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Serwanga J, Ankunda V, Sembera J, Kato L, Oluka GK, Baine C, Odoch G, Kayiwa J, Auma BO, Jjuuko M, Nsereko C, Cotten M, Onyachi N, Muwanga M, Lutalo T, Fox J, Musenero M, Kaleebu P. Rapid, early, and potent Spike-directed IgG, IgM, and IgA distinguish asymptomatic from mildly symptomatic COVID-19 in Uganda, with IgG persisting for 28 months. Front Immunol 2023; 14:1152522. [PMID: 37006272 PMCID: PMC10060567 DOI: 10.3389/fimmu.2023.1152522] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2023] [Indexed: 04/04/2023] Open
Abstract
Introduction Understanding how spike (S)-, nucleoprotein (N)-, and RBD-directed antibody responses evolved in mild and asymptomatic COVID-19 in Africa and their interactions with SARS-CoV-2 might inform development of targeted treatments and vaccines. Methods Here, we used a validated indirect in-house ELISA to characterise development and persistence of S- and N-directed IgG, IgM, and IgA antibody responses for 2430 SARS-CoV-2 rt-PCR-diagnosed Ugandan specimens from 320 mild and asymptomatic COVID-19 cases, 50 uninfected contacts, and 54 uninfected non-contacts collected weekly for one month, then monthly for 28 months. Results During acute infection, asymptomatic patients mounted a faster and more robust spike-directed IgG, IgM, and IgA response than those with mild symptoms (Wilcoxon rank test, p-values 0.046, 0.053, and 0.057); this was more pronounced in males than females. Spike IgG antibodies peaked between 25 and 37 days (86.46; IQR 29.47-242.56 BAU/ml), were significantly higher and more durable than N- and RBD IgG antibodies and lasted for 28 months. Anti-spike seroconversion rates consistently exceeded RBD and nucleoprotein rates. Spike- and RBD-directed IgG antibodies were positively correlated until 14 months (Spearman's rank correlation test, p-values 0.0001 to 0.05), although RBD diminished faster. Significant anti-spike immunity persisted without RBD. 64% and 59% of PCR-negative, non-infected non-contacts and suspects, exhibited baseline SARS-CoV-2 N-IgM serological cross-reactivity, suggesting undetected exposure or abortive infection. N-IgG levels waned after 787 days, while N-IgM levels remained undetectable throughout. Discussion Lower N-IgG seroconversion rates and the absence of N-IgM indicate that these markers substantially underestimate the prior exposure rates. Our findings provide insights into the development of S-directed antibody responses in mild and asymptomatic infections, with varying degrees of symptoms eliciting distinct immune responses, suggesting distinct pathogenic pathways. These longer-lasting data inform vaccine design, boosting strategies, and surveillance efforts in this and comparable settings.
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Affiliation(s)
- Jennifer Serwanga
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Violet Ankunda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jackson Sembera
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Gerald Kevin Oluka
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Geoffrey Odoch
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - John Kayiwa
- Department of Virology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Betty Oliver Auma
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Mark Jjuuko
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Christopher Nsereko
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Matthew Cotten
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nathan Onyachi
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Moses Muwanga
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Tom Lutalo
- Department of Epidemiology and Data Management, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julie Fox
- Guy’s and St Thomas’ National Health Services Foundation Trust, King’s College London, London, United Kingdom
| | - Monica Musenero
- Science, Technology, and Innovation Secretariat, Office of the President, Government of Uganda, Kampala, Uganda
| | - Pontiano Kaleebu
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
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202
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Takano T, Sato T, Kotaki R, Moriyama S, Fukushi S, Shinoda M, Kabasawa K, Shimada N, Kousaka M, Adachi Y, Onodera T, Terahara K, Isogawa M, Matsumura T, Shinkai M, Takahashi Y. Heterologous SARS-CoV-2 spike protein booster elicits durable and broad antibody responses against the receptor-binding domain. Nat Commun 2023; 14:1451. [PMID: 36922492 PMCID: PMC10016167 DOI: 10.1038/s41467-023-37128-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The immunogenicity of mRNA vaccines has not been well studied when compared to different vaccine modalities in the context of additional boosters. Here we show that longitudinal analysis reveals more sustained SARS-CoV-2 spike receptor-binding domain (RBD)-binding IgG titers with the breadth to antigenically distinct variants by the S-268019-b spike protein booster compared to the BNT162b2 mRNA homologous booster. The durability and breadth of RBD-angiotensin-converting enzyme 2 (ACE2) binding inhibitory antibodies are pronounced in the group without systemic adverse events (AEs) after the S-268019-b booster, leading to the elevated neutralizing activities against Omicron BA.1 and BA.5 variants in the stratified group. In contrast, BNT162b2 homologous booster elicited antibodies to spike N-terminal domain in proportion to the AE scores. High-dimensional immune profiling identifies early CD16+ natural killer cell dynamics with CCR3 upregulation, as one of the correlates for the distinct anti-RBD antibody responses by the S-268019-b booster. Our results illustrate the combinational effects of heterologous booster on the immune dynamics and the durability and breadth of recalled anti-RBD antibody responses against emerging virus variants.
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Affiliation(s)
- Tomohiro Takano
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Takashi Sato
- Tokyo Shinagawa Hospital, Tokyo, 140-8522, Japan
| | - Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Shuetsu Fukushi
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | - Mio Kousaka
- Tokyo Shinagawa Hospital, Tokyo, 140-8522, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kazutaka Terahara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Masanori Isogawa
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | | | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
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203
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Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports 2023; 18:636-653. [PMID: 36827975 PMCID: PMC9948283 DOI: 10.1016/j.stemcr.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.
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Affiliation(s)
- Lisiena Hysenaj
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samantha Little
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Melia Magnen
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kriti Bahl
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Oghenekevwe M Gbenedio
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Morgan Prinz
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Lauren Rodriguez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Leonard C Lupin-Jimenez
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Luke R Bonser
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nina K Serwas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Taha Y Taha
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Renuka Kumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jack Z Li
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Vivianne W Ding
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bharath Sreekumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Simoneau
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany
| | - Michael G Tomlinson
- School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Khajida Khan
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa
| | - Mark R Looney
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Jablons
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Matthay
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Krummel
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Johannes R Kratz
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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204
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Behbahanipour M, Benoit R, Navarro S, Ventura S. OligoBinders: Bioengineered Soluble Amyloid-like Nanoparticles to Bind and Neutralize SARS-CoV-2. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11444-11457. [PMID: 36890692 PMCID: PMC9969896 DOI: 10.1021/acsami.2c18305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become a primary health concern. Molecules that prevent viral entry into host cells by interfering with the interaction between SARS-CoV-2 spike (S) protein and the human angiotensin-converting enzyme 2 receptor (ACE2r) opened a promising avenue for virus neutralization. Here, we aimed to create a novel kind of nanoparticle that can neutralize SARS-CoV-2. To this purpose, we exploited a modular self-assembly strategy to engineer OligoBinders, soluble oligomeric nanoparticles decorated with two miniproteins previously described to bind to the S protein receptor binding domain (RBD) with high affinity. The multivalent nanostructures compete with the RBD-ACE2r interaction and neutralize SARS-CoV-2 virus-like particles (SC2-VLPs) with IC50 values in the pM range, preventing SC2-VLPs fusion with the membrane of ACE2r-expressing cells. Moreover, OligoBinders are biocompatible and significantly stable in plasma. Overall, we describe a novel protein-based nanotechnology that might find application in SARS-CoV-2 therapeutics and diagnostics.
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Affiliation(s)
- Molood Behbahanipour
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Roger Benoit
- Laboratory
of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Susanna Navarro
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Salvador Ventura
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, 08193 Barcelona, Spain
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205
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Rabaan AA, Al-Ahmed SH, Albayat H, Alwarthan S, Alhajri M, Najim MA, AlShehail BM, Al-Adsani W, Alghadeer A, Abduljabbar WA, Alotaibi N, Alsalman J, Gorab AH, Almaghrabi RS, Zaidan AA, Aldossary S, Alissa M, Alburaiky LM, Alsalim FM, Thakur N, Verma G, Dhawan M. Variants of SARS-CoV-2: Influences on the Vaccines' Effectiveness and Possible Strategies to Overcome Their Consequences. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:507. [PMID: 36984508 PMCID: PMC10051174 DOI: 10.3390/medicina59030507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
The immune response elicited by the current COVID-19 vaccinations declines with time, especially among the immunocompromised population. Furthermore, the emergence of novel SARS-CoV-2 variants, particularly the Omicron variant, has raised serious concerns about the efficacy of currently available vaccines in protecting the most vulnerable people. Several studies have reported that vaccinated people get breakthrough infections amid COVID-19 cases. So far, five variants of concern (VOCs) have been reported, resulting in successive waves of infection. These variants have shown a variable amount of resistance towards the neutralising antibodies (nAbs) elicited either through natural infection or the vaccination. The spike (S) protein, membrane (M) protein, and envelope (E) protein on the viral surface envelope and the N-nucleocapsid protein in the core of the ribonucleoprotein are the major structural vaccine target proteins against COVID-19. Among these targets, S Protein has been extensively exploited to generate effective vaccines against COVID-19. Hence, amid the emergence of novel variants of SARS-CoV-2, we have discussed their impact on currently available vaccines. We have also discussed the potential roles of S Protein in the development of novel vaccination approaches to contain the negative consequences of the variants' emergence and acquisition of mutations in the S Protein of SARS-CoV-2. Moreover, the implications of SARS-CoV-2's structural proteins were also discussed in terms of their variable potential to elicit an effective amount of immune response.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Shamsah H. Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif 32654, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mustafa A. Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
| | - Bashayer M. AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Wasl Al-Adsani
- Department of Medicine, Infectious Diseases Hospital, Kuwait City 63537, Kuwait
- Department of Infectious Diseases, Hampton Veterans Administration Medical Center, Hampton, VA 23667, USA
| | - Ali Alghadeer
- Department of Anesthesia, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Wesam A. Abduljabbar
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Nouf Alotaibi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Jameela Alsalman
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 435, Bahrain
| | - Ali H. Gorab
- Al Kuzama Primary Health Care Center, Al Khobar Health Network, Eastern Health Cluster, Al Khobar 34446, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ali A. Zaidan
- Gastroenterology Department, King Fahad Armed Forces Hospital, Jeddah 23831, Saudi Arabia
| | - Sahar Aldossary
- Pediatric Infectious Diseases, Women and Children’s Health Institute, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Lamees M. Alburaiky
- Pediatric Department, Safwa General Hospital, Eastern Health Cluster, Safwa 31921, Saudi Arabia
| | - Fatimah Mustafa Alsalim
- Department of Family Medicine, Primary Health Care, Qatif Health Cluster, Qatif 32434, Saudi Arabia
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Geetika Verma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India
- Trafford College, Altrincham, Manchester WA14 5PQ, UK
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206
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Naidoo DB, Chuturgoon AA. The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics. Mol Diagn Ther 2023; 27:193-226. [PMID: 36656511 PMCID: PMC9850341 DOI: 10.1007/s40291-022-00634-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2022] [Indexed: 01/20/2023]
Abstract
The infectious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Globally, there have been millions of infections and fatalities. Unfortunately, the virus has been persistent and a contributing factor is the emergence of several variants. The urgency to combat COVID-19 led to the identification/development of various diagnosis (polymerase chain reaction and antigen tests) and treatment (repurposed drugs, convalescent plasma, antibodies and vaccines) options. These treatments may treat mild symptoms and decrease the risk of life-threatening disease. Although these options have been fairly beneficial, there are some challenges and limitations, such as cost of tests/drugs, specificity, large treatment dosages, intravenous administration, need for trained personal, lengthy production time, high manufacturing costs, and limited availability. Therefore, the development of more efficient COVID-19 diagnostic and therapeutic options are vital. Nanobodies (Nbs) are novel monomeric antigen-binding fragments derived from camelid antibodies. Advantages of Nbs include low immunogenicity, high specificity, stability and affinity. These characteristics allow for rapid Nb generation, inexpensive large-scale production, effective storage, and transportation, which is essential during pandemics. Additionally, the potential aerosolization and inhalation delivery of Nbs allows for targeted treatment delivery as well as patient self-administration. Therefore, Nbs are a viable option to target SARS-CoV-2 and overcome COVID-19. In this review we discuss (1) COVID-19; (2) SARS-CoV-2; (3) the present conventional COVID-19 diagnostics and therapeutics, including their challenges and limitations; (4) advantages of Nbs; and (5) the numerous Nbs generated against SARS-CoV-2 as well as their diagnostic and therapeutic potential.
