross‐reactive antibodies and their relationship with COVID‐19 severity. We analyzed the neutralization of SARS‐CoV‐2, NL63, HKU1, and 229E in 38 COVID‐19 patients and 62 healthcare workers, and a further 182 samples to specifically study the relationship between SARS‐CoV‐2 and NL63. We found that although HCoV neutralization was very common there was little evidence that these antibodies neutralized SARS‐CoV‐2. Despite no evidence in cross‐neutralization, levels of NL63 neutralizing antibodies become elevated after exposure to SARS‐CoV‐2 through infection or following vaccination.
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Affiliation(s)
- David A Wells
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway
| | - Cecilia Di Genova
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway
| | - Alexander Sampson
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matteo Ferrari
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge
| | - George Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Peter Smith
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew Chan
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Javier Castillo-Olivares
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway
| | - Jonathan L Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge
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15
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Palmer P, Del Rosario JMM, da Costa KAS, Carnell GW, Huang CQ, Heeney JL, Temperton NJ, Wells DA. AutoPlate: Rapid Dose-Response Curve Analysis for Biological Assays. Front Immunol 2022; 12:681636. [PMID: 35222351 PMCID: PMC8866857 DOI: 10.3389/fimmu.2021.681636] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The emergence of COVID-19 has emphasised that biological assay data must be analysed quickly to develop safe, effective and timely vaccines/therapeutics. For viruses such as SARS-CoV-2, the primary way of measuring immune correlates of protection is through assays such as the pseudotype microneutralisation (pMN) assay, thanks to its safety and versatility. However, despite the presence of existing tools for data analysis such as PRISM and R the analysis of these assays remains cumbersome and time-consuming. We introduce an open-source R Shiny web application and R library (AutoPlate) to accelerate data analysis of dose-response curve immunoassays. Using example data from influenza studies, we show that AutoPlate improves on available analysis software in terms of ease of use, flexibility and speed. AutoPlate (https://philpalmer.shinyapps.io/AutoPlate/) is a tool for the use of laboratories and wider scientific community to accelerate the analysis of biological assays in the development of viral vaccines and therapeutics.
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Affiliation(s)
- Phil Palmer
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Joanne Marie M Del Rosario
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom.,Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila, Philippines
| | - Kelly A S da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - George W Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Chloe Q Huang
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Nigel J Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - David A Wells
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
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16
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Scherer KM, Mascheroni L, Carnell GW, Wunderlich LCS, Makarchuk S, Brockhoff M, Mela I, Fernandez-Villegas A, Barysevich M, Stewart H, Suau Sans M, George CL, Lamb JR, Kaminski-Schierle GS, Heeney JL, Kaminski CF. SARS-CoV-2 nucleocapsid protein adheres to replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress. Sci Adv 2022; 8:eabl4895. [PMID: 34995113 PMCID: PMC10954198 DOI: 10.1126/sciadv.abl4895] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Despite being the target of extensive research efforts due to the COVID-19 (coronavirus disease 2019) pandemic, relatively little is known about the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication within cells. We investigate and characterize the tightly orchestrated virus assembly by visualizing the spatiotemporal dynamics of the four structural SARS-CoV-2 proteins at high resolution. The nucleoprotein is expressed first and accumulates around folded endoplasmic reticulum (ER) membranes in convoluted layers that contain viral RNA replication foci. We find that, of the three transmembrane proteins, the membrane protein appears at the Golgi apparatus/ER-to-Golgi intermediate compartment before the spike and envelope proteins. Relocation of a lysosome marker toward the assembly compartment and its detection in transport vesicles of viral proteins confirm an important role of lysosomes in SARS-CoV-2 egress. These data provide insights into the spatiotemporal regulation of SARS-CoV-2 assembly and refine the current understanding of SARS-CoV-2 replication.
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Affiliation(s)
- Katharina M. Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lucia C. S. Wunderlich
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | - Marius Brockhoff
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Ana Fernandez-Villegas
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Max Barysevich
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Hazel Stewart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria Suau Sans
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Jacob R. Lamb
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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17
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Ali YM, Lynch NJ, Khatri P, Bamigbola IE, Chan ACY, Yabuki M, Demopulos GA, Heeney JL, Pai S, Baxendale H, Schwaeble WJ. Secondary Complement Deficiency Impairs Anti-Microbial Immunity to Klebsiella pneumoniae and Staphylococcus aureus During Severe Acute COVID-19. Front Immunol 2022; 13:841759. [PMID: 35572551 PMCID: PMC9094484 DOI: 10.3389/fimmu.2022.841759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 01/08/2023] Open
Abstract
A high incidence of secondary Klebsiella pneumoniae and Staphylococcus aureus infection were observed in patients with severe COVID-19. The cause of this predisposition to infection is unclear. Our data demonstrate consumption of complement in acute COVID-19 patients reflected by low levels of C3, C4, and loss of haemolytic activity. Given that the elimination of Gram-negative bacteria depends in part on complement-mediated lysis, we hypothesised that secondary hypocomplementaemia is rendering the antibody-dependent classical pathway activation inactive and compromises serum bactericidal activity (SBA). 217 patients with severe COVID-19 were studied. 142 patients suffered secondary bacterial infections. Klebsiella species were the most common Gram-negative organism, found in 58 patients, while S. aureus was the dominant Gram-positive organism found in 22 patients. Hypocomplementaemia was observed in patients with acute severe COVID-19 but not in convalescent survivors three months after discharge. Sera from patients with acute COVID-19 were unable to opsonise either K. pneumoniae or S. aureus and had impaired complement-mediated killing of Klebsiella. We conclude that hyperactivation of complement during acute COVID-19 leads to secondary hypocomplementaemia and predisposes to opportunistic infections.
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Affiliation(s)
- Youssif M. Ali
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- *Correspondence: Youssif M. Ali, ; Wilhelm J. Schwaeble,
| | - Nicholas J. Lynch
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Priyanka Khatri
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ifeoluwa E. Bamigbola
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Andrew C. Y. Chan
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Jonathan L. Heeney
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sumita Pai
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Helen Baxendale
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Wilhelm J. Schwaeble
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Youssif M. Ali, ; Wilhelm J. Schwaeble,
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18
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Castillo-Olivares J, Wells DA, Ferrari M, Chan ACY, Smith P, Nadesalingam A, Paloniemi M, Carnell GW, Ohlendorf L, Cantoni D, Mayora-Neto M, Palmer P, Tonks P, Temperton NJ, Peterhoff D, Neckermann P, Wagner R, Doffinger R, Kempster S, Otter AD, Semper A, Brooks T, Albecka A, James LC, Page M, Schwaeble W, Baxendale H, Heeney JL. Analysis of Serological Biomarkers of SARS-CoV-2 Infection in Convalescent Samples From Severe, Moderate and Mild COVID-19 Cases. Front Immunol 2021; 12:748291. [PMID: 34867975 PMCID: PMC8640495 DOI: 10.3389/fimmu.2021.748291] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Precision monitoring of antibody responses during the COVID-19 pandemic is increasingly important during large scale vaccine rollout and rise in prevalence of Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2) variants of concern (VOC). Equally important is defining Correlates of Protection (CoP) for SARS-CoV-2 infection and COVID-19 disease. Data from epidemiological studies and vaccine trials identified virus neutralising antibodies (Nab) and SARS-CoV-2 antigen-specific (notably RBD and S) binding antibodies as candidate CoP. In this study, we used the World Health Organisation (WHO) international standard to benchmark neutralising antibody responses and a large panel of binding antibody assays to compare convalescent sera obtained from: a) COVID-19 patients; b) SARS-CoV-2 seropositive healthcare workers (HCW) and c) seronegative HCW. The ultimate aim of this study is to identify biomarkers of humoral immunity that could be used to differentiate severe from mild or asymptomatic SARS-CoV-2 infections. Some of these biomarkers could be used to define CoP in further serological studies using samples from vaccination breakthrough and/or re-infection cases. Whenever suitable, the antibody levels of the samples studied were expressed in International Units (IU) for virus neutralisation assays or in Binding Antibody Units (BAU) for ELISA tests. In this work we used commercial and non-commercial antibody binding assays; a lateral flow test for detection of SARS-CoV-2-specific IgG/IgM; a high throughput multiplexed particle flow cytometry assay for SARS-CoV-2 Spike (S), Nucleocapsid (N) and Receptor Binding Domain (RBD) proteins); a multiplex antigen semi-automated immuno-blotting assay measuring IgM, IgA and IgG; a pseudotyped microneutralisation test (pMN) and an electroporation-dependent neutralisation assay (EDNA). Our results indicate that overall, severe COVID-19 patients showed statistically significantly higher levels of SARS-CoV-2-specific neutralising antibodies (average 1029 IU/ml) than those observed in seropositive HCW with mild or asymptomatic infections (379 IU/ml) and that clinical severity scoring, based on WHO guidelines was tightly correlated with neutralisation and RBD/S antibodies. In addition, there was a positive correlation between severity, N-antibody assays and intracellular virus neutralisation.
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Affiliation(s)
- Javier Castillo-Olivares
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David A. Wells
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Matteo Ferrari
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Andrew C. Y. Chan
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Peter Smith
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Minna Paloniemi
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - George W. Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Luis Ohlendorf
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Phil Palmer
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Tonks
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nigel J. Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Patrick Neckermann
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sarah Kempster
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | - Amanda Semper
- UK Health Security Agency, Porton Down, United Kingdom
| | - Tim Brooks
- UK Health Security Agency, Porton Down, United Kingdom
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Leo C. James
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mark Page
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Wilhelm Schwaeble
- Complement Laboratory, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Helen Baxendale
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Jonathan L. Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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19
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Lai M, Maori E, Quaranta P, Matteoli G, Maggi F, Sgarbanti M, Crucitta S, Pacini S, Turriziani O, Antonelli G, Heeney JL, Freer G, Pistello M. CRISPR/Cas9 Ablation of Integrated HIV-1 Accumulates Proviral DNA Circles with Reformed Long Terminal Repeats. J Virol 2021; 95:e0135821. [PMID: 34549986 PMCID: PMC8577360 DOI: 10.1128/jvi.01358-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/12/2021] [Accepted: 09/12/2021] [Indexed: 12/03/2022] Open
Abstract
Gene editing may be used to excise the human immunodeficiency virus type 1 (HIV-1) provirus from the host cell genome, possibly eradicating the infection. Here, using cells acutely or latently infected by HIV-1 and treated with long terminal repeat (LTR)-targeting CRISPR/Cas9, we show that the excised HIV-1 provirus persists for a few weeks and may rearrange in circular molecules. Although circular proviral DNA is naturally formed during HIV-1 replication, we observed that gene editing might increase proviral DNA circles with restored LTRs. These extrachromosomal elements were recovered and probed for residual activity through their transfection in uninfected cells. We discovered that they can be transcriptionally active in the presence of Tat and Rev. Although confirming that gene editing is a powerful tool to eradicate HIV-1 infection, this work highlights that, to achieve this goal, the LTRs must be cleaved in several pieces to avoid residual activity and minimize the risk of reintegration in the context of genomic instability, possibly caused by the off-target activity of Cas9. IMPORTANCE The excision of HIV-1 provirus from the host cell genome has proven feasible in vitro and, to some extent, in vivo. Among the different approaches, CRISPR/Cas9 is the most promising tool for gene editing. The present study underlines the remarkable effectiveness of CRISPR/Cas9 in removing the HIV-1 provirus from infected cells and investigates the fate of the excised HIV-1 genome. This study demonstrates that the free provirus may persist in the cell after editing and in appropriate circumstances may reactivate. As an episome, it might be transcriptionally active, especially in the presence of Tat and Rev. The persistence of the HIV-1 episome was strongly decreased by gene editing with multiple targets. Although gene editing has the potential to eradicate HIV-1 infection, this work highlights a potential issue that warrants further investigation.