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Affiliation(s)
- Dhaneshree Bestinee Naidoo
- Discipline of Medical Biochemistry and Chemical Pathology, Faculty of Health Sciences, Howard College, University of Kwa-Zulu Natal, Durban, 4013, South Africa
| | - Anil Amichund Chuturgoon
- Discipline of Medical Biochemistry and Chemical Pathology, Faculty of Health Sciences, Howard College, University of Kwa-Zulu Natal, Durban, 4013, South Africa.
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207
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Chen DY, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature 2023; 615:143-150. [PMID: 36630998 DOI: 10.1038/s41586-023-05697-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
The SARS-CoV-2 Omicron variant is more immune evasive and less virulent than other major viral variants that have so far been recognized1-12. The Omicron spike (S) protein, which has an unusually large number of mutations, is considered to be the main driver of these phenotypes. Here we generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron (BA.1 lineage) in the backbone of an ancestral SARS-CoV-2 isolate, and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escaped vaccine-induced humoral immunity, mainly owing to mutations in the receptor-binding motif; however, unlike naturally occurring Omicron, it efficiently replicated in cell lines and primary-like distal lung cells. Similarly, in K18-hACE2 mice, although virus bearing Omicron S caused less severe disease than the ancestral virus, its virulence was not attenuated to the level of Omicron. Further investigation showed that mutating non-structural protein 6 (nsp6) in addition to the S protein was sufficient to recapitulate the attenuated phenotype of Omicron. This indicates that although the vaccine escape of Omicron is driven by mutations in S, the pathogenicity of Omicron is determined by mutations both in and outside of the S protein.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Adams
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Markus Bosmann
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yachana Kataria
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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208
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Avdonin PP, Rybakova EY, Trufanov SK, Avdonin PV. SARS-CoV-2 Receptors and Their Involvement in Cell Infection. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2023; 17:1-11. [PMID: 37008884 PMCID: PMC10050803 DOI: 10.1134/s1990747822060034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 03/30/2023]
Abstract
The new coronavirus infection (COVID-19) pandemic caused by SARS-CoV-2 has many times surpassed the epidemics caused by SARS-CoV and MERS-CoV. The reason for this was the presence of sites in the protein sequence of SARS-CoV-2 that provide interaction with a broader range of receptor proteins on the host cell surface. In this review, we consider both already known receptors common to SARS-CoV and SARS-CoV-2 and new receptors specific to SARS-CoV-2.
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Affiliation(s)
- P. P. Avdonin
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - E. Yu. Rybakova
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - S. K. Trufanov
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - P. V. Avdonin
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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209
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Rachman A, Iriani A, Sukrisman L, Rajabto W, Mulansari NA, Lubis AM, Cahyanur R, Prasetyawati F, Priantono D, Rumondor BB, Betsy R, Juanputra S. A comparative study of the COVID-19 vaccine efficacy among cancer patients: mRNA versus non-mRNA. PLoS One 2023; 18:e0281907. [PMID: 36857323 PMCID: PMC9977046 DOI: 10.1371/journal.pone.0281907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/03/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Cancer patients have an increased risk of a severe COVID-19 infection with higher mortality rate. This study aimed to analyze the levels of anti-SARS-CoV-2 S-RBD IgG and NAB among cancer patients who were vaccinated with COVID-19 vaccines, either with BNT162b2, mRNA-1273, AZD1222/ChAdOx1nCoV-19, or Coronavac/BBIBP-CorV vaccines. METHOD A cross-sectional study was conducted among subjects with either solid or hematological cancers who had received two doses of either mRNA or non-mRNA vaccines within 6 months. The levels of anti-SARS-CoV-2 S-RBD IgG and NAb were analyzed using the Mindray Immunoassay Analyzer CL-900i. Statistical analysis was conducted using mean comparison and regression analysis. RESULT The mRNA-1273 vaccine had the highest median levels of S-RBD IgG and NAb, followed by BNT162b, ChAdOx1nCoV-19, and BBIBP-CorV/Coronavac. The levels of S-RBD IgG and NAb in subjects vaccinated with mRNA vaccines were significantly higher than those of non-mRNA vaccines when grouped based on their characteristics, including age, type of cancer, chemotherapy regimen, and comorbidity (p<0.05). Furthermore, the S-RBD IgG and NAb levels between the subjects vaccinated with non-mRNA vaccines and the subjects vaccinated with mRNA vaccines were significantly different (p<0.05). However, there was no significant difference between the same types of vaccines. This study demonstrated a very strong correlation between the level of S-RBD IgG and the level of NAb (R = 0.962; p<0.001). The level of anti-SARS-CoV-2 S-RBD IgG was consistently higher compared to the level of NAb. CONCLUSIONS Generally, mRNA vaccines produced significantly higher anti-SARS-CoV-2 S-RBD IgG and NAb levels than non-mRNA vaccines in cancer subjects.
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Affiliation(s)
- Andhika Rachman
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
- * E-mail:
| | - Anggraini Iriani
- Department of Clinical Pathology, Yarsi University, Jakarta, Indonesia
| | - Lugyanti Sukrisman
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Wulyo Rajabto
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Nadia Ayu Mulansari
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Anna Mira Lubis
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Rahmat Cahyanur
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Findy Prasetyawati
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Dimas Priantono
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Bayu Bijaksana Rumondor
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Rachelle Betsy
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Samuel Juanputra
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
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210
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Guo Y, Su X, Wu K, Yong KT. Numerical Analysis of Three-dimensional Nanodisk Array-based Surface Plasmon Resonance Biosensors for SARS-CoV-2 Detection. PLASMONICS (NORWELL, MASS.) 2023; 18:769-779. [PMID: 36852386 PMCID: PMC9947906 DOI: 10.1007/s11468-023-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
UNLABELLED With continuous mutations of SARS-CoV-2 virus, new highly contagious and fast-spreading variants have emerged, including Delta and Omicron. The popular label-free immunosensor based on surface plasmon resonance (SPR) technique can be used for real-time monitoring of the ligand-analyte or antibody-antigen interactions occurring on the sensor surface. In this work, an SPR-based biosensor combined with a nanodisk array was presented to enhance the sensitivity toward virus detection. The nanodisk arrays were employed to enhance the adsorption of molecules for better detection by increasing the SPR field. Four optimal sensing configurations of silver or gold nanodisks on gold thin films with different aspect ratios were achieved through systematic optimization of all parameters to yield the best sensor performance. The resonance angle can be modulated simply by the aspect ratio of nanodisk array. The sensitivity of the optimized sensors has been improved, and the detection limit is smaller than that of bare gold-based sensor. The multi-jump resonance angle curves at tiny refractive index can clearly distinguish the difference of trace concentrations, which is very important for the accurate detection of trace substances. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11468-023-01802-3.
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Affiliation(s)
- Yan Guo
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Xianglong Su
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Kaihua Wu
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Ken-Tye Yong
- School of Biomedical Engineering, The University of Sydney, Sydney, Australia
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211
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Taylor MK, Williams EP, Xue Y, Jenjaroenpun P, Wongsurawat T, Smith AP, Smith AM, Parvathareddy J, Kong Y, Vogel P, Cao X, Reichard W, Spruill-Harrell B, Samarasinghe AE, Nookaew I, Fitzpatrick EA, Smith MD, Aranha M, Smith JC, Jonsson CB. Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants. Viruses 2023; 15:611. [PMID: 36992320 PMCID: PMC10059853 DOI: 10.3390/v15030611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
The emergence and availability of closely related clinical isolates of SARS-CoV-2 offers a unique opportunity to identify novel nonsynonymous mutations that may impact phenotype. Global sequencing efforts show that SARS-CoV-2 variants have emerged and then been replaced since the beginning of the pandemic, yet we have limited information regarding the breadth of variant-specific host responses. Using primary cell cultures and the K18-hACE2 mouse, we investigated the replication, innate immune response, and pathology of closely related, clinical variants circulating during the first wave of the pandemic. Mathematical modeling of the lung viral replication of four clinical isolates showed a dichotomy between two B.1. isolates with significantly faster and slower infected cell clearance rates, respectively. While isolates induced several common immune host responses to infection, one B.1 isolate was unique in the promotion of eosinophil-associated proteins IL-5 and CCL11. Moreover, its mortality rate was significantly slower. Lung microscopic histopathology suggested further phenotypic divergence among the five isolates showing three distinct sets of phenotypes: (i) consolidation, alveolar hemorrhage, and inflammation, (ii) interstitial inflammation/septal thickening and peribronchiolar/perivascular lymphoid cells, and (iii) consolidation, alveolar involvement, and endothelial hypertrophy/margination. Together these findings show divergence in the phenotypic outcomes of these clinical isolates and reveal the potential importance of nonsynonymous mutations in nsp2 and ORF8.
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Affiliation(s)
- Mariah K. Taylor
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan P. Williams
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Yi Xue
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amanda P. Smith
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Amber M. Smith
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ying Kong
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Peter Vogel
- Veterinary Pathology Core Laboratory, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Briana Spruill-Harrell
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Amali E. Samarasinghe
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Elizabeth A. Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Micholas Dean Smith
- Center for Molecular Biophysics, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Michelle Aranha
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Jeremy C. Smith
- Center for Molecular Biophysics, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Regional Biocontainment Laboratory, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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212
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Du W, Janssens R, Mykytyn AZ, Li W, Drabek D, van Haperen R, Chatziandreou M, Rissmann M, van der Lee J, van Dortmondt M, Martin IS, van Kuppeveld FJM, Hurdiss DL, Haagmans BL, Grosveld F, Bosch BJ. Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants. Front Immunol 2023; 14:1111385. [PMID: 36895554 PMCID: PMC9990171 DOI: 10.3389/fimmu.2023.1111385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Emerging SARS-CoV-2 variants have accrued mutations within the spike protein rendering most therapeutic monoclonal antibodies against COVID-19 ineffective. Hence there is an unmet need for broad-spectrum mAb treatments for COVID-19 that are more resistant to antigenically drifted SARS-CoV-2 variants. Here we describe the design of a biparatopic heavy-chain-only antibody consisting of six antigen binding sites recognizing two distinct epitopes in the spike protein NTD and RBD. The hexavalent antibody showed potent neutralizing activity against SARS-CoV-2 and variants of concern, including the Omicron sub-lineages BA.1, BA.2, BA.4 and BA.5, whereas the parental components had lost Omicron neutralization potency. We demonstrate that the tethered design mitigates the substantial decrease in spike trimer affinity seen for escape mutations for the hexamer components. The hexavalent antibody protected against SARS-CoV-2 infection in a hamster model. This work provides a framework for designing therapeutic antibodies to overcome antibody neutralization escape of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rick Janssens
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Anna Z. Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Marianthi Chatziandreou
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melanie Rissmann
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Itziar Serna Martin
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniel L. Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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213
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da Costa HHM, Orts DJB, Moura AD, Duarte-Neto AN, Cirqueira CS, Réssio RA, Kanamura CT, Miguita K, Ferreira JE, Santos RTM, Adriani PP, Cunha-Junior JP, Astray RM, Catarino RM, Lancelotti M, Prudencio CR. RBD and Spike DNA-Based Immunization in Rabbits Elicited IgG Avidity Maturation and High Neutralizing Antibody Responses against SARS-CoV-2. Viruses 2023; 15:555. [PMID: 36851769 PMCID: PMC9959588 DOI: 10.3390/v15020555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/23/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023] Open
Abstract
Neutralizing antibodies (nAbs) are a critical part of coronavirus disease 2019 (COVID-19) research as they are used to gain insight into the immune response to severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) infections. Among the technologies available for generating nAbs, DNA-based immunization methods are an alternative to conventional protocols. In this pilot study, we investigated whether DNA-based immunization by needle injection in rabbits was a viable approach to produce a functional antibody response. We demonstrated that three doses of DNA plasmid carrying the gene encoding the full-length spike protein (S) or the receptor binding domain (RBD) of SARS-CoV-2 induced a time-dependent increase in IgG antibody avidity maturation. Moreover, the IgG antibodies displayed high cross neutralization by live SARS-CoV-2 and pseudoviruses neutralization assays. Thus, we established a simple, low cost and feasible DNA-based immunization protocol in rabbits that elicited high IgG avidity maturation and nAbs production against SARS-CoV-2, highlighting the importance of DNA-based platforms for developing new immunization strategies against SARS-CoV-2 and future emerging epidemics.
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Affiliation(s)
- Hernan H. M. da Costa
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
- Graduate Program Interunits in Biotechnology, University of São Paulo, São Paulo 05508-000, Brazil
| | - Diego J. B. Orts
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | - Andrew D. Moura
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | | | - Rodrigo A. Réssio
- Pathology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | - Karen Miguita
- Pathology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | | | - Patricia P. Adriani
- Skinzymes Biotechnology Ltd., São Paulo 05441-040, Brazil
- Laboratory of Nanopharmaceuticals and Delivery Systems, Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Jair P. Cunha-Junior
- Laboratory of Immunochemistry and Immunotechnology, Department of Immunology, Federal University of Uberlândia, Uberlândia 38405-317, Brazil
| | - Renato M. Astray
- Multi-Purpose Laboratory, Butantan Institute, São Paulo 05503-900, Brazil
| | | | - Marcelo Lancelotti
- Faculty of Pharmaceutical Sciences, Campinas State University, Campinas 13083-871, Brazil
| | - Carlos R. Prudencio
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
- Graduate Program Interunits in Biotechnology, University of São Paulo, São Paulo 05508-000, Brazil
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214
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Chen J, Li Y, Liu Z. Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101249. [PMID: 36714073 PMCID: PMC9869493 DOI: 10.1016/j.xcrp.2023.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.
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Affiliation(s)
- Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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215
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Leventopoulos M, Michou V, Kyprianidou C, Meristoudis C, Manias NG, Kavvadas HP, Nikolopoulos D, Tsilivakos V, Georgoulias G. Performance characteristics of the boson rapid SARS-cov-2 antigen test card vs RT-PCR: Cross-reactivity and emerging variants. Heliyon 2023; 9:e13642. [PMID: 36789386 PMCID: PMC9911158 DOI: 10.1016/j.heliyon.2023.e13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Background SARS-CoV-2 virus has undergone several mutations on its genome, since the onset of the pandemic. Multiple variants of concern (VOC) have emerged including Alpha, Beta, Gamma, and Delta with the more recent one being the Omicron (B.1.1.529). Specific rapid antigen tests (RADs) have been used for the detection of SARS-CoV-2. However, since the emergence of new VOCs, the performance characteristics of these RADs needs to be re-evaluated. Objectives The main purposes of this clinical study were to determine the diagnostic sensitivity and specificity of the BOSON Rapid Antigen Test compared to the gold standard real time RT-PCR and to determine the ability of the RAD to accurately depict different VOC. Additionally, the cross reactivity to other viruses and pathogen, as well as, the possible interference of non Covid-19 hospitalized patients for various causes, were investigated. Results A total of 623 individuals (symptomatic) were tested. The sensitivity, specificity and accuracy of the BOSON RAD was 95.27%, 100% and 98.45% (n = 448), meeting the WHO recommended standards. Additionally, the Delta (83.33%, Ct < 34) and Omicron (100%, Ct < 26) VOC were determined with high sensitivity. Also, there was no interference from hospitalized, non-Covid 19 patients, and no cross-reactivity was detected. Conclusions The study showed that this RAD could rapidly identify individuals with SARS-CoV-2, including those with the new dominant Omicron VOC, with no cross reactivity from other pathogens.
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Affiliation(s)
- Michail Leventopoulos
- Department of Cellular Biology and Immunology, Locus Medicus S.A., Athens, Greece,Corresponding author. Department of Cellular Biology and Immunology, Locus Medicus S.A., 246 Mesogeion Av., Cholargos, 155 61, Athens, Greece.