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Affiliation(s)
- Michele Lai
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eyal Maori
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paola Quaranta
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Giulia Matteoli
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | | | - Stefania Crucitta
- Pharmacology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Simone Pacini
- Hematology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ombretta Turriziani
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Giulia Freer
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Virology Unit, Pisa University Hospital, Pisa, Italy
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20
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Nadesalingam A, Cantoni D, Wells DA, Aguinam ET, Ferrari M, Smith P, Chan A, Carnell G, Ohlendorf L, Einhauser S, George C, Wagner R, Temperton N, Castillo-Olivares J, Baxendale H, Heeney JL. Paucity and discordance of neutralising antibody responses to SARS-CoV-2 VOCs in vaccinated immunodeficient patients and health-care workers in the UK. Lancet Microbe 2021; 2:e416-e418. [PMID: 34223399 PMCID: PMC8238451 DOI: 10.1016/s2666-5247(21)00157-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway, UK
| | - David A Wells
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Ernest T Aguinam
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Matteo Ferrari
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Peter Smith
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Andrew Chan
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - George Carnell
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Luis Ohlendorf
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Charlotte George
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Medway, UK
| | | | - Helen Baxendale
- Clinical Immunology Department, Royal Papworth NHS Foundation Trust, Cambridge, UK
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge CB3 OES, UK
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21
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Carnell GW, Ciazynska KA, Wells DA, Xiong X, Aguinam ET, McLaughlin SH, Mallery D, Ebrahimi S, Ceron-Gutierrez L, Asbach B, Einhauser S, Wagner R, James LC, Doffinger R, Heeney JL, Briggs JAG. SARS-CoV-2 Spike Protein Stabilized in the Closed State Induces Potent Neutralizing Responses. J Virol 2021; 95:e0020321. [PMID: 33963055 PMCID: PMC8274612 DOI: 10.1128/jvi.00203-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
The majority of SARS-CoV-2 vaccines in use or advanced development are based on the viral spike protein (S) as their immunogen. S is present on virions as prefusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described against both open and closed conformations. The long-term success of vaccination strategies depends upon inducing antibodies that provide long-lasting broad immunity against evolving SARS-CoV-2 strains. Here, we have assessed the results of immunization in a mouse model using an S protein trimer stabilized in the closed state to prevent full exposure of the receptor binding site and therefore interaction with the receptor. We compared this with other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induced a T cell response and long-lived, strongly neutralizing antibody responses against 2019 SARS-CoV-2 and variants of concern P.1 and B.1.351. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralizing responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, immune responses than open spikes and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. We suggest that closed spikes, together with their improved stability and storage properties, may be a valuable component of refined, next-generation vaccines. IMPORTANCE Vaccines in use against SARS-CoV-2 induce immune responses against the spike protein. There is intense interest in whether the antibody response induced by vaccines will be robust against new variants, as well as in next-generation vaccines for use in previously infected or immunized individuals. We assessed the use as an immunogen of a spike protein engineered to be conformationally stabilized in the closed state where the receptor binding site is occluded. Despite occlusion of the receptor binding site, the spike induces potently neutralizing sera against multiple SARS-CoV-2 variants. Antibodies are raised against a different pattern of epitopes to those induced by other spike constructs, preferring conformational epitopes present in the closed conformation. Closed spikes, or mRNA vaccines based on their sequence, can be a valuable component of next-generation vaccines.
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Affiliation(s)
- George W. Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - David A. Wells
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoli Xiong
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ernest T. Aguinam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Donna Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Leo C. James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - John A. G. Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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22
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Hauser A, Carnell G, Held K, Sulbaran G, Tischbierek N, Rogers L, Pollakis G, Tonks P, Hoelscher M, Ding S, Sanders RW, Geldmacher C, Sattentau Q, Weissenhorn W, Heeney JL, Peterhoff D, Wagner R. Stepwise Conformational Stabilization of a HIV-1 Clade C Consensus Envelope Trimer Immunogen Impacts the Profile of Vaccine-Induced Antibody Responses. Vaccines (Basel) 2021; 9:750. [PMID: 34358165 PMCID: PMC8310183 DOI: 10.3390/vaccines9070750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/16/2023] Open
Abstract
Stabilization of the HIV-1 Envelope glycoprotein trimer (Env) in its native pre-fusion closed conformation is regarded as one of several requirements for the induction of neutralizing antibody (nAb) responses, which, in turn, will most likely be a prerequisite for the development of an efficacious preventive vaccine. Here, we systematically analyzed how the stepwise stabilization of a clade C consensus (ConC) Env immunogen impacts biochemical and biophysical protein traits such as antigenicity, thermal stability, structural integrity, and particle size distribution. The increasing degree of conformational rigidification positively correlates with favorable protein characteristics, leading to optimized homogeneity of the protein preparations, increased thermal stability, and an overall favorable binding profile of structure-dependent broadly neutralizing antibodies (bnAbs) and non-neutralizing antibodies (non-nAbs). We confirmed that increasing the structural integrity and stability of the Env trimers positively correlates with the quality of induced antibody responses by the immunogens. These and other data contribute to the selection of ConCv5 KIKO as novel Env immunogens for use within the European Union's H2020 Research Consortium EHVA (European HIV Alliance) for further preclinical analysis and phase 1 clinical development.
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Affiliation(s)
- Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Guidenn Sulbaran
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Nadine Tischbierek
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - Lisa Rogers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology, and Immunology (CIMI), University of Liverpool, Liverpool L69 7BE, UK;
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU EZI), Liverpool L69 7BE, UK
| | - Paul Tonks
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Song Ding
- EuroVacc Foundation, 1105 BP Amsterdam, The Netherlands;
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Quentin Sattentau
- The Sir Willian Dunn School of Pathology, The University of Oxford, Oxford OX1 3RE, UK;
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
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23
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Ali YM, Ferrari M, Lynch NJ, Yaseen S, Dudler T, Gragerov S, Demopulos G, Heeney JL, Schwaeble WJ. Lectin Pathway Mediates Complement Activation by SARS-CoV-2 Proteins. Front Immunol 2021; 12:714511. [PMID: 34290717 PMCID: PMC8287855 DOI: 10.3389/fimmu.2021.714511] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 12/17/2022] Open
Abstract
Early and persistent activation of complement is considered to play a key role in the pathogenesis of COVID-19. Complement activation products orchestrate a proinflammatory environment that might be critical for the induction and maintenance of a severe inflammatory response to SARS-CoV-2 by recruiting cells of the cellular immune system to the sites of infection and shifting their state of activation towards an inflammatory phenotype. It precedes pathophysiological milestone events like the cytokine storm, progressive endothelial injury triggering microangiopathy, and further complement activation, and causes an acute respiratory distress syndrome (ARDS). To date, the application of antiviral drugs and corticosteroids have shown efficacy in the early stages of SARS-CoV-2 infection, but failed to ameliorate disease severity in patients who progressed to severe COVID-19 pathology. This report demonstrates that lectin pathway (LP) recognition molecules of the complement system, such as MBL, FCN-2 and CL-11, bind to SARS-CoV-2 S- and N-proteins, with subsequent activation of LP-mediated C3b and C4b deposition. In addition, our results confirm and underline that the N-protein of SARS-CoV-2 binds directly to the LP- effector enzyme MASP-2 and activates complement. Inhibition of the LP using an inhibitory monoclonal antibody against MASP-2 effectively blocks LP-mediated complement activation. FACS analyses using transfected HEK-293 cells expressing SARS-CoV-2 S protein confirm a robust LP-dependent C3b deposition on the cell surface which is inhibited by the MASP-2 inhibitory antibody. In light of our present results, and the encouraging performance of our clinical candidate MASP-2 inhibitor Narsoplimab in recently published clinical trials, we suggest that the targeting of MASP-2 provides an unsurpassed window of therapeutic efficacy for the treatment of severe COVID-19.
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Affiliation(s)
- Youssif M. Ali
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Matteo Ferrari
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J. Lynch
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | - Jonathan L. Heeney
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Wilhelm J. Schwaeble
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
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24
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Del Rosario JMM, da Costa KAS, Asbach B, Ferrara F, Ferrari M, Wells DA, Mann GS, Ameh VO, Sabeta CT, Banyard AC, Kinsley R, Scott SD, Wagner R, Heeney JL, Carnell GW, Temperton NJ. Exploiting Pan Influenza A and Pan Influenza B Pseudotype Libraries for Efficient Vaccine Antigen Selection. Vaccines (Basel) 2021; 9:741. [PMID: 34358157 PMCID: PMC8310092 DOI: 10.3390/vaccines9070741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/09/2021] [Revised: 06/09/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
We developed an influenza hemagglutinin (HA) pseudotype library encompassing Influenza A subtypes HA1-18 and Influenza B subtypes (both lineages) to be employed in influenza pseudotype microneutralization (pMN) assays. The pMN is highly sensitive and specific for detecting virus-specific neutralizing antibodies against influenza viruses and can be used to assess antibody functionality in vitro. Here we show the production of these viral HA pseudotypes and their employment as substitutes for wildtype viruses in influenza neutralization assays. We demonstrate their utility in detecting serum responses to vaccination with the ability to evaluate cross-subtype neutralizing responses elicited by specific vaccinating antigens. Our findings may inform further preclinical studies involving immunization dosing regimens in mice and may help in the creation and selection of better antigens for vaccine design. These HA pseudotypes can be harnessed to meet strategic objectives that contribute to the strengthening of global influenza surveillance, expansion of seasonal influenza prevention and control policies, and strengthening pandemic preparedness and response.
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Affiliation(s)
- Joanne Marie M. Del Rosario
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
- Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
| | - Kelly A. S. da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (B.A.); (R.W.)
| | - Francesca Ferrara
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
- Vector Development and Production Laboratory, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matteo Ferrari
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - David A. Wells
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Gurdip Singh Mann
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
| | - Veronica O. Ameh
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi P.M.B. 2373, Bene State, Nigeria;
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, P. Bag X04, Onderstepoort 0110, South Africa;
| | - Claude T. Sabeta
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, P. Bag X04, Onderstepoort 0110, South Africa;
- OIE Rabies Reference Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa
| | - Ashley C. Banyard
- Animal and Plant Health Agency (APHA), Department of Virology, Weybridge, Surrey KT15 3NB, UK;
| | - Rebecca Kinsley
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Simon D. Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (B.A.); (R.W.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Jonathan L. Heeney
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - George W. Carnell
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Nigel J. Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, UK; (J.M.M.D.R.); (K.A.S.d.C.); (F.F.); (G.S.M.); (S.D.S.)
- DIOSynVax, Cambridge CB3 0ES, UK; (M.F.); (D.A.W.); (R.K.); (J.L.H.); (G.W.C.)
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25
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Happi AN, Ogunsanya OA, Oguzie JU, Oluniyi PE, Olono AS, Heeney JL, Happi CT. Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa. Sci Rep 2021; 11:13689. [PMID: 34210997 PMCID: PMC8249450 DOI: 10.1038/s41598-021-91961-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.
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Affiliation(s)
- Anise N Happi
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria. .,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
| | - Olusola A Ogunsanya
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Alhaji S Olono
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jonathan L Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria. .,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
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26
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Favara DM, Ceron-Gutierrez ML, Carnell GW, Heeney JL, Corrie P, Doffinger R. Detection of breastmilk antibodies targeting SARS-CoV-2 nucleocapsid, spike and receptor-binding-domain antigens. Emerg Microbes Infect 2021; 9:2728-2731. [PMID: 33258732 PMCID: PMC7782901 DOI: 10.1080/22221751.2020.1858699] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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] [Indexed: 01/06/2023]
Abstract
A 40-year-old female was found to have strongly neutralizing SARS-CoV-2 breastmilk IgA and IgG antibodies reactive against multiple SARS-CoV-2 antigens at 2.5 months after documented infection with SARS-CoV-2. At 6.5 months following the infection, she remained positive for breastmilk and serum SARS-CoV-2 neutralizing antibodies. Holder breast milk pasteurization did not diminish SARS-CoV-2 antibody titres but it reduced its neutralizing capacity, while serum heat inactivation had no negative effect on SARS-CoV-2 serum antibody levels and neutralizing capacity. Current data on SARS-CoV-2 and breastmilk are reviewed.
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Affiliation(s)
- D M Favara
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Oncology, The Queen Elizabeth Hospital, The Queen Elizabeth Hospital King's Lynn NHS Foundation Trust, Kings Lynn, UK.,Department of Oncology, University of Cambridge, Cambridge, UK
| | - M L Ceron-Gutierrez
- Department of Immunology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - G W Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - P Corrie
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - R Doffinger
- Department of Immunology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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27
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Iles RK, Zmuidinaite R, Iles JK, Carnell G, Sampson A, Heeney JL. Development of a Clinical MALDI-ToF Mass Spectrometry Assay for SARS-CoV-2: Rational Design and Multi-Disciplinary Team Work. Diagnostics (Basel) 2020; 10:E746. [PMID: 32987950 PMCID: PMC7600155 DOI: 10.3390/diagnostics10100746] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country's population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high-throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology-multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct application to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 coronavirus detection-(Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; (1) ease of sampling, (2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution.