| | - Vassiliki Michou
- Department of Molecular Pathology and Genetics, Locus Medicus S.A., Athens, Greece
| | | | - Christos Meristoudis
- Department of Molecular Pathology and Genetics, Locus Medicus S.A., Athens, Greece
| | | | | | | | - Vassilis Tsilivakos
- Department of Cellular Biology and Immunology, Locus Medicus S.A., Athens, Greece
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216
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Ching WY, Adhikari P, Jawad B, Podgornik R. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Biomedicines 2023; 11:517. [PMID: 36831053 PMCID: PMC9953097 DOI: 10.3390/biomedicines11020517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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217
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Ali Z, Cardoza JV, Basak S, Narsaria U, Singh VP, Isaac SP, França TCC, LaPlante SR, George SS. Computational design of candidate multi-epitope vaccine against SARS-CoV-2 targeting structural (S and N) and non-structural (NSP3 and NSP12) proteins. J Biomol Struct Dyn 2023; 41:13348-13367. [PMID: 36744449 DOI: 10.1080/07391102.2023.2173297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 virus has created a global damage and has exposed the vulnerable side of scientific research towards novel diseases. The intensity of the pandemic is huge, with mortality rates of more than 6 million people worldwide in a span of 2 years. Considering the gravity of the situation, scientists all across the world are continuously attempting to create successful therapeutic solutions to combat the virus. Various vaccination strategies are being devised to ensure effective immunization against SARS-CoV-2 infection. SARS-CoV-2 spreads very rapidly, and the infection rate is remarkably high than other respiratory tract viruses. The viral entry and recognition of the host cell is facilitated by S protein of the virus. N protein along with NSP3 is majorly responsible for viral genome assembly and NSP12 performs polymerase activity for RNA synthesis. In this study, we have designed a multi-epitope, chimeric vaccine considering the two structural (S and N protein) and two non-structural proteins (NSP3 and NSP12) of SARS-CoV-2 virus. The aim is to induce immune response by generating antibodies against these proteins to target the viral entry and viral replication in the host cell. In this study, computational tools were used, and the reliability of the vaccine was verified using molecular docking, molecular dynamics simulation and immune simulation studies in silico. These studies demonstrate that the vaccine designed shows steady interaction with Toll like receptors with good stability and will be effective in inducing a strong and specific immune response in the body.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, India
| | | | | | | | - Vijay Pratap Singh
- Department of Physiotherapy, Kasturba Medical College, Mangalore, Manipal academy of higher education, Mangalore, Manipal, India
| | | | - Tanos C C França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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218
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Almeida B, Domingues C, Mascarenhas-Melo F, Silva I, Jarak I, Veiga F, Figueiras A. The Role of Cyclodextrins in COVID-19 Therapy-A Literature Review. Int J Mol Sci 2023; 24:2974. [PMID: 36769299 PMCID: PMC9918006 DOI: 10.3390/ijms24032974] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) emerged in December 2019 and quickly spread, giving rise to a pandemic crisis. Therefore, it triggered tireless efforts to identify the mechanisms of the disease, how to prevent and treat it, and to limit and hamper its global dissemination. Considering the above, the search for prophylactic approaches has led to a revolution in the reglementary pharmaceutical pipeline, with the approval of vaccines against COVID-19 in an unprecedented way. Moreover, a drug repurposing scheme using regulatory-approved antiretroviral agents is also being pursued. However, their physicochemical characteristics or reported adverse events have sometimes limited their use. Hence, nanotechnology has been employed to potentially overcome some of these challenges, particularly cyclodextrins. Cyclodextrins are cyclic oligosaccharides that present hydrophobic cavities suitable for complexing several drugs. This review, besides presenting studies on the inclusion of antiviral drugs in cyclodextrins, aims to summarize some currently available prophylactic and therapeutic schemes against COVID-19, highlighting those that already make use of cyclodextrins for their complexation. In addition, some new therapeutic approaches are underscored, and the potential application of cyclodextrins to increase their promising application against COVID-19 will be addressed. This review describes the instances in which the use of cyclodextrins promotes increased bioavailability, antiviral action, and the solubility of the drugs under analysis. The potential use of cyclodextrins as an active ingredient is also covered. Finally, toxicity and regulatory issues as well as future perspectives regarding the use of cyclodextrins in COVID-19 therapy will be provided.
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Affiliation(s)
- Beatriz Almeida
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Cátia Domingues
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- LAQV-REQUIMTE, Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Filipa Mascarenhas-Melo
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- LAQV-REQUIMTE, Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Inês Silva
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ivana Jarak
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Francisco Veiga
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- LAQV-REQUIMTE, Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana Figueiras
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- LAQV-REQUIMTE, Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
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Capistrano KJ, Richner J, Schwartz J, Mukherjee SK, Shukla D, Naqvi AR. Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166612. [PMID: 36481486 PMCID: PMC9721271 DOI: 10.1016/j.bbadis.2022.166612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
A significant number of SARS-CoV-2-infected individuals naturally overcome viral infection, suggesting the existence of a potent endogenous antiviral mechanism. As an innate defense mechanism, microRNA (miRNA) pathways in mammals have evolved to restrict viruses, besides regulating endogenous mRNAs. In this study, we systematically examined the complete repertoire of human miRNAs for potential binding sites on SARS-CoV-2 Wuhan-Hu-1, Beta, Delta, and Omicron. Human miRNA and viral genome interaction were analyzed using RNAhybrid 2.2 with stringent parameters to identify highly bonafide miRNA targets. Using publicly available data, we filtered for miRNAs expressed in lung epithelial cells/tissue and oral keratinocytes, concentrating on the miRNAs that target SARS-CoV-2 S protein mRNAs. Our results show a significant loss of human miRNA and SARS-CoV-2 interactions in Omicron (130 miRNAs) compared to Wuhan-Hu-1 (271 miRNAs), Beta (279 miRNAs), and Delta (275 miRNAs). In particular, hsa-miR-3150b-3p and hsa-miR-4784 show binding affinity for S protein of Wuhan strain but not Beta, Delta, and Omicron. Loss of miRNA binding sites on N protein was also observed for Omicron. Through Ingenuity Pathway Analysis (IPA), we examined the experimentally validated and highly predicted functional role of these miRNAs. We found that hsa-miR-3150b-3p and hsa-miR-4784 have several experimentally validated or highly predicted target genes in the Toll-like receptor, IL-17, Th1, Th2, interferon, and coronavirus pathogenesis pathways. Focusing on the coronavirus pathogenesis pathway, we found that hsa-miR-3150b-3p and hsa-miR-4784 are highly predicted to target MAPK13. Exploring miRNAs to manipulate viral genome/gene expression can provide a promising strategy with successful outcomes by targeting specific VOCs.
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Affiliation(s)
- Kristelle J Capistrano
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Justin Richner
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Joel Schwartz
- Molecular Pathology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sunil K Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepak Shukla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA; Department of Ophthalmology and Visual Sciences, Ocular Virology Laboratory, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA.
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220
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Das T, Mukhopadhyay C. Identification of possible binding modes of SARS-CoV-2 spike N-terminal domain for ganglioside GM1. Chem Phys Lett 2023; 812:140260. [PMID: 36532818 PMCID: PMC9744490 DOI: 10.1016/j.cplett.2022.140260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Coarse-grained molecular dynamics simulations of the lipid bilayer mixture of POPC and cholesterol were carried out in the presence and absence of ganglioside monosialo 1 (GM1) with N - terminal domain (NTD) of SARS-CoV-2 spike glycoprotein. The interactions of GM1 with two different NTD orientations were compared. NTD orientation I compactly bind GM1 predominantly through the sialic acid and the external galactose moieties providing more restriction to GM1 mobility whereas orientation II is more distributed on the lipid surface and due to the relaxed mobility of GM1 there, presumably, the NTD receptor penetrates more through the membrane.
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Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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221
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Baier CJ, Barrantes FJ. Role of cholesterol-recognition motifs in the infectivity of SARS-CoV-2 variants. Colloids Surf B Biointerfaces 2023; 222:113090. [PMID: 36563415 PMCID: PMC9743692 DOI: 10.1016/j.colsurfb.2022.113090] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
The presence of linear amino acid motifs with the capacity to recognize the neutral lipid cholesterol, known as Cholesterol Recognition/interaction Amino acid Consensus sequence (CRAC), and its inverse or mirror image, CARC, has recently been reported in the primary sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S homotrimeric glycoprotein. These motifs also occur in the two other pathogenic coronaviruses, SARS-CoV, and Middle-East respiratory syndrome CoV (MERS-CoV), most conspicuously in the transmembrane domain, the fusion peptide, the amino-terminal domain, and the receptor binding domain of SARS-CoV-2 S protein. Here we analyze the presence of cholesterol-recognition motifs in these key regions of the spike glycoprotein in the pathogenic CoVs. We disclose the inherent pathophysiological implications of the cholesterol motifs in the virus-host cell interactions and variant infectivity.
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Affiliation(s)
- Carlos Javier Baier
- Laboratorio de Toxicología, Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR), Universidad Nacional del Sur (UNS), Consejo de Investigaciones Científicas y Técnicas (CONICET), Departamento de Biología, Bioquímica y Farmacia (DBByF), San Juan 670, B8000ICN Bahía Blanca, Argentina,Correspondence to: INBIOSUR-CONICET-UNS, DBByF, San Juan 670, B8000ICN Bahía Blanca, Buenos Aires, Argentina
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, BIOMED UCA-CONICET, 1600 Av. A. Moreau de Justo, C1107AAZ Buenos Aires, Argentina,Correspondence to: BIOMED UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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222
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Cao Y, Jian F, Wang J, Yu Y, Song W, Yisimayi A, Wang J, An R, Chen X, Zhang N, Wang Y, Wang P, Zhao L, Sun H, Yu L, Yang S, Niu X, Xiao T, Gu Q, Shao F, Hao X, Xu Y, Jin R, Shen Z, Wang Y, Xie XS. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature 2023; 614:521-529. [PMID: 36535326 PMCID: PMC9931576 DOI: 10.1038/s41586-022-05644-7] [Citation(s) in RCA: 266] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA.5 (ref. 1). Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such sudden convergent evolution and its effect on humoral immunity remain unclear. Here we demonstrate that these convergent mutations can cause evasion of neutralizing antibody drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2-binding capability. BQ.1.1.10 (BQ.1.1 + Y144del), BA.4.6.3, XBB and CH.1.1 are the most antibody-evasive strains tested. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies isolated from individuals who had BA.2 and BA.5 breakthrough infections2,3. Owing to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection reduced the diversity of the neutralizing antibody binding sites and increased proportions of non-neutralizing antibody clones, which, in turn, focused humoral immune pressure and promoted convergent evolution in the RBD. Moreover, we show that the convergent RBD mutations could be accurately inferred by deep mutational scanning profiles4,5, and the evolution trends of BA.2.75 and BA.5 subvariants could be well foreseen through constructed convergent pseudovirus mutants. These results suggest that current herd immunity and BA.5 vaccine boosters may not efficiently prevent the infection of Omicron convergent variants.
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Affiliation(s)
- Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | | | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | - Ran An
- Changping Laboratory, Beijing, P. R. China
| | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Na Zhang
- Changping Laboratory, Beijing, P. R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P. R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | | | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Xiaohua Hao
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China.
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S. Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep 2023; 42:111964. [PMID: 36640338 PMCID: PMC9812370 DOI: 10.1016/j.celrep.2022.111964] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages threatened the efficacy of vaccine-elicited antibodies and acquired increased binding to several mammalian ACE2 receptors. Cryoelectron microscopy (cryo-EM) analysis of the BA.2 spike (S) glycoprotein in complex with mouse ACE2 (mACE2) identifies BA.1- and BA.2-mutated residues Q493R, N501Y, and Y505H as complementing non-conserved residues between human and mouse ACE2, rationalizing the enhanced S protein-mACE2 interaction for Omicron variants. Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 amino-terminal domain (NTD) reveal a dramatic reorganization of the highly antigenic N1 loop into a β-strand, providing an explanation for decreased binding of the BA.2 S protein to antibodies isolated from BA.1-convalescent patients. Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly evolving Omicron variant landscape.