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Affiliation(s)
- Ray K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
- NISAD, Medicon Village, SE-223 81 Lund, Sweden
| | - Raminta Zmuidinaite
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jason K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Alex Sampson
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
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Zurnic I, Hütter S, Lehmann U, Stanke N, Reh J, Kern T, Lindel F, Gerresheim G, Hamann M, Müllers E, Lesbats P, Cherepanov P, Serrao E, Engelman A, Lindemann D, Da Silva Santos C, Tartour K, Cimarelli A, Burdick R, Chen J, Sastri J, Hu WS, Pathak V, Keppler OT, Pradeau K, Eiler S, Levy N, Lennon S, Cianferani S, Emiliani S, Ruff M, Parissi V, Rato S, Rausell A, Munoz M, Telenti A, Ciuffi A, Zhyvoloup A, Melamed A, Anderson I, Planas D, Kriston-Vizi J, Ketteler R, Lee CH, Merritt A, Ancuta P, Bangham C, Fassati A, Rodari A, Van Driessche B, Galais M, Delacourt N, Fauquenoy S, Vanhulle C, Kula A, Burny A, Rohr O, Van Lint C, van Montfort T, van der Sluis R, Speijer D, Berkhout B, Meng B, Rutkowski A, Berry N, Dölken L, Lever A, Schuster T, Asbach B, Wagner R, Gross C, Wiesmann V, Kalmer M, Wittenberg T, Gettemans J, Thoma-Kress AK, Li M, Freed EO, Liu SL, Müller J, Münch J, Sewald X, Uchil P, Ladinsky M, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka T, Brehm M, Greiner D, Mempel T, Bjorkman P, Kumar P, Mothes W, Joas S, Parrish E, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Sauermann U, Töpfer K, Schultheiss T, Bosinger S, Silvestri G, Apetrei C, Huot N, Müller-Trutwin M, Sauter D, Hahn BH, Stahl-Hennig C, Kirchhoff F, Schumann G, Jung-Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Canadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Gerdes P, Merkert S, Pulgarin A, Bock A, Held U, Witthuhn A, Haase A, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez J, Faulkner GJ, Hurst T, Katzourakis A, Magiorkinis G, Schott K, Derua R, Seifried J, Reuter A, Schmitz H, Tondera C, Brandariz-Nuñez A, Diaz-Griffero F, Janssens V, König R, Baldauf HM, Stegmann L, Schwarz SM, Trotard M, Martin M, Lenzi G, Burggraf M, Pan X, Fregoso OI, Lim ES, Abraham L, Erikson E, Nguyen L, Ambiel I, Rutsch F, Kim B, Emerman M, Fackler OT, Wittmann S, Behrendt R, Volkmann B, Eissmann K, Gramberg T, Bolduan S, Koppensteiner H, Regensburg S, Brack-Werner R, Draenert R, Schindler M, Ducroux A, Xu S, Ponnurangam A, Franz S, Malassa A, Ewald E, Goffinet C, Fung SY, Chan CP, Yuen CK, Kok KH, Chan CP, Jin DY, Dittmer U, Kmiec D, Iyer S, Stürzel C, Hahn B, Ariumi Y, Yasuda-Inoue M, Kawano K, Tateishi S, Turelli P, Compton A, Roy N, Porrot F, Billet A, Casartelli N, Yount J, Liang C, Schwartz O, Magnus C, Reh L, Moore P, Uhr T, Weber J, Morris L, Trkola A, Grindberg RV, Schlaepfer E, Schreiber G, Simon V, Speck RF, Debyser Z, Vranckx L, Demeulemeester J, Saleh S, Verdin E, Cereseto A, Christ F, Gijsbers R, Wang G, Zhao N, Das AT, Köstler J, Perdiguero B, Esteban M, Jacobs BL, Montefiori DC, LaBranche CC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Landucci G, Forthal DN, Seaman MS, Hawkins N, Self SG, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo AD, Ding S, Heeney JL, Pantaleo G, Stab V, Ensser A, Tippler B, Burton D, Tenbusch M, Überla K, Alter G, Lofano G, Dugast AS, Kulkarni V, Suscovich T, Opazo T, Barraza F, Herrera D, Garces A, Schwenke T, Tapia D, Cancino J, Arriagada G, Haußner C, Damm D, Rohrhofer A, Schmidt B, Eichler J, Midgley R, Wheeldon J, Piguet V, Khopkar P, Rohamare M, Kulkarni S, Godinho-Santos A, Hance A, Goncalves J, Mammano F, Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M, Wamara J, Bannert N, Mesplede T, Osman N, Anstett K, Liang JC, Pham HT, Wainberg M, Shao W, Shan J, Kearney M, Wu X, Maldarelli F, Mellors J, Luke B, Coffin J, Hughes S, Fricke T, Opp S, Shepard C, Ivanov D, Valle-Casuso J, Kanja M, Cappy P, Negroni M, Lener D, Knyazhanskaya E, Anisenko A, Zatsepin T, Gottikh M, Komkov A, Minervina A, Nugmanov G, Nazarov V, Khodosevich K, Mamedov I, Lebedev Y, Colomer-Lluch M, Serra-Moreno R, Sarracino A, Gharu L, Pasternak A, Marcello A, McCartin AM, Kulkarni A, Le Douce V, Gautier V, Baeyens A, Naessens E, Van Nuffel A, Weening K, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B, Mok HP, Norton N, Fun A, Hirst J, Wills M, Miklik D, Senigl F, Hejnar J, Sakuragi JI, Sakuragi S, Yokoyama M, Shioda T, Sato H, Bodem J, Moschall R, Denk S, Erkelenz S, Schenk C, Schaal H, Donhauser N, Socher E, Millen S, Sticht H, Gross C, Mann M, Wei G, Betts MJ, Liu Y, Kehl T, Russell RB, Löchelt M, Hohn O, Mostafa S, Hanke K, Norley S, Chen CY, Shingai M, Borrego P, Taveira N, Strebel K, Hellmund C, Meng B, Friedrich M, Hahn F, Setz C, Rauch P, Fraedrich K, Matthaei A, Henklein P, Traxdorf M, Fossen T, Schubert U, Khwaja A, Galilee M, Alian A, Schwalbe B, Hauser H, Schreiber M, Scherpenisse M, Cho YK, Kim J, Jeong D, Trejbalova K, Benesova M, Kucerova D, Vernerova Z, Amouroux R, Hajkova P, Elleder D, Hron T, Farkasova H, Padhi A, Paces J, Zhu H, Gifford R, Murcia P, Carrozza ML, Niewiadomska AM, Mazzei M, Abi-Said M, Hughes J, Hué S, Gifford R, Obasa A, Jacobs G, Engelbrecht S, Mack K, Starz K, Geyer M, Bibollet-Ruche F, Stürzel C, Leoz M, Plantier JC, Argaw-Denboba A, Balestrieri E, Serafino A, Bucci I, Cipriani C, Spadafora C, Sinibaldi-Vallebona P, Matteucci C, Jayashree SN, Neogi U, Chhangani AK, Rathore SS, Mathur BRJ, Abati A, Koç BT, Oğuzoğlu TÇ, Shimauchi T, Caucheteux S, Turpin J, Finsterbusch K, Tokura Y, Souriant S, Balboa L, Pingris K, Kviatcowsky D, Raynaud-Messina B, Cougoule C, Mercier I, Kuroda M, González-Montaner P, Inwentarz S, Moraña EJ, del Carmen Sasiain M, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Vérollet C, Herrmann A, Thomas D, Bouzas NF, Lahaye X, Bhargava A, Satoh T, Gentili M, Cerboni S, Silvin A, Conrad C, Ahmed-Belkacem H, Rodriguez EC, Guichou JF, Bosquet N, Piel M, Le Grand R, King M, Pawlotsky JM, Manel N, Hofmann H, Vanwalscappel B, Bloch N, Landau N, Indik S, Hagen B, Valle-Casuso JC, Allouch A, David A, Barré-Sinoussi F, Benkirane M, Pancino G, Saez-Cirion A, Lee WY, Sloan R, Schulte B, Opp S, Blomberg J, Vargiu L, Rodriguez-Tomé P, Tramontano E, Sperber G, Kumari N, Ammosova T, Diaz S, Oneal P, Nekhai S, Fahrny A, Gers-Huber G, Audigé A, Jayaprakash A, Sachidanandam R, Hernandez M, Dillon-White M, Souriant S, Pingris K, Raynaud-Messina B, Cougoule C, Mercier I, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Maze E, Ham C, Almond N, Towers G, Belshaw R, de Sousa-Pereira P, Abrantes J, Pizzato M, Esteves PJ, Kahle T, Schmitt S, Merkel L, Reuter N, Stamminger T, Rosa ID, Bishop K, Spinazzola A, Groom H, Vieyres G, Müsken M, Zillinger T, Hornung V, Barchet W, Häussler S, Pietschmann T, Javed A, Leuchte N, Salinas G, Opitz L, Sopper S, Mummert C, Hofmann C, Hückelhoven AG, Bergmann S, Müller-Schmucker SM, Harrer EG, Dörrie J, Schaft N, Harrer T, Cardinaux L, Zahno ML, Vogt HR, Zanoni R, Bertoni G, Muenchhoff M, Goulder P, Keppler O, Rebensburg S, Helfer M, Zhang Y, Chen H, Bernier A, Gosselin A, Routy JP, Wöhrl B, Schneider A, Corona A, Spöring I, Jordan M, Buchholz B, Maccioni E, Di Santo R, Schweimer K, Schölz C, Weinert B, Wagner S, Beli P, Miyake Y, Qi J, Jensen L, Streicher W, McCarthy A, Westwood N, Lain S, Cox J, Matthias P, Mann M, Bradner J, Choudhary C, Stern M, Valletta E, Frezza C, Marino-Merlo F, Grelli S, Serafino AL, Mastino A, Macchi B, Kaulfuß M, Windmann S, Bayer W, Mikasi S, Jacobs G, Heß R, Bonsmann MSG, Kirschning C, Lepenies B, Kolenbrander A, Temchura V, Iijima K, Kobayashi J, Ishizaka Y. Proceedings of the Frontiers of Retrovirology Conference 2016. Retrovirology 2016. [PMCID: PMC5046194 DOI: 10.1186/s12977-016-0294-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oral presentations Session 1: Entry & uncoating O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection Oliver T. Keppler Session 2: Reverse transcription & integration O5 Structure and function of HIV-1 integrase post translational modifications Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure Vincent Parissi Session 3: Transcription and latency O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylvain Fauquenoy, Caroline Vanhulle, Anna Kula, Arsène Burny, Olivier Rohr, Carine Van Lint O10 Tissue-specific dendritic cells differentially modulate latent HIV-1 reservoirs Thijs van Montfort, Renee van der Sluis, Dave Speijer, Ben Berkhout Session 4: RNA trafficking & packaging O11 A novel cis-acting element affecting HIV replication Bo Meng, Andrzej Rutkowski, Neil Berry, Lars Dölken, Andrew Lever O12 Tolerance of HIV’s late gene expression towards stepwise codon adaptation Thomas Schuster, Benedikt Asbach, Ralf Wagner Session 5: Assembly & release O13 Importance of the tax-inducible actin-bundling protein fascin for transmission of human T cell leukemia virus Type 1 (HTLV-1) Christine Gross, Veit Wiesmann, Martina Kalmer, Thomas Wittenberg, Jan Gettemans, Andrea K. Thoma-Kress O14 Lentiviral nef proteins antagonize TIM-mediated inhibition of viral release Minghua Li, Eric O. Freed, Shan-Lu Liu Session 6: Pathogenesis & evolution O15 SEVI and semen prolong the half-life of HIV-1 Janis Müller, Jan Münch O16 CD169+ macrophages mediate retrovirus trans-infection of permissive lymphocytes to establish infection in vivo Xaver Sewald, Pradeep Uchil, Mark Ladinsky, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas Murooka, Michael Brehm, Dale Greiner, Thorsten Mempel, Pamela Bjorkman, Priti Kumar, Walther Mothes O17 Efficient replication of a vpu containing SIVagm construct in African Green Monkeys requires an HIV-1 nef gene Simone Joas, Erica Parrish, Clement Wesley Gnanadurai, Edina Lump, Christina M. Stürzel, Nicholas F. Parrish, Ulrike Sauermann, Katharina Töpfer, Tina Schultheiss, Steven Bosinger, Guido Silvestri, Cristian Apetrei, Nicholas Huot, Michaela Müller-Trutwin, Daniel Sauter, Beatrice H. Hahn, Christiane Stahl-Hennig, Frank Kirchhoff O18 Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression Gerald Schumann, Sabine Jung-Klawitter, Nina V. Fuchs, Kyle R. Upton, Martin Muñoz-Lopez, Ruchi Shukla, Jichang Wang, Marta Garcia-Canadas, Cesar Lopez-Ruiz, Daniel J. Gerhardt, Attila Sebe, Ivana Grabundzija, Patricia Gerdes, Sylvia Merkert, Andres Pulgarin, Anja Bock, Ulrike Held, Anett Witthuhn, Alexandra Haase, Ernst J. Wolvetang, Ulrich Martin, Zoltán Ivics, Zsuzsanna Izsvák, J. Garcia-Perez, Geoffrey J. Faulkner O19 NF-κB activation induces expression of human endogenous retrovirus and particle production Tara Hurst, Aris Katzourakis, Gkikas Magiorkinis Session 7a and b: Innate sensing & intrinsic immunity O20 Identification of the phosphatase acting on T592 in SAMHD1 during M/G1 transition Kerstin Schott, Rita Derua, Janna Seifried, Andreas Reuter, Heike Schmitz, Christiane Tondera, Alberto Brandariz-Nuñez, Felipe Diaz-Griffero, Veerle Janssens, Renate König O21 Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells Hanna-Mari Baldauf, Lena Stegmann, Sarah-Marie Schwarz, Maud Trotard, Margarethe Martin, Gina Lenzi, Manja Burggraf, Xiaoyu Pan, Oliver I. Fregoso, Efrem S. Lim, Libin Abraham, Elina Erikson, Laura Nguyen, Ina Ambiel, Frank Rutsch, Renate König, Baek Kim, Michael Emerman, Oliver T. Fackler, Oliver T. Keppler O22 The role of SAMHD1 in antiviral restriction and immune sensing in the mouse Sabine Wittmann, Rayk Behrendt, Bianca Volkmann, Kristin Eissmann, Thomas Gramberg O23 T cells expressing reduced restriction factors are preferentially infected in therapy naïve HIV-1 patients Sebastian Bolduan, Herwig Koppensteiner, Stefanie Regensburg, Ruth Brack-Werner, Rika Draenert, Michael Schindler O24 cGAS-mediated innate immunity spreads through HIV-1 env-induced membrane fusion sites from infected to uninfected primary HIV-1 target cells Aurélie Ducroux, Shuting Xu, Aparna Ponnurangam, Sergej Franz, Angelina Malassa, Ellen Ewald, Christine Goffinet O25 Perturbation of innate RNA and DNA sensing by human T cell leukemia virus type 1 oncoproteins Sin-Yee Fung, Ching-Ping Chan, Chun-Kit Yuen, Kin-Hang Kok, Chin-Ping Chan, Dong-Yan Jin O26 Induction and anti-viral activity of Interferon α subtypes in HIV-1 infection Ulf Dittmer O27 Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance Dorota Kmiec, Shilpa Iyer, Christina Stürzel, Daniel Sauter, Beatrice Hahn, Frank Kirchhoff O28 DNA repair protein Rad18 restricts HIV-1 and LINE-1 life cycle Yasuo Ariumi, Mariko Yasuda-Inoue, Koudai Kawano, Satoshi Tateishi, Priscilla Turelli O29 Natural mutations in IFITM3 allow escape from post-translational regulation and toggle antiviral specificity Alex Compton, Nicolas Roy, Françoise Porrot, Anne Billet, Nicoletta Casartelli, Jacob Yount, Chen Liang, Oliver Schwartz Session 8: Adaptive immunity & immune evasion O30 Observing evolution in HIV-1 infection: phylogenetics and mutant selection windows to infer the influence of the autologous antibody response on the viral quasispecies Carsten Magnus, Lucia Reh, Penny Moore, Therese Uhr, Jacqueline Weber, Lynn Morris, Alexandra Trkola O31 Dose and subtype specific analyses of the anti-HIV effects of IFN-alpha family members Rashel V. Grindberg, Erika Schlaepfer, Gideon Schreiber, Viviana Simon, Roberto F. Speck Session 9: Novel antiviral strategies O32 LEDGIN-mediated inhibition of the integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV Zeger Debyser, Lenard Vranckx, Jonas Demeulemeester, Suha Saleh, Eric Verdin, Anna Cereseto, Frauke Christ, Rik Gijsbers O33 NKG2D-mediated clearance of reactivated viral reservoirs by natural killer cells O34 Inhibition of HIV reactivation in brain cells by AAV-mediated delivery of CRISPR/Cas9 O35 CRISPR-Cas9 as antiviral: potent HIV-1 inhibition, but rapid virus escape and the subsequent design of escape-proof antiviral strategies Ben Berkhout, Gang Wang, Na Zhao, Atze T. Das Session 10: Recent advances in HIV vaccine development O36 Priming with a potent HIV-1 DNA vaccine frames the quality of T cell and antibody responses prior to a poxvirus and protein boost Benedikt Asbach, Josef Köstler, Beatriz Perdiguero, Mariano Esteban, Bertram L. Jacobs, David C. Montefiori, Celia C. LaBranche, Nicole L. Yates, Georgia D. Tomaras, Guido Ferrari, Kathryn E. Foulds, Mario Roederer, Gary Landucci, Donald N. Forthal, Michael S. Seaman, Natalie Hawkins, Steven G. Self, Sanjay Phogat, James Tartaglia, Susan W. Barnett, Brian Burke, Anthony D. Cristillo, Song Ding, Jonathan L. Heeney, Giuseppe Pantaleo, Ralf Wagner O37 Passive immunisation with a neutralising antibody against HIV-1 Env prevents infection of the first cells in a mucosal challenge rhesus monkey model Christiane Stahl-Hennig, Viktoria Stab, Armin Ensser, Ulrike Sauermann, Bettina Tippler, Dennis Burton, Matthias Tenbusch, Klaus Überla O38 HIV antibody Fc-glycoforms drive B cell affinity maturation Galit Alter, Giuseppe Lofano, Anne-Sophie Dugast, Viraj Kulkarni, Todd Suscovich Poster presentations Topic 1: Entry & uncoating P1 Dynein light chain is required for murine leukemia virus infection Tatiana Opazo, Felipe Barraza, Diego Herrera, Andrea Garces, Tomas Schwenke, Diego Tapia, Jorge Cancino, Gloria Arriagada P2 Peptide paratope mimics of the broadly neutralising HIV-1 antibody b12 Christina Haußner, Dominik Damm, Anette Rohrhofer, Barbara Schmidt, Jutta Eichler P3 Investigating cellular pathways involved in the transmission of HIV-1 between dendritic cells and T cells using RNAi screening techniques Rebecca Midgley, James Wheeldon, Vincent Piguet P4 Co-receptor tropism in HIV-1, HIV-2 monotypic and dual infections Priyanka Khopkar, Megha Rohamare, Smita Kulkarni P5 Characterisation of the role of CIB1 and CIB2 as HIV-1 helper factors Ana Godinho-Santos, Allan Hance, Joao Goncalves, Fabrizio Mammano P6 Buffering deleterious polymorphisms in the highly constrained C2 region of HIV-1 envelope by the flexible V3 domain Romain Gasser, Meriem Hamoudi, Martina Pellicciotta, Zhicheng Zhou, Clara Visdeloup, Philippe Colin, Martine Braibant, Bernard Lagane, Matteo Negroni P7 Entry inhibition of HERV-K(HML-2) by an Env-IgG fusion protein Jula Wamara, Norbert Bannert Topic 2: Reverse transcription & integration P8 The R263K/H51Y resistance substitutions in HIV integrase decreases levels of integrated HIV DNA over time Thibault Mesplede, Nathan Osman, Kaitlin Anstett, Jiaming Calvin Liang, Hanh Thi Pham, Mark Wainberg P9 The Retrovirus Integration Database (RID) Wei Shao, Jigui Shan, Mary Kearney, Xiaolin Wu, Frank Maldarelli, John Mellors, Brian Luke, John Coffin, Stephen Hughes P10 The small molecule 3G11 inhibits HIV-1 reverse transcription Thomas Fricke, Silvana Opp, Caitlin Shepard, Dmitri Ivanov, Baek Kim, Jose Valle-Casuso, Felipe Diaz-Griffero P11 Dual and opposite regulation of HIV-1 integration by hRAD51: impact on therapeutical approaches using homologous DNA repair modulators Vincent Parissi P12 A flexible motif essential for integration by HIV-1 integrase Marine Kanja, Pierre Cappy, Matteo Negroni, Daniela Lener P13 Interaction between HIV-1 integrase and the host protein Ku70: identification of the binding site and study of the influence on integrase-proteasome interplay Ekaterina Knyazhanskaya, Andrey Anisenko, Timofey Zatsepin, Marina Gottikh P14 Normalisation based method for deep sequencing of somatic retroelement integrations in human genome Alexander Komkov, Anastasia Minervina, Gaiaz Nugmanov, Vadim Nazarov, Konstantin Khodosevich, Ilgar Mamedov, Yuri Lebedev Topic 3: Transcription and latency P15 BCA2/RABRING7 restricts HIV-1 transcription by preventing the nuclear translocation of NF-κB Marta Colomer-Lluch, Ruth Serra-Moreno P16 MATR3 post-transcriptional regulation of HIV-1 transcription during latency Ambra Sarracino, Anna Kula, Lavina Gharu, Alexander Pasternak, Carine Van Lint, Alessandro Marcello P17 HIV-1 tat intersects the SUMO pathway to regulate HIV-1 promoter activity Ann Marie McCartin, Anurag Kulkarni, Valentin Le Douce, Virginie Gautier P18 Conservation in HIV-1 Vpr guides tertiary gRNA folding and alternative splicing Ann Baeyens, Evelien Naessens, Anouk Van Nuffel, Karin Weening, Anne-Marie Reilly, Eva Claeys, Wim Trypsteen, Linos Vandekerckhove, Sven Eyckerman, Kris Gevaert, Bruno Verhasselt P19 The majority of reactivatable latent HIV are genetically distinct Hoi Ping Mok, Nicholas Norton, Axel Fun, Jack Hirst, Mark Wills, Andrew Lever P20 Do mutations in the tat exonic splice enhancer contribute to HIV-1 latency? Nicholas Norton, Hoi Ping Mok, Jack Hirst, Andrew Lever P21 Culture-to-Ct: A fast and direct RT-qPCR HIV gene reactivation screening method using primary T cell culture Valentin Le Douce, Ann Marie McCartin, Virginie Gautier P22 A novel approach to define populations of early silenced proviruses Dalibor Miklik, Filip Senigl, Jiri Hejnar Topic 4: RNA trafficking & packaging P23 Functional analysis of the structure and conformation of HIV-1 genome RNA DIS Jun-ichi Sakuragi, Sayuri Sakuragi, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato P24 Regulation of foamy viral env splicing controls gag and pol expression Jochen Bodem, Rebecca Moschall, Sarah Denk, Steffen Erkelenz, Christian Schenk, Heiner Schaal Topic 5: Assembly & release P25 Transfer of HTLV-1 p8 to target T cells depends on VASP: a novel interaction partner of p8 Norbert Donhauser, Ellen Socher, Sebastian Millen, Heinrich Sticht, Andrea K. Thoma-Kress P26 COL4A1 and COL4A2 are novel HTLV-1 tax targets with a putative role in virus transmission Christine Gross, Sebastian Millen, Melanie Mann, Klaus Überla, Andrea K. Thoma-Kress P27 The C terminus of foamy virus gag protein is required for particle formation, and virus budding: starting assembly at the C terminus? Guochao Wei, Matthew J. Betts, Yang Liu, Timo Kehl, Robert B. Russell, Martin Löchelt P28 Generation of an antigen-capture ELISA and analysis of Rec and Staufen-1 effects on HERV-K(HML-2) virus particle production Oliver Hohn, Saeed Mostafa, Kirsten Hanke, Stephen Norley, Norbert Bannert P29 Antagonism of BST-2/tetherin is a conserved function of primary HIV-2 Env glycoproteins Chia-Yen Chen, Masashi Shingai, Pedro Borrego, Nuno Taveira, Klaus Strebel P30 Mutations in the packaging signal region of the HIV-1 genome cause a late domain mutant phenotype Chris Hellmund, Bo Meng, Andrew Lever P31 p6 regulates membrane association of HIV-1 gag Melanie Friedrich, Friedrich Hahn, Christian Setz, Pia Rauch, Kirsten Fraedrich, Alina Matthaei, Petra Henklein, Maximilian Traxdorf, Torgils Fossen, Ulrich Schubert Topic 6: Pathogenesis & evolution P32 Molecular and structural basis of protein evolution during viral adaptation Aya Khwaja, Meytal Galilee, Akram Alian P33 HIV-1 enhancement and neutralisation by soluble gp120 and its role for the selection of the R5-tropic “best fit” Birco Schwalbe, Heiko Hauser, Michael Schreiber P34 An insertion of seven amino acids in the Env cytoplasmic tail of Human Immunodeficiency Virus type 2 (HIV-2) selected during disease progression enhances viral replication François Dufrasne, Mara Lucchetti, Patrick Goubau, Jean Ruelle P35 Cell-associated HIV-1 unspliced to multiply spliced RNA ratio at 12 weeks ART correlates with markers of immune activation and apoptosis and predicts the CD4 T-cell count at 96 weeks ART Mirte Scherpenisse, Ben Berkhout, Alexander Pasternak P36 Faster progression in non-B subtype HIV-1-infected patients than Korean subclade of subtype B is accompanied by higher variation and no induction of gross deletion in non-B nef gene by Korean red ginseng treatment Young-Keol Cho, Jungeun Kim, Daeun Jeong P37 Aberrant expression of ERVWE1 endogenous retrovirus and overexpression of TET dioxygenases are characteristic features of seminoma Katerina Trejbalova, Martina Benesova, Dana Kucerova, Zdenka Vernerova, Rachel Amouroux, Petra Hajkova, Jiri Hejnar P38 Life history of the oldest lentivirus: characterisation of ELVgv integrations and the TRIM5 selection pattern in dermoptera Daniel Elleder, Tomas Hron, Helena Farkasova, Abinash Padhi, Jan Paces P39 Characterisation of a highly divergent endogenous retrovirus in the equine germ line Henan Zhu, Robert Gifford, Pablo Murcia P40 The emergence of pandemic retroviral infection in small ruminants Maria Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir Abi-Said, Joseph Hughes, Stéphane Hué, Robert Gifford P41 Near full-length genome (NFLG) Characterisation of HIV-1 subtype B identified in South Africa Adetayo Obasa, Graeme Jacobs, Susan Engelbrecht P42 Acquisition of Vpu-mediated tetherin antagonism by an HIV-1 group O strain Katharina Mack, Kathrin Starz, Daniel Sauter, Matthias Geyer, Frederic Bibollet-Ruche, Christina Stürzel, Marie Leoz, Jean Christophe Plantier, Beatrice H. Hahn, Frank Kirchhoff P43 The human endogenous retrovirus type K is involved in cancer stem cell markers expression and in human melanoma malignancy Ayele Argaw-Denboba, Emanuela Balestrieri, Annalucia Serafino, Ilaria Bucci, Chiara Cipriani, Corrado Spadafora, Paolo Sinibaldi-Vallebona, Claudia Matteucci P44 Natural infection of Indian non-human primates by unique