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Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Faezeh Vahdatihassani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Gandeeva Therapeutics, Inc., Burnaby, BC V5C 6N5, Canada.
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224
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Manrique PD, Chakraborty S, Henderson R, Edwards RJ, Mansbach R, Nguyen K, Stalls V, Saunders C, Mansouri K, Acharya P, Korber B, Gnanakaran S. Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design. iScience 2023; 26:105855. [PMID: 36590900 PMCID: PMC9791713 DOI: 10.1016/j.isci.2022.105855] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022] Open
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike's stability. Taken together, the network approach serves as a valuable tool to evaluate communication "hot-spots" in proteins to guide design of stable immunogens.
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Affiliation(s)
- Pedro D. Manrique
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Rachael Mansbach
- Physics Department, Concordia University, Montreal, QC H4B IR6, Canada
| | - Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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225
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Qin R, An C, Chen W. Physical-Chemical Regulation of Membrane Receptors Dynamics in Viral Invasion and Immune Defense. J Mol Biol 2023; 435:167800. [PMID: 36007627 PMCID: PMC9394170 DOI: 10.1016/j.jmb.2022.167800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/13/2022] [Accepted: 08/18/2022] [Indexed: 02/04/2023]
Abstract
Mechanical cues dynamically regulate membrane receptors functions to trigger various physiological and pathological processes from viral invasion to immune defense. These cues mainly include various types of dynamic mechanical forces and the spatial confinement of plasma membrane. However, the molecular mechanisms of how they couple with biochemical cues in regulating membrane receptors functions still remain mysterious. Here, we review recent advances in methodologies of single-molecule biomechanical techniques and in novel biomechanical regulatory mechanisms of critical ligand recognition of viral and immune receptors including SARS-CoV-2 spike protein, T cell receptor (TCR) and other co-stimulatory immune receptors. Furthermore, we provide our perspectives of the general principle of how force-dependent kinetics determine the dynamic functions of membrane receptors and of biomechanical-mechanism-driven SARS-CoV-2 neutralizing antibody design and TCR engineering for T-cell-based therapies.
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Affiliation(s)
- Rui Qin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Chenyi An
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-Machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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226
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Chen DY, Kenney D, Chin CV, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.10.13.512134. [PMID: 36263066 PMCID: PMC9580375 DOI: 10.1101/2022.10.13.512134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The recently identified, globally predominant SARS-CoV-2 Omicron variant (BA.1) is highly transmissible, even in fully vaccinated individuals, and causes attenuated disease compared with other major viral variants recognized to date. The Omicron spike (S) protein, with an unusually large number of mutations, is considered the major driver of these phenotypes. We generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron in the backbone of an ancestral SARS-CoV-2 isolate and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S.
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227
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Venkatakrishnan AJ, Anand P, Lenehan PJ, Ghosh P, Suratekar R, Silvert E, Pawlowski C, Siroha A, Chowdhury DR, O'Horo JC, Yao JD, Pritt BS, Norgan AP, Hurt RT, Badley AD, Halamka J, Soundararajan V. Expanding repertoire of SARS-CoV-2 deletion mutations contributes to evolution of highly transmissible variants. Sci Rep 2023; 13:257. [PMID: 36604461 PMCID: PMC9815892 DOI: 10.1038/s41598-022-26646-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and performed whole-genome viral sequencing from 102 COVID-19 patients, including 43 vaccine breakthrough infections. We identified 92 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a 3-month window. Deletions in the Spike protein N-terminal domain were highly enriched for these 'surge-associated mutations' (Odds Ratio = 14.19, 95% CI 6.15-32.75, p value = 3.41 × 10-10). Based on a longitudinal analysis of mutational prevalence globally, we found an expanding repertoire of Spike protein deletions proximal to an antigenic supersite in the N-terminal domain that may be one of the key contributors to the evolution of highly transmissible variants. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences from 102 patients and identified 107 unique mutations, including 78 substitutions and 29 deletions. In five patients, we identified distinct deletions between residues 85-90, which reside within a linear B cell epitope. Deletions in this region arose contemporaneously on a diverse background of variants across the globe since December 2020. Overall, our findings based on genomic-epidemiology and clinical surveillance suggest that the genomic deletion of dispensable antigenic regions in SARS-CoV-2 may contribute to the evasion of immune responses and the evolution of highly transmissible variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Venky Soundararajan
- nference, Cambridge, MA, 02139, USA.
- nference Labs, Bengaluru, Karnataka, India.
- Anumana, Cambridge, MA, 02139, USA.
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228
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Wang D, Chen Y, Xiang S, Hu H, Zhan Y, Yu Y, Zhang J, Wu P, Liu FY, Kai T, Ding P. Recent advances in immunoassay technologies for the detection of human coronavirus infections. Front Cell Infect Microbiol 2023; 12:1040248. [PMID: 36683684 PMCID: PMC9845787 DOI: 10.3389/fcimb.2022.1040248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the seventh coronavirus (CoV) that has spread in humans and has become a global pandemic since late 2019. Efficient and accurate laboratory diagnostic methods are one of the crucial means to control the development of the current pandemic and to prevent potential future outbreaks. Although real-time reverse transcription-polymerase chain reaction (rRT-PCR) is the preferred laboratory method recommended by the World Health Organization (WHO) for diagnosing and screening SARS-CoV-2 infection, the versatile immunoassays still play an important role for pandemic control. They can be used not only as supplemental tools to identify cases missed by rRT-PCR, but also for first-line screening tests in areas with limited medical resources. Moreover, they are also indispensable tools for retrospective epidemiological surveys and the evaluation of the effectiveness of vaccination. In this review, we summarize the mainstream immunoassay methods for human coronaviruses (HCoVs) and address their benefits, limitations, and applications. Then, technical strategies based on bioinformatics and advanced biosensors were proposed to improve the performance of these methods. Finally, future suggestions and possibilities that can lead to higher sensitivity and specificity are provided for further research.
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Affiliation(s)
- Danqi Wang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Yuejun Chen
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Shan Xiang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Huiting Hu
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Yujuan Zhan
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ying Yu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Jingwen Zhang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Fei Yue Liu
- Department of Economics and Management, ChangSha University, Changsha, Hunan, China
| | - Tianhan Kai
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
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229
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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230
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Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction. Mol Divers 2023; 27:45-57. [PMID: 35243596 PMCID: PMC8893242 DOI: 10.1007/s11030-022-10405-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/08/2022] [Indexed: 02/08/2023]
Abstract
In India, during the second wave of the COVID-19 pandemic, the breakthrough infections were mainly caused by the SARS-COV-2 delta variant (B.1.617.2). It was reported that, among majority of the infections due to the delta variant, only 9.8% percent cases required hospitalization, whereas only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections cases were observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Downregulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant resulted in structural instability of ORF8 dimer caused by disruption of hydrogen bonds and salt bridges as revealed by structural analysis and MD simulation studies. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild-type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 of SARS-CoV-2 delta variant may not be hindering the MHC-I expression thereby resulting in a better immune response against the SARS-CoV-2 delta variant, which partly explains the possible reason for sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India.
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231
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Cheng ZJ, Li B, Zhan Z, Zhao Z, Xue M, Zheng P, Lyu J, Hu C, He J, Chen R, Sun B. Clinical Application of Antibody Immunity Against SARS-CoV-2: Comprehensive Review on Immunoassay and Immunotherapy. Clin Rev Allergy Immunol 2023; 64:17-32. [PMID: 35031959 PMCID: PMC8760112 DOI: 10.1007/s12016-021-08912-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
The current COVID-19 global pandemic poses immense challenges to global health, largely due to the difficulty to detect infection in the early stages of the disease, as well as the current lack of effective antiviral therapy. Research and understanding of the human immune system can provide important theoretical and technical support for the clinical diagnosis and treatment of COVID-19, the clinical implementations of which include immunoassays and immunotherapy, which play a crucial role in the fight against the pandemic. This review consolidates the current scientific evidence for immunoassay, which includes multiple methods of detecting antigen and antibody against SARS-CoV-2. We compared the characteristics, advantages and disadvantages, and clinical applications of these three detection techniques. In addition to detecting viral infections, knowledge on the body's immunity against the virus is desirable; thus, the immunotherapy-based neutralizing antibody (nAb) detection methods were discussed. We also gave a brief introduction to the new immunoassay technology such as biosensing. This was followed by an in-depth and extensive review on a variety of immunotherapy methods. It includes convalescent plasma therapy, neutralizing antibody-based treatments targeting different regions of SARS-CoV-2, immunotherapy targeted on the host cell including inhibiting the host cell receptor and cytokine storm, as well as cocktail antibodies, cross-neutralizing antibodies, and immunotherapy based on cross-reactivity between viral epitopes and autoepitopes and autoantibody. Despite the development of various immunological testing methods and antibody therapies, the current global situation of COVID-19 is still tense. We need more efficient detection methods and more reliable antibody therapies. The up-to-date knowledge on therapeutic strategies will likely help clinicians worldwide to protect patients from life-threatening viral infections.