lentiviruses S. Nandi Jayashree, Ujjwal Neogi, Anil K. Chhangani, Shravan Sing Rathore, Bajrang R. J. Mathur P45 Free cervical cancer screening among HIV-positive women receiving antiretroviral treatment in Nigeria Adeyemi Abati P46 Molecular evolutionary status of feline immunodeficiency virus in Turkey B. Taylan Koç, Tuba Çiğdem Oğuzoğlu Topic 7: Innate sensing & intrinsic immunity P47 Cell-to-cell contact with HTLV-1-infected T cells reduces dendritic cell immune functions and contributes to infection in trans. Takatoshi Shimauchi, Stephan Caucheteux, Jocelyn Turpin, Katja Finsterbusch, Charles Bangham, Yoshiki Tokura, Vincent Piguet P48 Deciphering the mechanisms of HIV-1 exacerbation induced by Mycobacterium tuberculosis in monocytes/macrophages Shanti Souriant, Luciana Balboa, Karine Pingris, Denise Kviatcowsky, Brigitte Raynaud-Messina, Céline Cougoule, Ingrid Mercier, Marcelo Kuroda, Pablo González-Montaner, Sandra Inwentarz, Eduardo Jose Moraña, Maria del Carmen Sasiain, Olivier Neyrolles, Isabelle Maridonneau-Parini, Geanncarlo Lugo-Villarino, Christel Vérollet P49 The SAMHD1-mediated inhibition of LINE-1 retroelements is regulated by phosphorylation Alexandra Herrmann, Sabine Wittmann, Caitlin Shepard, Dominique Thomas, Nerea Ferreirós Bouzas, Baek Kim, Thomas Gramberg P50 Activities of nuclear envelope protein SUN2 in HIV infection Xavier Lahaye, Anvita Bhargava, Takeshi Satoh, Matteo Gentili, Silvia Cerboni, Aymeric Silvin, Cécile Conrad, Hakim Ahmed-Belkacem, Elisa C. Rodriguez, Jean-François Guichou, Nathalie Bosquet, Matthieu Piel, Roger Le Grand, Megan King, Jean-Michel Pawlotsky, Nicolas Manel P51 Activation of TLR7/8 with a small molecule agonist induces a novel restriction to HIV-1 infection of monocytes Henning Hofmann, Benedicte Vanwalscappel, Nicolin Bloch, Nathaniel Landau P52 Steady state between the DNA polymerase and Rnase H domain activities of reverse transcriptases determines the sensitivity of retroviruses to inhibition by APOBEC3 proteins Stanislav Indik, Benedikt Hagen P53 HIV restriction in mature dendritic cells is related to p21 induction and p21-mediated control of the dNTP pool and SAMHD1 activity. José Carlos Valle-Casuso, Awatef Allouch, Annie David, Françoise Barré-Sinoussi, Michaela Müller-Trutwin, Monsef Benkirane, Gianfranco Pancino, Asier Saez-Cirion P54 IFITM protens restrict HIV-1 protein synthesis Wing-Yiu Lee, Chen Liang, Richard Sloan P55 Characterisation and functional analysis of the novel restriction factor Serinc5 Bianca Schulte, Silvana Opp, Felipe Diaz-Griffero P56 piRNA sequences are common in Human Endogenous Retroviral Sequences (HERVs): An antiretroviral restriction mechanism? Jonas Blomberg, Luana Vargiu, Patricia Rodriguez-Tomé, Enzo Tramontano, Göran Sperber P57 Ferroportin restricts HIV-1 infection in sickle cell disease Namita Kumari, Tatiana Ammosova, Sharmeen Diaz, Patricia Oneal, Sergei Nekhai P58 APOBEC3G modulates the response to antiretroviral drugs in humanized mice Audrey Fahrny, Gustavo Gers-Huber, Annette Audigé, Roberto F. Speck, Anitha Jayaprakash, Ravi Sachidanandam, Matt Hernandez, Marsha Dillon-White, Viviana Simon P59 High-throughput epigenetic analysis of evolutionarily young endogenous retrovirus presents in the mule deer (Odocoileus hemionus) genome Tomas Hron, Helena Farkasova, Daniel Elleder P60 Characterisation of the expression of novel endogenous retroviruses and immune interactions in a macaque model Neil Berry, Emmanuel Maze, Claire Ham, Neil Almond, Greg Towers, Robert Belshaw P61 HIV-1 restriction by orthologs of SERINC3 and SERINC5 Patrícia de Sousa-Pereira, Joana Abrantes, Massimo Pizzato, Pedro J. Esteves, Oliver T. Fackler, Oliver T. Keppler, Hanna-Mari Baldauf P62 TRIM19/PML restricts HIV infection in a cell type-dependent manner Bianca Volkmann, Tanja Kahle, Kristin Eissmann, Alexandra Herrmann, Sven Schmitt, Sabine Wittmann, Laura Merkel, Nina Reuter, Thomas Stamminger, Thomas Gramberg P63 Recent invasion of the mule deer genome by a retrovirus Helena Farkasova, Tomas Hron, Daniel Elleder P64 Does the antiviral protein SAMHD1 influence mitochondrial function? Ilaria Dalla Rosa, Kate Bishop, Antonella Spinazzola, Harriet Groom P65 cGAMP transfers intercellularly via HIV-1 Env-mediated cell–cell fusion sites and triggers an innate immune response in primary target cells Shuting Xu, Aurélie Ducroux, Aparna Ponnurangam, Sergej Franz, Gabrielle Vieyres, Mathias Müsken, Thomas Zillinger, Angelina Malassa, Ellen Ewald, Veit Hornung, Winfried Barchet, Susanne Häussler, Thomas Pietschmann, Christine Goffinet P66 Pre-infection transcript levels of FAM26F in PBMCS inform about overall plasma viral load in acute and postacute phase after SIV-infection Ulrike Sauermann, Aneela Javed, Nicole Leuchte, Gabriela Salinas, Lennart Opitz, Christiane Stahl-Hennig, Sieghart Sopper P67 Sequence-function analysis of three T cell receptors targeting the HIV-1 p17 epitope SLYNTVATL Christiane Mummert, Christian Hofmann, Angela G. Hückelhoven, Silke Bergmann, Sandra M. Müller-Schmucker, Ellen G. Harrer, Jan Dörrie, Niels Schaft, Thomas Harrer P68 An immunodominant region of the envelope glycoprotein of small ruminant lentiviruses may function as decoy antigen Laure Cardinaux, M.-L. Zahno, H.-R. Vogt, R. Zanoni, G. Bertoni P69 Impact of immune activation, immune exhaustion, broadly neutralising antibodies and viral reservoirs on disease progression in HIV-infected children Maximilian Muenchhoff, Philip Goulder, Oliver Keppler Topic 9: Novel antiviral strategies P70 Identification of natural compounds as new antiviral products by bioassay-guided fractionation Alexandra Herrmann, Stephanie Rebensburg, Markus Helfer, Michael Schindler, Ruth Brack-Werner P71 The PPARG antagonism disconnects the HIV replication and effector functions in Th17 cells Yuwei Zhang, Huicheng Chen, Delphine Planas, Annie Bernier, Annie Gosselin, Jean-Pierre Routy, Petronela Ancuta P72 Characterisation of a multiresistant subtype AG reverse transcriptase: AZT resistance, sensitivity to RNase H inhibitors and inhibitor binding Birgitta Wöhrl, Anna Schneider, Angela Corona, Imke Spöring, Mareike Jordan, Bernd Buchholz, Elias Maccioni, Roberto Di Santo, Jochen Bodem, Enzo Tramontano, Kristian Schweimer P73 Insigths into the acetylation pattern of HDAC inhibitors and their potential role in HIV therapy Christian Schölz, Brian Weinert, Sebastian Wagner, Petra Beli, Yasuyuki Miyake, Jun Qi, Lars Jensen, Werner Streicher, Anna McCarthy, Nicholas Westwood, Sonia Lain, Jürgen Cox, Patrick Matthias, Matthias Mann, James Bradner, Chunaram Choudhary P74 HPV-derived and seminal amyloid peptides enhance HIV-1 infection and impair the efficacy of broadly neutralising antibodies and antiretroviral drugs Marcel Stern, Oliver T. Keppler P75 D(−)lentiginosine inhibits both proliferation and virus expression in cells infected by HTLV-1 in vitro Elena Valletta, Caterina Frezza, Claudia Matteucci, Francesca Marino-Merlo, Sandro Grelli, Anna Lucia Serafino, Antonio Mastino, Beatrice Macchi P76 HIV-1 resistance analyses of the Cape Winelands districts, South Africa Sello Mikasi, Graeme Jacobs, Susan Engelbrecht Topic 10: Recent advances in HIV vaccine development P77 Induction of complex retrovirus antigen-specific immune responses by adenovirus-based vectors depends on the order of vector administration Meike Kaulfuß, Sonja Windmann, Wibke Bayer P78 Direct impact of structural properties of HIV-1 Env on the regulation of the humoral immune response Rebecca Heß, Michael Storcksdieck gen. Bonsmann, Viktoria Stab, Carsten Kirschning, Bernd Lepenies, Matthias Tenbusch, Klaus Überla P79 Lentiviral virus-like particles mediate gerenration of T-follicular helper cells in vitro Anne Kolenbrander, Klaus Überla, Vladimir Temchura P80 Recruitment of HIV-1 Vpr to DNA damage sites and protection of proviral DNA from nuclease activity Kenta Iijima, Junya Kobayashi, Yukihito Ishizaka
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Greenwood EJD, Schmidt F, Kondova I, Niphuis H, Hodara VL, Clissold L, McLay K, Guerra B, Redrobe S, Giavedoni LD, Lanford RE, Murthy KK, Rouet F, Heeney JL. Simian Immunodeficiency Virus Infection of Chimpanzees (Pan troglodytes) Shares Features of Both Pathogenic and Non-pathogenic Lentiviral Infections. PLoS Pathog 2015; 11:e1005146. [PMID: 26360709 PMCID: PMC4567047 DOI: 10.1371/journal.ppat.1005146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 03/11/2015] [Accepted: 08/12/2015] [Indexed: 01/08/2023] Open
Abstract
The virus-host relationship in simian immunodeficiency virus (SIV) infected chimpanzees is thought to be different from that found in other SIV infected African primates. However, studies of captive SIVcpz infected chimpanzees are limited. Previously, the natural SIVcpz infection of one chimpanzee, and the experimental infection of six chimpanzees was reported, with limited follow-up. Here, we present a long-term study of these seven animals, with a retrospective re-examination of the early stages of infection. The only clinical signs consistent with AIDS or AIDS associated disease was thrombocytopenia in two cases, associated with the development of anti-platelet antibodies. However, compared to uninfected and HIV-1 infected animals, SIVcpz infected animals had significantly lower levels of peripheral blood CD4+ T-cells. Despite this, levels of T-cell activation in chronic infection were not significantly elevated. In addition, while plasma levels of β2 microglobulin, neopterin and soluble TNF-related apoptosis inducing ligand (sTRAIL) were elevated in acute infection, these markers returned to near-normal levels in chronic infection, reminiscent of immune activation patterns in ‘natural host’ species. Furthermore, plasma soluble CD14 was not elevated in chronic infection. However, examination of the secondary lymphoid environment revealed persistent changes to the lymphoid structure, including follicular hyperplasia in SIVcpz infected animals. In addition, both SIV and HIV-1 infected chimpanzees showed increased levels of deposition of collagen and increased levels of Mx1 expression in the T-cell zones of the lymph node. The outcome of SIVcpz infection of captive chimpanzees therefore shares features of both non-pathogenic and pathogenic lentivirus infections. The HIV-1/AIDS pandemic is the result of cross-species transmission of simian immunodeficiency virus (SIVcpz) from chimpanzees to humans. Many African primates are infected with SIV, but those studied in captivity generally do not develop disease. However, wild chimpanzees infected with SIVcpz are at increased risk of death and may develop an AIDS-like disease. It has therefore been suggested that the viral features which SIVcpz and HIV-1 share, that differentiate them from other species’ SIV, may be critical in the development of disease in both humans and chimpanzees. Here, we present a long-term follow-up of 7 SIVcpz infected chimpanzees, housed in primate centres in the US and Europe, under similar conditions to other studied models. These animals did not develop an AIDS-like disease, after up to 25 years of infection, and showed features similar to other species where disease rarely develops, such as limited immune activation in the blood. However, they also had significantly reduced CD4+ T-cells and disruption to the secondary lymphoid tissues, normally associated with pathogenic primate lentiviral infections. Thus, while SIVcpz infection of chimpanzees shares features of both pathogenic and non-pathogenic infections, disease has not developed in captivity.