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Affiliation(s)
- Zhangkai J. Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Bizhou Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Zhiqing Zhan
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Zifan Zhao
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Mingshan Xue
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Peiyan Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Jiali Lyu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Chundi Hu
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
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232
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Li Y, Xu S, Ye Q, Chi H, Guo Z, Chen J, Wu M, Fan B, Li B, Qin C, Liu Z. Rational Development of Hypervalent Glycan Shield-Binding Nanoparticles with Broad-Spectrum Inhibition against Fatal Viruses Including SARS-CoV-2 Variants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2202689. [PMID: 36377484 PMCID: PMC9839850 DOI: 10.1002/advs.202202689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/22/2022] [Indexed: 05/31/2023]
Abstract
Infectious virus diseases, particularly coronavirus disease 2019, have posed a severe threat to public health, whereas the developed therapeutic and prophylactic strategies are seriously challenged by viral evolution and mutation. Therefore, broad-spectrum inhibitors of viruses are highly demanded. Herein, an unprecedented antiviral strategy is reported, targeting the viral glycan shields with hypervalent mannose-binding nanoparticles. The nanoparticles exhibit a unique double-punch mechanism, being capable of not only blocking the virus-receptor interaction but also inducing viral aggregation, thereby allowing for inhibiting the virus entry and facilitating the phagocytosis of viruses. The nanoparticles exhibit potent and broad-spectrum antiviral efficacy to multiple pseudoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its major variants (D614G, N501Y, N439K, Δ69-70, Delta, and Omicron; lentiviruses expressing only the spike proteins), as well as other vital viruses (human immunodeficiency virus 1 and Lassa virus), with apparent EC50 values around the 10-9 m level. Significantly, the broad-spectrum inhibition of authentic viruses of both wild-type SARS-CoV-2 and Delta variants is confirmed. Therefore, this hypervalent glycan-shield targeting strategy opens new access to broad-spectrum viral inhibition.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Shuxin Xu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Qing Ye
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Hang Chi
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
| | - Mei Wu
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Baochao Fan
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of AgricultureNanjing210014P. R. China
| | - Bin Li
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of AgricultureNanjing210014P. R. China
| | - Cheng‐Feng Qin
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071P. R. China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023P. R. China
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233
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Li E, Han Q, Bi J, Wei S, Wang S, Zhang Y, Liu J, Feng N, Wang T, Wu J, Yang S, Zhao Y, Liu B, Yan F, Xia X. Therapeutic equine hyperimmune antibodies with high and broad-spectrum neutralizing activity protect rodents against SARS-CoV-2 infection. Front Immunol 2023; 14:1066730. [PMID: 36875106 PMCID: PMC9981790 DOI: 10.3389/fimmu.2023.1066730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
The emergence of SARS-CoV-2 variants stresses the continued need for broad-spectrum therapeutic antibodies. Several therapeutic monoclonal antibodies or cocktails have been introduced for clinical use. However, unremitting emerging SARS-CoV-2 variants showed reduced neutralizing efficacy by vaccine induced polyclonal antibodies or therapeutic monoclonal antibodies. In our study, polyclonal antibodies and F(ab')2 fragments with strong affinity produced after equine immunization with RBD proteins produced strong affinity. Notably, specific equine IgG and F(ab')2 have broad and high neutralizing activity against parental virus, all SARS-CoV-2 variants of concern (VOCs), including B.1.1,7, B.1.351, B.1.617.2, P.1, B.1.1.529 and BA.2, and all variants of interest (VOIs) including B.1.429, P.2, B.1.525, P.3, B.1.526, B.1.617.1, C.37 and B.1.621. Although some variants weaken the neutralizing ability of equine IgG and F(ab')2 fragments, they still exhibited superior neutralization ability against mutants compared to some reported monoclonal antibodies. Furthermore, we tested the pre-exposure and post-exposure protective efficacy of the equine immunoglobulin IgG and F(ab')2 fragments in lethal mouse and susceptible golden hamster models. Equine immunoglobulin IgG and F(ab')2 fragments effectively neutralized SARS-CoV-2 in vitro, fully protected BALB/c mice from the lethal challenge, and reduced golden hamster's lung pathological change. Therefore, equine pAbs are an adequate, broad coverage, affordable and scalable potential clinical immunotherapy for COVID-19, particularly for SARS-CoV-2 VOCs or VOIs.
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Affiliation(s)
- Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiuxue Han
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin Agriculture University, Changchun, China
| | - Jinhao Bi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shimeng Wei
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ying Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun Wu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Liu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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234
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogenic human coronavirus that belongs to the sarbecovirus lineage of the genus Betacoronavirus. The ancestor strain has evolved into a number of variants of concern, with the Omicron variant of concern now having many distinct sublineages. The ongoing COVID-19 pandemic caused by SARS-CoV-2 has caused serious damage to public health and the global economy, and one strategy to combat COVID-19 has been the development of broadly neutralizing antibodies for prophylactic and therapeutic use. Many are in preclinical and clinical development, and a few have been approved for emergency use. Here we summarize neutralizing antibodies that target four key regions within the SARS-CoV-2 spike (S) protein, namely the N-terminal domain and the receptor-binding domain in the S1 subunit, and the stem helix region and the fusion peptide region in the S2 subunit. Understanding the characteristics of these broadly neutralizing antibodies will accelerate the development of new antibody therapeutics and provide guidance for the rational design of next-generation vaccines.
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235
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Li M, Ren Y, Aw ZQ, Chen B, Yang Z, Lei Y, Cheng L, Liang Q, Hong J, Yang Y, Chen J, Wong YH, Wei J, Shan S, Zhang S, Ge J, Wang R, Dong JZ, Chen Y, Shi X, Zhang Q, Zhang Z, Chu JJH, Wang X, Zhang L. Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Nat Commun 2022; 13:7957. [PMID: 36575191 PMCID: PMC9792944 DOI: 10.1038/s41467-022-35642-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
As SARS-CoV-2 Omicron and other variants of concern (VOCs) continue spreading worldwide, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with potency against diverse VOCs including Omicron subvariants BA.1, BA.2 and BA.4/5, SARS-CoV-1, and major sarbecoviruses. Crystal structure analysis of one representative nanobody, 3-2A2-4, discovers a highly conserved epitope located between the cryptic and the outer face of the receptor binding domain (RBD), distinctive from the receptor ACE2 binding site. Cryo-EM and biochemical evaluation reveal that 3-2A2-4 interferes structural alteration of RBD required for ACE2 binding. Passive delivery of 3-2A2-4 protects K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. Identification of these unique nanobodies will inform the development of next generation antibody therapies and design of pan-sarbecovirus vaccines.
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Affiliation(s)
- Mingxi Li
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yifei Ren
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhen Qin Aw
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Bo Chen
- NB BIOLAB Co., Ltd, Chengdu, 611137, China
| | - Ziqing Yang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yuqing Lei
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Qingtai Liang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Junxian Hong
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yiling Yang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jing Chen
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi Hao Wong
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Jing Wei
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Sisi Shan
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Senyan Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruoke Wang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | | | | | - Xuanling Shi
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Justin Jang Hann Chu
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
- Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Linqi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, NexVac Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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236
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Sharma G, Song LF, Merz KM. Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. J Chem Inf Model 2022; 62:6574-6585. [PMID: 35118864 PMCID: PMC8848506 DOI: 10.1021/acs.jcim.1c01283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 01/07/2023]
Abstract
The recent outbreak of COVID-19 infection started in Wuhan, China, and spread across China and beyond. Since the WHO declared COVID-19 a pandemic (March 11, 2020), three vaccines and only one antiviral drug (remdesivir) have been approved (Oct 22, 2020) by the FDA. The coronavirus enters human epithelial cells by the binding of the densely glycosylated fusion spike protein (S protein) to a receptor (angiotensin-converting enzyme 2, ACE2) on the host cell surface. Therefore, inhibiting the viral entry is a promising treatment pathway for preventing or ameliorating the effects of COVID-19 infection. In the current work, we have used all-atom molecular dynamics (MD) simulations to investigate the influence of the MLN-4760 inhibitor on the conformational properties of ACE2 and its interaction with the receptor-binding domain (RBD) of SARS-CoV-2. We have found that the presence of an inhibitor tends to completely/partially open the ACE2 receptor where the two subdomains (I and II) move away from each other, while the absence results in partial or complete closure. The current study increases our understanding of ACE inhibition by MLN-4760 and how it modulates the conformational properties of ACE2.
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Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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237
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Characterization of Systemic and Mucosal Humoral Immune Responses to an Adjuvanted Intranasal SARS-CoV-2 Protein Subunit Vaccine Candidate in Mice. Vaccines (Basel) 2022; 11:vaccines11010030. [PMID: 36679875 PMCID: PMC9865305 DOI: 10.3390/vaccines11010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Continuous viral evolution of SARS-CoV-2 has resulted in variants capable of immune evasion, vaccine breakthrough infections and increased transmissibility. New vaccines that invoke mucosal immunity may provide a solution to reducing virus transmission. Here, we evaluated the immunogenicity of intranasally administered subunit protein vaccines composed of a stabilized SARS-CoV-2 spike trimer or the receptor binding domain (RBD) adjuvanted with either cholera toxin (CT) or an archaeal lipid mucosal adjuvant (AMVAD). We show robust induction of immunoglobulin (Ig) G and IgA responses in plasma, nasal wash and bronchoalveolar lavage in mice only when adjuvant is used in the vaccine formulation. While the AMVAD adjuvant was more effective at inducing systemic antibodies against the RBD antigen than CT, CT was generally more effective at inducing overall higher IgA and IgG titers against the spike antigen in both systemic and mucosal compartments. Furthermore, vaccination with adjuvanted spike led to superior mucosal IgA responses than with the RBD antigen and produced broadly targeting neutralizing plasma antibodies against ancestral, Delta and Omicron variants in vitro; whereas adjuvanted RBD elicited a narrower antibody response with neutralizing activity only against ancestral and Delta variants. Our study demonstrates that intranasal administration of an adjuvanted protein subunit vaccine in immunologically naïve mice induced both systemic and mucosal neutralizing antibody responses that were most effective at neutralizing SARS-CoV-2 variants when the trimeric spike was used as an antigen compared to RBD.
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238
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Bowen JE, Park YJ, Stewart C, Brown JT, Sharkey WK, Walls AC, Joshi A, Sprouse KR, McCallum M, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Nguyen AW, Silva RP, Huang Y, Low JS, Jerak J, Tiles SW, Ahmed K, Shariq A, Dan JM, Zhang Z, Weiskopf D, Sette A, Snell G, Posavad CM, Iqbal NT, Geffner J, Bandera A, Gori A, Sallusto F, Maynard JA, Crotty S, Van Voorhis WC, Simmerling C, Grifantini R, Chu HY, Corti D, Veesler D. SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Sci Immunol 2022; 7:eadf1421. [PMID: 36356052 PMCID: PMC9765460 DOI: 10.1126/sciimmunol.adf1421] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022]
Abstract
Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies and engineering strategies. We show here that vaccines containing prefusion-stabilizing S mutations elicit antibody responses in humans with enhanced recognition of S and the S1 subunit relative to postfusion S as compared with vaccines lacking these mutations or natural infection. Prefusion S and S1 antibody binding titers positively and equivalently correlated with neutralizing activity, and depletion of S1-directed antibodies completely abrogated plasma neutralizing activity. We show that neutralizing activity is almost entirely directed to the S1 subunit and that variant cross-neutralization is mediated solely by receptor binding domain-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants than current technologies.
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Affiliation(s)
- John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William K. Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Nicholas M. Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Ignacio G. Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Annalee W. Nguyen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Rui P. Silva
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Yimin Huang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Asefa Shariq
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | | | - Christine M. Posavad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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239
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Li J, Liang T, Hei A, Wang X, Li H, Yu X, Zhao R, Gao P, Fang C, Zhou J, Li M, He E, Skog S. Novel neutralizing chicken IgY antibodies targeting 17 potent conserved peptides identified by SARS-CoV-2 proteome microarray, and future prospects. Front Immunol 2022; 13:1074077. [PMID: 36618358 PMCID: PMC9815496 DOI: 10.3389/fimmu.2022.1074077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction An approach toward novel neutralizing IgY polyclonal antibodies (N-IgY-pAb) against SARS-CoV-2 S-ECD was developed. Material and methods The novel N-IgY-pAb and its intranasal spray response against the wild type ("'WH-Human 1") SARS-CoV-2 virus, variants of Delta or Omicron were up to 98%. Unique virus peptides binding to N-IgY-pAb were screened by a SARS-CoV-2 proteome microarray. Results Seventeen mutation-free peptides with a Z-score > 3.0 were identified as potent targets from a total of 966 peptides. The new findings show that one is in the RBM domain (461LKPFERDISTEIYQA475 ), two are in the NTD domain (21RTQLPPAYTNSFTRG35, 291CALDPLSETKCTLKS305) four are in the C1/2-terminal (561PFQQFGRDIADTTDA575,571DTTDAVRDPQTLEIL585,581TLEILDITPCSFGGV595, 661ECDIPIGAGICASYQ675 ), three are in the S1/S2 border (741YICGDSTECSNLLLQ755, 811KPSKRSFIEDLLFNK825, 821LLFNKVTLADAGFIK835) one target is in HR2 (1161SPDVDLGDISGINAS1175) and one is in HR2-TM (1201QELGKYEQYIKWPWY1215). Moreover, five potential peptides were in the NSP domain: nsp3-55 (1361SNEKQEILGTVSWNL1375), nsp14-50 (614HHANEYRLYLDAYNM642, ORF10-3 (21MNSRNYIAQVDVVNFNLT38, ORF7a-1(1MKIILFLALITLATC15) and ORF7a-12 (1116TLCFTLKRKTE121). Discussion and conclusion We concluded that the N-IgY-pAb could effectively neutralize the SARS-CoV-2. The new findings of seventeen potent conserved peptides are extremely important for developing new vaccines and "cocktails" of neutralizing Abs for efficient treatments for patients infected with SARS-CoV-2.
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Affiliation(s)
- Jin Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ailian Hei
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Xiangbin Wang
- SciProtech Co., Ltd, Beijing Changping Science Park, Beijing, China
| | - Huijun Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Centre, National Centre for Protein Sciences-Beijing (PHOENIX Centre), Beijing Institute of LifeOmics, Beijing, China
| | - Rui Zhao
- SciProtech Co., Ltd, Beijing Changping Science Park, Beijing, China
| | - Peng Gao
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Cong Fang
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Ji Zhou
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Maogang Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Ellen He
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Sven Skog
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China,*Correspondence: Sven Skog,
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240
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Cocherie T, Zafilaza K, Leducq V, Marot S, Calvez V, Marcelin AG, Todesco E. Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Microorganisms 2022; 11:30. [PMID: 36677322 PMCID: PMC9866527 DOI: 10.3390/microorganisms11010030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations.
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Affiliation(s)
| | | | | | | | | | | | - Eve Todesco
- Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Virologie, 75013 Paris, France
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241
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Zapata-Cardona MI, Flórez-Álvarez L, Lopera TJ, Chvatal-Medina M, Zapata-Builes W, Diaz FJ, Aguilar-Jimenez W, Taborda N, Hernandez JC, Rugeles MT. Neutralizing antibody titers to Omicron six months after vaccination with BNT162b2 in Colombia. Front Immunol 2022; 13:1102384. [PMID: 36618393 PMCID: PMC9811190 DOI: 10.3389/fimmu.2022.1102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of the Omicron variant has generated concerns about the efficacy of COVID-19 vaccines. We evaluated the serum neutralizing activity of antibodies against the Omicron (lineage BA.1.1) by plaque reduction neutralizing test, as well as its correlation with age and gender, in a Colombian cohort six months after being vaccinated with BNT162b2 (Pfizer/BioNTech). Compared to all other variants analyzed, a significantly lower neutralizing activity (p<0.001) was observed against Omicron. Interestingly, older individuals exhibited lower titers against Omicron than those younger than 40. No statistical differences in neutralizing activity were observed according to gender. Our results showed that two doses of BNT162b2 might not provide robust protection against the Omicron variant over time. It is necessary to consider including changes in the composition of the vaccines to protect against new emerging variants of SARS-CoV-2 and campaigns to implement additional booster vaccinations.
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Affiliation(s)
- María I. Zapata-Cardona
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tulio J. Lopera
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Francisco J. Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Natalia Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Juan C. Hernandez
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,*Correspondence: Maria T. Rugeles,
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Stocks BB, Thibeault MP, L’Abbé D, Stuible M, Durocher Y, Melanson JE. Production and Characterization of a SARS-CoV-2 Nucleocapsid Protein Reference Material. ACS MEASUREMENT SCIENCE AU 2022; 2:620-628. [PMID: 36785774 PMCID: PMC9662649 DOI: 10.1021/acsmeasuresciau.2c00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/02/2023]
Abstract
Rapid antigen tests have become a widely used COVID-19 diagnostic tool with demand accelerating in response to the highly contagious SARS-CoV-2 Omicron variant. Hundreds of such test kits are approved for use worldwide, predominantly reporting on the presence of the viral nucleocapsid (N) protein, yet the comparability among manufacturers remains unclear and the need for reference standards is recognized. To address this lack of standardization, the National Research Council Canada has developed a SARS-CoV-2 nucleocapsid protein reference material solution, NCAP-1. Reference value determination for N protein content was realized by amino acid analysis (AAA) via double isotope dilution liquid chromatography-tandem mass spectrometry (LC-ID-MS/MS) following acid hydrolysis of the protein, in conjunction with UV spectrophotometry based on tryptophan and tyrosine absorbance at 280 nm. The homogeneity of the material was established through spectrophotometric absorbance readings at 280 nm. The molar concentration of the N protein in NCAP-1 was 10.0 ± 1.9 μmol L-1 (k = 2, 95% confidence interval). Reference mass concentration and mass fraction values were subsequently calculated using the protein molecular weight and density of the NCAP-1 solution. Changes to protein higher-order structure, probed by size-exclusion liquid chromatography (LC-SEC) with UV detection, were used to evaluate transportation and storage stabilities. LC-SEC revealed nearly 90% of the N protein in the material is present as a mixture of hexamers and tetramers. The remaining low molecular weight species (<30 kDa) were interrogated by top-down mass spectrometry and determined to be autolysis products homologous to those previously documented for N protein of the original SARS-CoV [Biochem. Biophys. Res. Commun.2008t, 377, 429-433].
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Affiliation(s)
- Bradley B. Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
| | - Marie-Pier Thibeault
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
| | - Denis L’Abbé
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Matthew Stuible
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Yves Durocher
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Jeremy E. Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
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243
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Yamamoto Y, Nakano Y, Murae M, Shimizu Y, Sakai S, Ogawa M, Mizukami T, Inoue T, Onodera T, Takahashi Y, Wakita T, Fukasawa M, Miyazaki S, Noguchi K. Direct Inhibition of SARS-CoV-2 Spike Protein by Peracetic Acid. Int J Mol Sci 2022; 24:20. [PMID: 36613459 PMCID: PMC9820423 DOI: 10.3390/ijms24010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Peracetic acid (PAA) disinfectants are effective against a wide range of pathogenic microorganisms, including bacteria, fungi, and viruses. Several studies have shown the efficacy of PAA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, its efficacy in SARS-CoV-2 variants and the molecular mechanism of action of PAA against SARS-CoV-2 have not been investigated. SARS-CoV-2 infection depends on the recognition and binding of the cell receptor angiotensin-converting enzyme 2 (ACE2) via the receptor-binding domain (RBD) of the spike protein. Here, we demonstrated that PAA effectively suppressed pseudotyped virus infection in the Wuhan type and variants, including Delta and Omicron. Similarly, PAA reduced the authentic viral load of SARS-CoV-2. Computational analysis suggested that the hydroxyl radicals produced by PAA cleave the disulfide bridges in the RBD. Additionally, the PAA treatment decreased the abundance of the Wuhan- and variant-type spike proteins. Enzyme-linked immunosorbent assay showed direct inhibition of RBD-ACE2 interactions by PAA. In conclusion, the PAA treatment suppressed SARS-CoV-2 infection, which was dependent on the inhibition of the interaction between the spike RBD and ACE2 by inducing spike protein destabilization. Our findings provide evidence of a potent disinfection strategy against SARS-CoV-2.