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Affiliation(s)
| | - Fabian Schmidt
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ivanela Kondova
- Division of Pathology and Microbiology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Henk Niphuis
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Vida L. Hodara
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Southwest National Primate Research Center, San Antonio, Texas, United States of America
| | - Leah Clissold
- The Genome Analysis Centre (TGAC), Norwich, United Kingdom
| | - Kirsten McLay
- The Genome Analysis Centre (TGAC), Norwich, United Kingdom
| | - Bernadette Guerra
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Sharon Redrobe
- Twycross Zoo - East Midland Zoological Society, Atherstone, United Kingdom
| | - Luis D. Giavedoni
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Southwest National Primate Research Center, San Antonio, Texas, United States of America
| | - Robert E. Lanford
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Southwest National Primate Research Center, San Antonio, Texas, United States of America
| | - Krishna K. Murthy
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - François Rouet
- Laboratoire de Rétrovirologie, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL. Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data. PLoS One 2015; 10:e0129059. [PMID: 26098299 PMCID: PMC4476701 DOI: 10.1371/journal.pone.0129059] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 09/10/2014] [Accepted: 05/04/2015] [Indexed: 12/18/2022] Open
Abstract
The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.
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Affiliation(s)
- Gordon M. Daly
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Richard M. Leggett
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR47UH, United Kingdom
| | - William Rowe
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Samuel Stubbs
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | - Maxim Wilkinson
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
| | | | - Mario Caccamo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR47UH, United Kingdom
| | - William Bernal
- Institute of Liver Studies, King's College Hospital, Denmark Hill, London, SE59RS, United Kingdom
| | - Jonathan L. Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom
- * E-mail:
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Swamy M, Abeler-Dörner L, Chettle J, Mahlakõiv T, Goubau D, Chakravarty P, Ramsay G, Reis e Sousa C, Staeheli P, Blacklaws BA, Heeney JL, Hayday AC. Intestinal intraepithelial lymphocyte activation promotes innate antiviral resistance. Nat Commun 2015; 6:7090. [PMID: 25987506 PMCID: PMC4479038 DOI: 10.1038/ncomms8090] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 09/12/2014] [Accepted: 03/27/2015] [Indexed: 12/13/2022] Open
Abstract
Unrelenting environmental challenges to the gut epithelium place particular demands on the local immune system. In this context, intestinal intraepithelial lymphocytes (IEL) compose a large, highly conserved T cell compartment, hypothesized to provide a first line of defence via cytolysis of dysregulated intestinal epithelial cells (IEC) and cytokine-mediated re-growth of healthy IEC. Here we show that one of the most conspicuous impacts of activated IEL on IEC is the functional upregulation of antiviral interferon (IFN)-responsive genes, mediated by the collective actions of IFNs with other cytokines. Indeed, IEL activation in vivo rapidly provoked type I/III IFN receptor-dependent upregulation of IFN-responsive genes in the villus epithelium. Consistent with this, activated IEL mediators protected cells against virus infection in vitro, and pre-activation of IEL in vivo profoundly limited norovirus infection. Hence, intraepithelial T cell activation offers an overt means to promote the innate antiviral potential of the intestinal epithelium.
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Affiliation(s)
- Mahima Swamy
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
- Peter Gorer Department of Immunobiology, King's College London, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
- Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lucie Abeler-Dörner
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
- Peter Gorer Department of Immunobiology, King's College London, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - James Chettle
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Tanel Mahlakõiv
- Institute of Virology, University Medical Center, Freiburg D-79104, Germany
- Spemann Graduate School of Biology and Medicine, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Delphine Goubau
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
| | - Probir Chakravarty
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
| | - George Ramsay
- Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Caetano Reis e Sousa
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
| | - Peter Staeheli
- Institute of Virology, University Medical Center, Freiburg D-79104, Germany
| | - Barbara A. Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Adrian C. Hayday
- Immunosurveillance lab, Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, UK
- Peter Gorer Department of Immunobiology, King's College London, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
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Sholukh AM, Watkins JD, Vyas HK, Gupta S, Lakhashe SK, Thorat S, Zhou M, Hemashettar G, Bachler BC, Forthal DN, Villinger F, Sattentau QJ, Weiss RA, Agatic G, Corti D, Lanzavecchia A, Heeney JL, Ruprecht RM. Defense-in-depth by mucosally administered anti-HIV dimeric IgA2 and systemic IgG1 mAbs: complete protection of rhesus monkeys from mucosal SHIV challenge. Vaccine 2015; 33:2086-95. [PMID: 25769884 DOI: 10.1016/j.vaccine.2015.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 10/03/2014] [Revised: 02/03/2015] [Accepted: 02/07/2015] [Indexed: 12/19/2022]
Abstract
Although IgA is the most abundantly produced immunoglobulin in humans, its role in preventing HIV-1 acquisition, which occurs mostly via mucosal routes, remains unclear. In our passive mucosal immunizations of rhesus macaques (RMs), the anti-HIV-1 neutralizing monoclonal antibody (nmAb) HGN194, given either as dimeric IgA1 (dIgA1) or dIgA2 intrarectally (i.r.), protected 83% or 17% of the RMs against i.r. simian-human immunodeficiency virus (SHIV) challenge, respectively. Data from the RV144 trial implied that vaccine-induced plasma IgA counteracted the protective effector mechanisms of IgG1 with the same epitope specificity. We thus hypothesized that mucosal dIgA2 might diminish the protection provided by IgG1 mAbs targeting the same epitope. To test our hypothesis, we administered HGN194 IgG1 intravenously (i.v.) either alone or combined with i.r. HGN194 dIgA2. We enrolled SHIV-exposed, persistently aviremic RMs protected by previously administered nmAbs; RM anti-human IgG responses were undetectable. However, low-level SIV Gag-specific proliferative T-cell responses were found. These animals resemble HIV-exposed, uninfected humans, in which local and systemic cellular immune responses have been observed. HGN194 IgG1 and dIgA2 used alone and the combination of the two neutralized the challenge virus equally well in vitro. All RMs given only i.v. HGN194 IgG1 became infected. In contrast, all RMs given HGN194 IgG1+dIgA2 were completely protected against high-dose i.r. SHIV-1157ipEL-p challenge. These data imply that combining suboptimal defenses at the mucosal and systemic levels can completely prevent virus acquisition. Consequently, active vaccination should focus on defense-in-depth, a strategy that seeks to build up defensive fall-back positions well behind the fortified frontline.
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Affiliation(s)
- Anton M Sholukh
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jennifer D Watkins
- Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Hemant K Vyas
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sandeep Gupta
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine School of Medicine, Irvine, CA, USA
| | - Samir K Lakhashe
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Swati Thorat
- Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Mingkui Zhou
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | | | - Donald N Forthal
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine School of Medicine, Irvine, CA, USA
| | - Francois Villinger
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA; Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Quentin J Sattentau
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | | | - Davide Corti
- Humabs BioMed SA, Bellinzona 6500, Switzerland; Institute for Research in Biomedicine, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Bellinzona 6500, Switzerland; Eidgenoessische Technische Hochschule, Zurich CH-8093, Switzerland
| | - Jonathan L Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Ruth M Ruprecht
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA; Southwest National Primate Research Center, San Antonio, TX, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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Mooij P, Koopman G, Drijfhout JW, Nieuwenhuis IG, Beenhakker N, Koestler J, Bogers WMJM, Wagner R, Esteban M, Pantaleo G, Heeney JL, Jacobs BL, Melief CJM. Synthetic long peptide booster immunization in rhesus macaques primed with replication-competent NYVAC-C-KC induces a balanced CD4/CD8 T-cell and antibody response against the conserved regions of HIV-1. J Gen Virol 2015; 96:1478-1483. [PMID: 25667320 DOI: 10.1099/vir.0.000074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/26/2015] [Indexed: 12/16/2022] Open
Abstract
The Thai trial (RV144) indicates that a prime-boost vaccine combination that induces both T-cell and antibody responses may be desirable for an effective HIV vaccine. We have previously shown that immunization with synthetic long peptides (SLP), covering the conserved parts of SIV, induced strong CD4 T-cell and antibody responses, but only modest CD8 T-cell responses. To generate a more balanced CD4/CD8 T-cell and antibody response, this study evaluated a pox-vector prime/SLP boost strategy in rhesus macaques. Priming with a replication-competent NYVAC, encoding HIV-1 clade C gag, pol and nef, induced modest IFNγ T-cell immune responses, predominantly directed against HIV-1 Gag. Booster immunization with SLP, covering the conserved parts of HIV-1 Gag, Pol and Env, resulted in a more than 10-fold increase in IFNγ ELISpot responses in four of six animals, which were predominantly HIV-1 Pol-specific. The animals showed a balanced polyfunctional CD4 and CD8 T-cell response and high Ab titres.
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Affiliation(s)
- Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Ivonne G Nieuwenhuis
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Niels Beenhakker
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Josef Koestler
- University of Regensburg, Franz-Josef-Strauss Allee 11, D93053 Regensburg, Germany
| | - Willy M J M Bogers
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Ralf Wagner
- University of Regensburg, Franz-Josef-Strauss Allee 11, D93053 Regensburg, Germany
| | | | - Giuseppe Pantaleo
- Swiss Vaccine Research Institute, Lausanne, Switzerland.,Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jonathan L Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | | | - Cornelis J M Melief
- ISA pharmaceuticals, J.H. Oortweg 19-21, 2333 CH Leiden, The Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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Lai RPJ, Hock M, Radzimanowski J, Tonks P, Hulsik DL, Effantin G, Seilly DJ, Dreja H, Kliche A, Wagner R, Barnett SW, Tumba N, Morris L, LaBranche CC, Montefiori DC, Seaman MS, Heeney JL, Weissenhorn W. A fusion intermediate gp41 immunogen elicits neutralizing antibodies to HIV-1. J Biol Chem 2014; 289:29912-26. [PMID: 25160627 PMCID: PMC4208001 DOI: 10.1074/jbc.m114.569566] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/01/2014] [Indexed: 11/06/2022] Open
Abstract
The membrane-proximal external region (MPER) of the human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein subunit gp41 is targeted by potent broadly neutralizing antibodies 2F5, 4E10, and 10E8. These antibodies recognize linear epitopes and have been suggested to target the fusion intermediate conformation of gp41 that bridges viral and cellular membranes. Anti-MPER antibodies exert different degrees of membrane interaction, which is considered to be the limiting factor for the generation of such antibodies by immunization. Here we characterize a fusion intermediate conformation of gp41 (gp41(int)-Cys) and show that it folds into an elongated ∼ 12-nm-long extended structure based on small angle x-ray scattering data. Gp41(int)-Cys was covalently linked to liposomes via its C-terminal cysteine and used as immunogen. The gp41(int)-Cys proteoliposomes were administered alone or in prime-boost regimen with trimeric envelope gp140(CA018) in guinea pigs and elicited high anti-gp41 IgG titers. The sera interacted with a peptide spanning the MPER region, demonstrated competition with broadly neutralizing antibodies 2F5 and 4E10, and exerted modest lipid binding, indicating the presence of MPER-specific antibodies. Although the neutralization potency generated solely by gp140(CA018) was higher than that induced by gp41(int)-Cys, the majority of animals immunized with gp41(int)-Cys proteoliposomes induced modest breadth and potency in neutralizing tier 1 pseudoviruses and replication-competent simian/human immunodeficiency viruses in the TZM-bl assay as well as responses against tier 2 HIV-1 in the A3R5 neutralization assay. Our data thus demonstrate that liposomal gp41 MPER formulation can induce neutralization activity, and the strategy serves to improve breadth and potency of such antibodies by improved vaccination protocols.
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Affiliation(s)
- Rachel P J Lai
- From the Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Miriam Hock
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France, CNRS, UVHCI, F-38000 Grenoble, France
| | - Jens Radzimanowski
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France, CNRS, UVHCI, F-38000 Grenoble, France
| | - Paul Tonks
- From the Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - David Lutje Hulsik
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France, CNRS, UVHCI, F-38000 Grenoble, France
| | - Gregory Effantin
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France, CNRS, UVHCI, F-38000 Grenoble, France
| | - David J Seilly
- From the Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Hanna Dreja
- From the Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
| | - Alexander Kliche
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Susan W Barnett
- Novartis Vaccines and Diagnostics Inc., Cambridge, Massachusetts 02139
| | - Nancy Tumba
- National Institute for Communicable Diseases, Centre for HIV and Sexually Transmitted Infections, 1 Modderfontein Road, Sandringham 2131, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases, Centre for HIV and Sexually Transmitted Infections, 1 Modderfontein Road, Sandringham 2131, South Africa
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, and
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, and
| | - Michael S Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115
| | - Jonathan L Heeney
- From the Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom,
| | - Winfried Weissenhorn
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France, CNRS, UVHCI, F-38000 Grenoble, France,
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35
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Bogers WM, Oostermeijer H, Mooij P, Koopman G, Verschoor EJ, Davis D, Ulmer JB, Brito LA, Cu Y, Banerjee K, Otten GR, Burke B, Dey A, Heeney JL, Shen X, Tomaras GD, Labranche C, Montefiori DC, Liao HX, Haynes B, Geall AJ, Barnett SW. Potent immune responses in rhesus macaques induced by nonviral delivery of a self-amplifying RNA vaccine expressing HIV type 1 envelope with a cationic nanoemulsion. J Infect Dis 2014; 211:947-55. [PMID: 25234719 DOI: 10.1093/infdis/jiu522] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [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: 02/06/2023] Open
Abstract
Self-amplifying messenger RNA (mRNA) of positive-strand RNA viruses are effective vectors for in situ expression of vaccine antigens and have potential as a new vaccine technology platform well suited for global health applications. The SAM vaccine platform is based on a synthetic, self-amplifying mRNA delivered by a nonviral delivery system. The safety and immunogenicity of an HIV SAM vaccine encoding a clade C envelope glycoprotein formulated with a cationic nanoemulsion (CNE) delivery system was evaluated in rhesus macaques. The HIV SAM vaccine induced potent cellular immune responses that were greater in magnitude than those induced by self-amplifying mRNA packaged in a viral replicon particle (VRP) or by a recombinant HIV envelope protein formulated with MF59 adjuvant, anti-envelope binding (including anti-V1V2), and neutralizing antibody responses that exceeded those induced by the VRP vaccine. These studies provide the first evidence in nonhuman primates that HIV vaccination with a relatively low dose (50 µg) of formulated self-amplifying mRNA is safe and immunogenic.