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Affiliation(s)
- Yuichiro Yamamoto
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
| | - Yoshio Nakano
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
| | - Mana Murae
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshimi Shimizu
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Department of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2, Nakano, Nakano-ku, Tokyo 164-8530, Japan
| | - Shota Sakai
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Motohiko Ogawa
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomoharu Mizukami
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuya Inoue
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
| | - Taishi Onodera
- Reseach Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshimasa Takahashi
- Reseach Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Masayoshi Fukasawa
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Satoru Miyazaki
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
| | - Kohji Noguchi
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Chiba, Japan
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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244
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.15.520606. [PMID: 36561191 PMCID: PMC9774213 DOI: 10.1101/2022.12.15.520606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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245
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McLean GR, Zhang Y, Ndoyi R, Martin A, Winer J. Rapid Quantification of SARS-CoV-2 Neutralising Antibodies Using Time-Resolved Fluorescence Immunoassay. Vaccines (Basel) 2022; 10:vaccines10122149. [PMID: 36560559 PMCID: PMC9785461 DOI: 10.3390/vaccines10122149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The quantification of neutralising antibodies (NAb) for SARS-CoV-2 has become an important tool for monitoring protective immunity following infection or immunisation. In this study, we evaluated using World-Health-Organisation-standard immunoglobulin preparations, a novel point-of-care test that quantitates NAb by time-resolved fluorescent immunoassay. The assay provided robust data of binding antibody units (BAU) in 15 min that were well correlated with NAb values obtained by traditional in vitro neutralisation assay. The data also correlated well to spike-receptor-binding domain-binding antibodies over a broad range of plasma dilutions. The assay was extremely sensitive, able to detect positive samples after dilution 1:10,000 and over a wide range of BAU. Assay specificity was estimated at 96% using Pre-COVID-19 serum samples when applying a cut-off value of 47 BAU/mL, although readings of up to 100 BAU/mL could be considered borderline. This point-of-care diagnostic test is useful for rapid population screening and includes the use of capillary blood samples. Furthermore, it provides results for SARS-CoV-2 NAb in 15 min, which can inform immediate decisions regarding protective immunity levels and the need for continued COVID immunisations.
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Affiliation(s)
- Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
- Correspondence:
| | - Yueke Zhang
- PremaLabs Diagnostics UK Ltd., London W1J 6ER, UK
| | - Rene Ndoyi
- PremaLabs Diagnostics UK Ltd., London W1J 6ER, UK
| | - Adam Martin
- PremaLabs Diagnostics UK Ltd., London W1J 6ER, UK
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246
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Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
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Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
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247
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Liang H, Nian X, Wu J, Liu D, Feng L, Lu J, Peng Y, Zhou Z, Deng T, Liu J, Ji D, Qiu R, Lin L, Zeng Y, Xia F, Hu Y, Li T, Duan K, Li X, Wang Z, Zhang Y, Zhang H, Zhu C, Wang S, Wu X, Wang X, Li Y, Huang S, Mao M, Guo H, Yang Y, Jia R, Xufang J, Wang X, Liang S, Qiu Z, Zhang J, Ding Y, Li C, Zhang J, Fu D, He Y, Zhou D, Li C, Zhang J, Yu D, Yang XM. COVID-19 vaccination boosts the potency and breadth of the immune response against SARS-CoV-2 among recovered patients in Wuhan. Cell Discov 2022; 8:131. [PMID: 36494338 PMCID: PMC9734167 DOI: 10.1038/s41421-022-00496-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
The immunity of patients who recover from coronavirus disease 2019 (COVID-19) could be long lasting but persist at a lower level. Thus, recovered patients still need to be vaccinated to prevent reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or its mutated variants. Here, we report that the inactivated COVID-19 vaccine can stimulate immunity in recovered patients to maintain high levels of anti-receptor-binding domain (RBD) and anti-nucleocapsid protein (NP) antibody titers within 9 months, and high neutralizing activity against the prototype, Delta, and Omicron strains was observed. Nevertheless, the antibody response decreased over time, and the Omicron variant exhibited more pronounced resistance to neutralization than the prototype and Delta strains. Moreover, the intensity of the SARS-CoV-2-specific CD4+ T cell response was also increased in recovered patients who received COVID-19 vaccines. Overall, the repeated antigen exposure provided by inactivated COVID-19 vaccination greatly boosted both the potency and breadth of the humoral and cellular immune responses against SARS-CoV-2, effectively protecting recovered individuals from reinfection by circulating SARS-CoV-2 and its variants.
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Affiliation(s)
- Hong Liang
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Xuanxuan Nian
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Junzheng Wu
- Chengdu Rongsheng Pharmaceuticals Co., Ltd., Chengdu, Sichuan, China
| | - Dong Liu
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Lu Feng
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Jia Lu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Yan Peng
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Zhijun Zhou
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Tao Deng
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Jing Liu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Deming Ji
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Ran Qiu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Lianzhen Lin
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Yan Zeng
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Fei Xia
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Yong Hu
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Taojing Li
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Kai Duan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Xinguo Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Zejun Wang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Yong Zhang
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Hang Zhang
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Chen Zhu
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Shang Wang
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Xiao Wu
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Xiang Wang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Yuwei Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Shihe Huang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China
| | - Min Mao
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Huanhuan Guo
- Wuxue Wusheng Plasma Collection Center, Wuxue, Hubei, China
| | - Yunkai Yang
- China National Biotec Group Company Limited, Beijing, China
| | - Rui Jia
- China National Biotec Group Company Limited, Beijing, China
| | - Jingwei Xufang
- China National Biotec Group Company Limited, Beijing, China
| | - Xuewei Wang
- China National Biotec Group Company Limited, Beijing, China
| | | | - Zhixin Qiu
- Wuhan Biobank Co., Ltd., Wuhan, Hubei, China
| | - Juan Zhang
- Wuhan Biobank Co., Ltd., Wuhan, Hubei, China
| | - Yaling Ding
- Chengdu Rongsheng Pharmaceuticals Co., Ltd., Chengdu, Sichuan, China
| | - Chunyan Li
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Jin Zhang
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Daoxing Fu
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Yanlin He
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China
| | - Dongbo Zhou
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China
| | - Cesheng Li
- Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd., Wuhan, Hubei, China.
| | - Jiayou Zhang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China.
- Wuhan Institute of Biological Products Co., Ltd., Wuhan, Hubei, China.
| | - Ding Yu
- Beijing Tiantan Biological Products Co., Ltd., Beijing, China.
- Chengdu Rongsheng Pharmaceuticals Co., Ltd., Chengdu, Sichuan, China.
| | - Xiao-Ming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, Hubei, China.
- China National Biotec Group Company Limited, Beijing, China.
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248
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A bispecific nanobody dimer broadly neutralizes SARS-CoV-1 & 2 variants of concern and offers substantial protection against Omicron via low-dose intranasal administration. Cell Discov 2022; 8:132. [PMID: 36494344 PMCID: PMC9734137 DOI: 10.1038/s41421-022-00497-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Current SARS-CoV-2 Omicron subvariants impose a heavy burden on global health systems by evading immunity from most developed neutralizing antibodies and vaccines. Here, we identified a nanobody (aSA3) that strongly cross-reacts with the receptor binding domain (RBD) of both SARS-CoV-1 and wild-type (WT) SARS-CoV-2. The dimeric construct of aSA3 (aSA3-Fc) tightly binds and potently neutralizes both SARS-CoV-1 and WT SARS-CoV-2. Based on X-ray crystallography, we engineered a bispecific nanobody dimer (2-3-Fc) by fusing aSA3-Fc to aRBD-2, a previously identified broad-spectrum nanobody targeting an RBD epitope distinct from aSA3. 2-3-Fc exhibits single-digit ng/mL neutralizing potency against all major variants of concerns including BA.5. In hamsters, a single systemic dose of 2-3-Fc at 10 mg/kg conferred substantial efficacy against Omicron infection. More importantly, even at three low doses of 0.5 mg/kg, 2-3-Fc prophylactically administered through the intranasal route drastically reduced viral RNA loads and completely eliminated infectious Omicron particles in the trachea and lungs. Finally, we discovered that 2(Y29G)-3-Fc containing a Y29G substitution in aRBD-2 showed better activity than 2-3-Fc in neutralizing BA.2.75, a recent Omicron subvariant that emerged in India. This study expands the arsenal against SARS-CoV-1, provides potential therapeutic and prophylactic candidates that fully cover major SARS-CoV-2 variants, and may offer a simple preventive approach against Omicron and its subvariants.
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249
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Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. PLoS Comput Biol 2022; 18:e1010230. [DOI: 10.1371/journal.pcbi.1010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/19/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Antibody epitope mapping of viral proteins plays a vital role in understanding immune system mechanisms of protection. In the case of class I viral fusion proteins, recent advances in cryo-electron microscopy and protein stabilization techniques have highlighted the importance of cryptic or ‘alternative’ conformations that expose epitopes targeted by potent neutralizing antibodies. Thorough epitope mapping of such metastable conformations is difficult but is critical for understanding sites of vulnerability in class I fusion proteins that occur as transient conformational states during viral attachment and fusion. We introduce a novel method Accelerated class I fusion protein Epitope Mapping (AxIEM) that accounts for fusion protein flexibility to improve out-of-sample prediction of discontinuous antibody epitopes. Harnessing data from previous experimental epitope mapping efforts of several class I fusion proteins, we demonstrate that accuracy of epitope prediction depends on residue environment and allows for the prediction of conformation-dependent antibody target residues. We also show that AxIEM can identify common epitopes and provide structural insights for the development and rational design of vaccines.
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Liu Y, Arase H. Neutralizing and enhancing antibodies against SARS-CoV-2. Inflamm Regen 2022; 42:58. [PMID: 36471381 PMCID: PMC9720987 DOI: 10.1186/s41232-022-00233-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The high transmissibility and rapid global spread of SARS-CoV-2 since 2019 has led to a huge burden on healthcare worldwide. Anti-SARS-CoV-2 neutralizing antibodies play an important role in not only protecting against infection but also in clearing the virus and are essential to providing long-term immunity. On the other hand, antibodies against the virus are not always protective. With the emergence of SARS-CoV-2 immune escape variants, vaccine design strategies as well as antibody-mediated therapeutic approaches have become more important. We review some of the findings on SARS-CoV-2 antibodies, focusing on both basic research and clinical applications.
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Affiliation(s)
- Yafei Liu
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
| | - Hisashi Arase
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
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