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Affiliation(s)
- Willy M Bogers
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | - Petra Mooij
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Gerrit Koopman
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | - David Davis
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | - Yen Cu
- Novartis Vacccines, Cambridge, Massachusetts
| | | | | | - Brian Burke
- Novartis Vacccines, Cambridge, Massachusetts
| | - Antu Dey
- Novartis Vacccines, Cambridge, Massachusetts
| | - Jonathan L Heeney
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | | | - Georgia D Tomaras
- Duke Human Vaccine Institute Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Celia Labranche
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - David C Montefiori
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Hua-Xin Liao
- Duke Human Vaccine Institute Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Barton Haynes
- Duke Human Vaccine Institute Department of Medicine, Duke University Medical Center, Durham, North Carolina
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36
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Benen TD, Tonks P, Kliche A, Kapzan R, Heeney JL, Wagner R. Development and immunological assessment of VLP-based immunogens exposing the membrane-proximal region of the HIV-1 gp41 protein. J Biomed Sci 2014; 21:79. [PMID: 25160824 PMCID: PMC4256929 DOI: 10.1186/s12929-014-0079-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 08/11/2014] [Indexed: 11/10/2022] Open
Abstract
Background The membrane-proximal external region (MPER) of HIV-1 gp41 is particularly conserved and target for the potent broadly neutralizing monoclonal antibodies (bnMAbs) 2F5, 4E10 and 10E8. Epitope focusing and stabilization present promising strategies to enhance the quality of immune responses to specific epitopes. Results The aim of this work was to design and evaluate novel immunogens based on the gp41 MPER with the potential to elicit cross-clade neutralizing antibodies. For that purpose, gp41 was truncated N-terminally in order to dispose immunodominant, non-neutralizing sites and enhance the exposure of conserved regions. To stabilize a trimeric conformation, heterologous GCN4 and HA2 zipper domains were fused based on an in silico “best-fit” model to the protein’s amino terminus. Cell surface exposure of resulting proteins and their selective binding to bnMAbs 2F5 and 4E10 could be shown by cytometric analyses. Incorporation into VLPs and preservation of antigenic structures were verified by electron microscopy, and the oligomeric state was successfully stabilized by zipper domains. These gp41 immunogens were evaluated for antigenicity in an immunization study in rabbits primed with homologous DNA expression plasmids and boosted with virus-like particle (VLP) proteins. Low titers of anti-MPER antibodies were measured by IgG ELISA, and low neutralizing activity could be detected against a clade C and B viral isolate in sera. Conclusions Thus, although neutralizing titers were very moderate, induction of cross-clade neutralizing antibodies seems possible following immunization with MPER-focusing immunogens. However, further refinement of MPER presentation and immunogenicity is clearly needed to induce substantial neutralization responses to these epitopes. Electronic supplementary material The online version of this article (doi:10.1186/s12929-014-0079-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Ralf Wagner
- Molecular Microbiology and Gene Therapy Unit, Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany.
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37
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Verstrepen BE, Verschoor EJ, Fagrouch ZC, Mooij P, de Groot NG, Bontrop RE, Bogers WM, Heeney JL, Koopman G. Strong vaccine-induced CD8 T-cell responses have cytolytic function in a chimpanzee clearing HCV infection. PLoS One 2014; 9:e95103. [PMID: 24740375 PMCID: PMC3989318 DOI: 10.1371/journal.pone.0095103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/22/2014] [Indexed: 12/16/2022] Open
Abstract
A single correlate of effective vaccine protection against chronic HCV infection has yet to be defined. In this study, we analyzed T-cell responses in four chimpanzees, immunized with core-E1-E2-NS3 and subsequently infected with HCV1b. Viral clearance was observed in one animal, while the other three became chronically infected. In the animal that cleared infection, NS3-specific CD8 T-cell responses were observed to be more potent in terms of frequency and polyfunctionality of cytokine producing cells. Unique to this animal was the presence of killing-competent CD8 T-cells, specific for NS31258–1272, being presented by the chimpanzee MHC class I molecule Patr-A*03∶01, and a high affinity recognition of this epitope. In the animals that became chronically infected, T-cells were able to produce cytokines against the same peptide but no cytolysis could be detected. In conclusion, in the animal that was able to clear HCV infection not only cytokine production was observed but also cytolytic potential against specific MHC class I/peptide-combinations.
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Affiliation(s)
- Babs E. Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ernst J. Verschoor
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Zahra C. Fagrouch
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G. de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E. Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Willy M. Bogers
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
- * E-mail:
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38
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Abstract
Subclinical infection of murine norovirus (MNV) was detected in a mixed breeding group of WT and Stat1(-/-) mice with no outward evidence of morbidity or mortality. Investigations revealed the presence of an attenuated MNV variant that did not cause cytopathic effects in RAW264.7 cells or death in Stat1(-/-) mice. Histopathological analysis of tissues from WT, heterozygous and Stat1(-/-) mice revealed a surprising spectrum of lesions. An infectious molecular clone was derived directly from faeces (MNV-O7) and the sequence analysis confirmed it was a member of norovirus genogroup V. Experimental infection with MNV-O7 induced a subclinical infection with no weight loss in Stat1(-/-) or WT mice, and recapitulated the clinical and pathological picture of the naturally infected colony. Unexpectedly, by day 54 post-infection, 50 % of Stat1(-/-) mice had cleared MNV-O7. In contrast, all WT mice remained infected persistently. Most significantly, this was associated with liver lesions in all the subclinically infected WT mice. These data confirmed that long-term persistence in WT mice is established with specific variants of MNV and that despite a subclinical presentation, active foci of acute inflammation persist within the liver. The data also showed that STAT1-dependent responses are not required to protect mice from lethal infection with all strains of MNV.
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Affiliation(s)
- Amita Shortland
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK
| | - James Chettle
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK
| | - Joy Archer
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK
| | - Kathryn Wood
- Nuffield Department of Surgical Sciences, University of Oxford, Level 6, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Dalan Bailey
- Institute of Biomedical Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge CB2 2QQ, UK
| | - Barbara A Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK
| | - Jonathan L Heeney
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK
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Greenwood EJD, Schmidt F, Liégeois F, Kondova I, Herbert A, Ngoubangoye B, Rouet F, Heeney JL. Loss of memory CD4+ T-cells in semi-wild mandrills (Mandrillus sphinx) naturally infected with species-specific simian immunodeficiency virus SIVmnd-1. J Gen Virol 2013; 95:201-212. [PMID: 24214347 PMCID: PMC3917062 DOI: 10.1099/vir.0.059808-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Simian immunodeficiency virus (SIV) infection is found in a number of African primate species and is thought to be generally non-pathogenic. However, studies of wild primates are limited to two species, with SIV infection appearing to have a considerably different outcome in each. Further examination of SIV-infected primates exposed to their natural environment is therefore warranted. We performed a large cross-sectional study of a cohort of semi-wild mandrills with naturally occurring SIV infection, including 39 SIV-negative and 33 species-specific SIVmnd-1-infected animals. This study was distinguished from previous reports by considerably greater sample size, examination of exclusively naturally infected animals in semi-wild conditions and consideration of simian T-lymphotropic virus (STLV) status in addition to SIVmnd-1 infection. We found that SIVmnd-1 infection was associated with a significant and progressive loss of memory CD4+ T-cells. Limited but significant increases in markers of immune activation in the T-cell populations, significant increases in plasma neopterin and changes to B-cell subsets were also observed in SIV-infected animals. However, no increase in plasma soluble CD14 was observed. Histological examination of peripheral lymph nodes suggested that SIVmnd-1 infection was not associated with a significant disruption of the lymph node architecture. Whilst this species has evolved numerous strategies to resist the development of AIDS, significant effects of SIV infection could be observed when examined in a natural environment. STLVmnd-1 infection also had significant effects on some markers relevant to understanding SIV infection and thus should be considered in studies of SIV infection of African primates where present.
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Affiliation(s)
- Edward J D Greenwood
- University of Cambridge, Department of Veterinary Medicine, Cambridge CB3 0ES, UK
| | - Fabian Schmidt
- University of Cambridge, Department of Veterinary Medicine, Cambridge CB3 0ES, UK
| | - Florian Liégeois
- Institut de Recherches pour le Développement, UMI 233, Montpellier, BP64501, France.,Centre International de Recherches Médicales de Franceville, Laboratoire de Rétrovirologie, Franceville, BP769, Gabon
| | - Ivanela Kondova
- Biomedical Primate Research Centre, Division of Pathology and Microbiology, Rijswijk 2288 GJ, The Netherlands
| | - Anaïs Herbert
- Centre International de Recherches Médicales de Franceville, Centre de Primatologie, Franceville, BP769, Gabon
| | - Barthelemy Ngoubangoye
- Centre International de Recherches Médicales de Franceville, Centre de Primatologie, Franceville, BP769, Gabon
| | - François Rouet
- Institut Pasteur du Cambodge, Unité VIH/Hépatites, 5 Boulevard Monivong, BP 983 Phnom-Penh, Cambodia.,Centre International de Recherches Médicales de Franceville, Laboratoire de Rétrovirologie, Franceville, BP769, Gabon
| | - Jonathan L Heeney
- University of Cambridge, Department of Veterinary Medicine, Cambridge CB3 0ES, UK
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Davis D, Koornstra W, Fagrouch Z, Verschoor EJ, Heeney JL, Bogers WMJM. In vitro neutralization of low dose inocula at physiological concentrations of a monoclonal antibody which protects macaques against SHIV challenge. PLoS One 2013; 8:e72702. [PMID: 23977339 PMCID: PMC3745472 DOI: 10.1371/journal.pone.0072702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Passive transfer of antibodies can be protective in the simian human immunodeficiency virus (SHIV)--rhesus macaque challenge model. The human monoclonal antibody IgG1 b12 neutralizes human immunodeficiency type 1 (HIV-1) in vitro and protects against challenge by SHIV. Our hypothesis is that neutralizing antibodies can only completely inactivate a relatively small number of infectious virus. METHODS AND FINDINGS We have used GHOST cell assays to quantify individual infectious events with HIV-1SF162 and its SHIV derivatives: the relatively neutralization sensitive SHIV(SF162P4) isolate and the more resistant SHIV(SF162P3). A plot of the number of fluorescent GHOST cells with increasing HIV-1SF162 dose is not linear. It is likely that with high-dose inocula, infection with multiple virus produces additive fluorescence in individual cells. In studies of the neutralization kinetics of IgG1 b12 against these isolates, events during the absorption phase of the assay, as well as the incubation phase, determine the level of neutralization. It is possible that complete inactivation of a virus is limited to the time it is exposed on the cell surface. Assays can be modified so that neutralization of these very low doses of virus can be quantified. A higher concentration of antibody is required to neutralize the same dose of resistant SHIV(SF162P3) than the sensitive SHIV(SF162P4). In the absence of selection during passage, the density of the CCR5 co-receptor on the GHOST cell surface is reduced. Changes in the CD4 : CCR5 density ratio influence neutralization. CONCLUSIONS Low concentrations of IgG1 b12 completely inactivate small doses of the neutralization resistant SHIV(SF162P3). Assays need to be modified to quantify this effect. Results from modified assays may predict protection following repeated low-dose shiv challenges in rhesus macaques. It should be possible to induce this level of antibody by vaccination so that modified assays could predict the outcome of human trials.
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Affiliation(s)
- David Davis
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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41
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Baker KS, Leggett RM, Bexfield NH, Alston M, Daly G, Todd S, Tachedjian M, Holmes CEG, Crameri S, Wang LF, Heeney JL, Suu-Ire R, Kellam P, Cunningham AA, Wood JLN, Caccamo M, Murcia PR. Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. Virology 2013; 441:95-106. [PMID: 23562481 PMCID: PMC3667569 DOI: 10.1016/j.virol.2013.03.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [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: 01/19/2013] [Revised: 02/21/2013] [Accepted: 03/11/2013] [Indexed: 12/12/2022]
Abstract
Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.
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Affiliation(s)
- Kate S Baker
- University of Cambridge, Department of Veterinary Medicine, Madingley Rd, Cambridge, Cambridgeshire, CB3 0ES, United Kingdom.
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42
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Bogers WM, Oostermeijer H, Mooij P, Koopman G, Verschoor E, Davis D, Heeney JL, Cu Y, Banerjee K, Burke B, Dey A, Geall A, Barnett SW. Macaques primed with self-amplifying RNA vaccines expressing HIV-1 envelope and boosted with recombinant protein show potent T- and B-cell responses. Retrovirology 2012. [PMCID: PMC3441294 DOI: 10.1186/1742-4690-9-s2-p24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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43
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Bexfield NH, Watson PJ, Aguirre-Hernandez J, Sargan DR, Tiley L, Heeney JL, Kennedy LJ. DLA class II alleles and haplotypes are associated with risk for and protection from chronic hepatitis in the English Springer spaniel. PLoS One 2012; 7:e42584. [PMID: 22870335 PMCID: PMC3411618 DOI: 10.1371/journal.pone.0042584] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 07/09/2012] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis (CH) is common in dogs in the United Kingdom. An increased prevalence of the disease is seen in the English Springer spaniel (ESS), and this breed suffer from a severe form with young to middle aged female dogs being predisposed. The disease shares histological features with those of human viral hepatitis, although the specific aetiological agent has not yet been identified. The aim of the current study was to investigate whether dog leucocyte antigen (DLA) class II alleles and haplotypes are associated with susceptibility/resistance to CH in the ESS. Sequence-based genotyping of the polymorphic exon 2 from DLA-DRB1, -DQA1 and -DQB1 class II loci were performed in 66 ESSs with CH and 84 healthy controls. There was a significant difference in the distribution of the protective alleles DRB1*00501 (3.0% vs. 12.0%, odds ratio [OR] = 0.23, 95% confidence interval [CI] = 0.06–0.74) and DQB1*00501 (3.8% vs. 12.0%, OR = 0.29, 95% CI = 0.09–0.85) between cases and controls. The haplotype DLA-DRB1*00501/DQA1*00301/DQB1*00501 was present in 11.9% of controls and 3.0% of cases and was significantly associated with protection against disease development (OR = 0.26, 95% CI = 0.08–0.80). There was a significant difference in the distribution of the risk alleles DRB1*00601 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) and DQB1*00701 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) between cases and controls. A risk haplotype (DLA-DRB1*00601/DQA1*005011/DQB1*00701) was present in 14.4% of cases and 6.5% of controls and conferred an elevated risk of developing CH with an OR of 3.13 (95% CI = 1.20–8.26). These results demonstrate that DLA class II is significantly associated with risk and protection from developing CH in ESSs.
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Affiliation(s)
- Nicholas H Bexfield
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
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Lai RPJ, Seaman MS, Tonks P, Wegmann F, Seilly DJ, Frost SDW, LaBranche CC, Montefiori DC, Dey AK, Srivastava IK, Sattentau Q, Barnett SW, Heeney JL. Mixed adjuvant formulations reveal a new combination that elicit antibody response comparable to Freund's adjuvants. PLoS One 2012; 7:e35083. [PMID: 22509385 PMCID: PMC3324409 DOI: 10.1371/journal.pone.0035083] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 12/02/2011] [Accepted: 03/08/2012] [Indexed: 12/04/2022] Open
Abstract
Adjuvant formulations capable of inducing high titer and high affinity antibody responses would provide a major advance in the development of vaccines to viral infections such as HIV-1. Although oil-in-water emulsions, such as Freund's adjuvant (FCA/FIA), are known to be potent, their toxicity and reactogenicity make them unacceptable for human use. Here, we explored different adjuvants and compared their ability to elicit antibody responses to FCA/FIA. Recombinant soluble trimeric HIV-1 gp140 antigen was formulated in different adjuvants, including FCA/FIA, Carbopol-971P, Carbopol-974P and the licensed adjuvant MF59, or combinations of MF59 and Carbopol. The antigen-adjuvant formulation was administered in a prime-boost regimen into rabbits, and elicitation of antigen binding and neutralizing antibodies (nAbs) was evaluated. When used individually, only FCA/FIA elicited significantly higher titer of nAbs than the control group (gp140 in PBS (p<0.05)). Sequential prime-boost immunizations with different adjuvants did not offer improvements over the use of FCA/FIA or MF59. Remarkably however, the concurrent use of the combination of Carbopol-971P and MF59 induced potent adjuvant activity with significantly higher titer nAbs than FCA/FIA (p<0.05). This combination was not associated with any obvious local or systemic adverse effects. Antibody competition indicated that the majority of the neutralizing activities were directed to the CD4 binding site (CD4bs). Increased antibody titers to the gp41 membrane proximal external region (MPER) and gp120 V3 were detected when the more potent adjuvants were used. These data reveal that the combination of Carbopol-971P and MF59 is unusually potent for eliciting nAbs to a variety of HIV-1 nAb epitopes.
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Affiliation(s)
- Rachel P. J. Lai
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Paul Tonks
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Frank Wegmann
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - David J. Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Simon D. W. Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Antu K. Dey
- Novartis Vaccines and Diagnostics Inc., Massachusetts, United States of America
| | | | - Quentin Sattentau
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Susan W. Barnett
- Novartis Vaccines and Diagnostics Inc., Massachusetts, United States of America
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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45
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Koopman G, Beenhakker N, Hofman S, Walther-Jallow L, Mäkitalo B, Mooij P, Anderson J, Verschoor E, Bogers WM, Heeney JL, Spetz AL. Immunization with apoptotic pseudovirus transduced cells induces both cellular and humoral responses: A proof of concept study in macaques. Vaccine 2012; 30:2523-34. [DOI: 10.1016/j.vaccine.2012.01.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/11/2012] [Accepted: 01/29/2012] [Indexed: 11/29/2022]
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46
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Dey AK, Burke B, Sun Y, Hartog K, Heeney JL, Montefiori D, Srivastava IK, Barnett SW. Use of a polyanionic carbomer, Carbopol971P, in combination with MF59, improves antibody responses to HIV-1 envelope glycoprotein. Vaccine 2012; 30:2749-59. [PMID: 22366638 DOI: 10.1016/j.vaccine.2012.02.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 02/09/2012] [Accepted: 02/11/2012] [Indexed: 12/20/2022]
Abstract
Identification of optimal antigen(s) and adjuvant combination(s) to elicit potent, protective, and long-lasting immunity has been a major challenge for the development of effective vaccines against chronic viral pathogens, such as HIV-1, for which there are not yet any licensed vaccines. Here we describe the use of a novel adjuvant approach employing Carbopol 971P(®) NF (hereafter referred to as Carbopol971P), a cross-linked polyanionic carbomer, in combination with the Novartis proprietary oil-in-water adjuvant, MF59, as a potentially safe and effective adjuvant to augment humoral immune responses to the HIV-1 envelope glycoprotein (Env). Intramuscular immunization of small animals with recombinant Env glycoprotein (gp140) formulated in Carbopol971P plus MF59 gave significantly higher titers of binding and virus neutralizing antibodies as compared to immunization using gp140 with either MF59 or Carbopol971P alone. In addition, the antibodies generated were of higher avidity. Importantly, the use of Carbopol971P plus MF59 did not cause any serious adverse reactions or any obvious health problems in animals upon intramuscular administration. Hence, the Carbopol971P plus MF59 adjuvant formulation may provide a benefit for future vaccine applications.
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Affiliation(s)
- Antu K Dey
- Novartis Vaccines & Diagnostics, 45 Sidney Street, Cambridge, MA 02139, USA.
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47
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Davis D, Koornstra W, Mortier D, Fagrouch Z, Verschoor EJ, Heeney JL, Bogers WMJM. Protection in macaques immunized with HIV-1 candidate vaccines can be predicted using the kinetics of their neutralizing antibodies. PLoS One 2011; 6:e28974. [PMID: 22216149 PMCID: PMC3247218 DOI: 10.1371/journal.pone.0028974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 10/20/2011] [Accepted: 11/17/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A vaccine is needed to control the spread of human immunodeficiency virus type 1 (HIV-1). An in vitro assay that can predict the protection induced by a vaccine would facilitate the development of such a vaccine. A potential candidate would be an assay to quantify neutralization of HIV-1. METHODS AND FINDINGS We have used sera from rhesus macaques that have been immunized with HIV candidate vaccines and subsequently challenged with simian human immunodeficiency virus (SHIV). We compared neutralization assays with different formats. In experiments with the standardized and validated TZMbl assay, neutralizing antibody titers against homologous SHIV(SF162P4) pseudovirus gave a variable correlation with reductions in plasma viremia levels. The target cells used in the assays are not just passive indicators of virus infection but are actively involved in the neutralization process. When replicating virus was used with GHOST cell assays, events during the absorption phase, as well as the incubation phase, determine the level of neutralization. Sera that are associated with protection have properties that are closest to the traditional concept of neutralization: the concentration of antibody present during the absorption phase has no effect on the inactivation rate. In GHOST assays, events during the absorption phase may inactivate a fixed number, rather than a proportion, of virus so that while complete neutralization can be obtained, it can only be found at low doses particularly with isolates that are relatively resistant to neutralization. CONCLUSIONS Two scenarios have the potential to predict protection by neutralizing antibodies at concentrations that can be induced by vaccination: antibodies that have properties close to the traditional concept of neutralization may protect against a range of challenge doses of neutralization sensitive HIV isolates; a window of opportunity also exists for protection against isolates that are more resistant to neutralization but only at low challenge doses.
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Affiliation(s)
- David Davis
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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48
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Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L, Alexander GJM, Bernal W, Heeney JL. A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS One 2011; 6:e28879. [PMID: 22216131 PMCID: PMC3244418 DOI: 10.1371/journal.pone.0028879] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [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: 08/26/2011] [Accepted: 11/16/2011] [Indexed: 12/22/2022] Open
Abstract
Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples.
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Affiliation(s)
- Gordon M. Daly
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Nick Bexfield
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Judith Heaney
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Sam Stubbs
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Antonia P. Mayer
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Anne Palser
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nizar Drou
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Mario Caccamo
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Laurence Tiley
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Graeme J. M. Alexander
- Department of Hepatology, Addenbrookes Hospital, Cambridge University Hospitals National Health Services Foundation Trust, Cambridge, United Kingdom
| | - William Bernal
- Institute of Liver Studies, King's College London School of Medicine, King's College Hospital, Denmark Hill, London, United Kingdom
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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49
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Verstrepen BE, Depla E, Rollier CS, Mares G, Drexhage JAR, Priem S, Verschoor EJ, Koopman G, Granier C, Dreux M, Cosset FL, Maertens G, Heeney JL. Clearance of genotype 1b hepatitis C virus in chimpanzees in the presence of vaccine-induced E1-neutralizing antibodies. J Infect Dis 2011; 204:837-44. [PMID: 21849281 PMCID: PMC3156919 DOI: 10.1093/infdis/jir423] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence indicates that neutralizing antibodies play an important role in protection from chronic hepatitis C virus (HCV) infection. Efforts to elicit such responses by immunization with intact heterodimeric E1E2 envelope proteins have met with limited success. To determine whether antigenic sites, which are not exposed by the combined E1E2 heterodimer structure, are capable of eliciting neutralizing antibody responses, we expressed and purified each as separate recombinant proteins E1 and E2, from which the immunodominant hypervariable region (HVR-1) was deleted. Immunization of chimpanzees with either E1 or E2 alone induced antigen-specific T-helper cytokines of similar magnitude. Unexpectedly, the capacity to neutralize HCV was observed in E1 but not in animals immunized with E2 devoid of HVR-1. Furthermore, in vivo only E1-vaccinated animals exposed to the heterologous HCV-1b inoculum cleared HCV infection.
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Affiliation(s)
- Babs E Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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50
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Rosenwirth B, Kondova I, Niphuis H, Greenwood EJD, Schmidt F, Verschoor EJ, Wittmann S, Heeney JL, Bogers WMJM, Fickenscher H, Koopman G. Herpesvirus saimiri infection of rhesus macaques: a model for acute rhadinovirus-induced t-cell transformation and oncogenesis. J Med Virol 2011; 83:1938-50. [PMID: 21915869 DOI: 10.1002/jmv.22197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Herpesvirus saimiri (HVS) causes acute lymphoma and leukemia upon experimental infection of various monkey species. HVS strain C488 is also capable of transforming human T-lymphocytes to stable growth in culture. The most susceptible species for oncogenesis are New World primates, in particular the cottontop tamarin (Saguinus oedipus). However, Old World monkeys such as macaques are the most used animal model for the close-to-human situation. The limited data on HVS infection in Old World monkeys prompted us to investigate susceptibility to infection and disease induction by HVS in macaques. After having established that rhesus macaques can be infected productively, and that rhesus T-cells can be transformed in vivo by HVS, we observed induction of lymphoma in all inoculated animals. Pre-existing humoral immunity in part of the rhesus colony capable of blocking HVS infection could be overcome by preselecting rhesus macaques for lack of this immunity of unknown origin. HVS infection of rhesus macaques as compared to that of New World monkeys has the advantages that disease progression is more prolonged, and larger blood volumes can be collected, which allows more extended analyses. Also, rhesus monkeys are the best immunologically and immunogenetically characterized primate species next to humans. This model could be useful for the evaluation of candidate tumor vaccines and to test novel approaches for cancer immunotherapy. In addition, HVS infection of macaques could eventually be useful as a surrogate model to address certain questions in rhadinovirus-induced human cancer such as effusion lymphoma or Kaposi's sarcoma.
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