751
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Mandolesi M, Sheward DJ, Hanke L, Ma J, Pushparaj P, Perez Vidakovics L, Kim C, Àdori M, Lenart K, Loré K, Castro Dopico X, Coquet JM, McInerney GM, Karlsson Hedestam GB, Murrell B. SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses. Cell Rep Med 2021; 2:100252. [PMID: 33842900 PMCID: PMC8020888 DOI: 10.1016/j.xcrm.2021.100252] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/05/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022]
Abstract
The outbreak and spread of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) is a current global health emergency, and effective prophylactic vaccines are needed urgently. The spike glycoprotein of SARS-CoV-2 mediates entry into host cells, and thus is the target of neutralizing antibodies. Here, we show that adjuvanted protein immunization with soluble SARS-CoV-2 spike trimers, stabilized in prefusion conformation, results in potent antibody responses in mice and rhesus macaques, with neutralizing antibody titers exceeding those typically measured in SARS-CoV-2 seropositive humans by more than one order of magnitude. Neutralizing antibody responses were observed after a single dose, with exceptionally high titers achieved after boosting. A follow-up to monitor the waning of the neutralizing antibody responses in rhesus macaques demonstrated durable responses that were maintained at high and stable levels at least 4 months after boosting. These data support the development of adjuvanted SARS-CoV-2 prefusion-stabilized spike protein subunit vaccines.
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Affiliation(s)
- Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Junjie Ma
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Klara Lenart
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Karin Loré
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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752
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Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls SM, Ansari MA, Abeler-Dörner L, Moore CE, Peto TEA, Eyre DW, Shaw R, Simmonds P, Buck D, Todd JA, Connor TR, Ashraf S, da Silva Filipe A, Shepherd J, Thomson EC, Bonsall D, Fraser C, Golubchik T. SARS-CoV-2 within-host diversity and transmission. Science 2021; 372:eabg0821. [PMID: 33688063 PMCID: PMC8128293 DOI: 10.1126/science.abg0821] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.
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Affiliation(s)
- Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Mariateresa de Cesare
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Monique Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Newton Otecko
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Jessica Lynch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Stephen Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Nicholas Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
- Gibraltar Health Authority, Gibraltar, UK
| | - Matilde Mori
- School of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Rebecca Williams
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Gabrielle Vernet
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Catrin E Moore
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Timothy E A Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - David W Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Big Data Institute, Nuffield Department of Public Health, University of Oxford, Old Road Campus, Oxford OX3 7FL, UK
| | - Robert Shaw
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF10 4BZ, UK
- Cardiff University School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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753
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Shen X, Tang H, McDanal C, Wagh K, Fischer W, Theiler J, Yoon H, Li D, Haynes BF, Sanders KO, Gnanakaran S, Hengartner N, Pajon R, Smith G, Glenn GM, Korber B, Montefiori DC. SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. Cell Host Microbe 2021; 29:529-539.e3. [PMID: 33705729 PMCID: PMC7934674 DOI: 10.1016/j.chom.2021.03.002] [Citation(s) in RCA: 266] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
All current vaccines for COVID-19 utilize ancestral SARS-CoV-2 spike with the goal of generating protective neutralizing antibodies. The recent emergence and rapid spread of several SARS-CoV-2 variants carrying multiple spike mutations raise concerns about possible immune escape. One variant, first identified in the United Kingdom (B.1.1.7, also called 20I/501Y.V1), contains eight spike mutations with potential to impact antibody therapy, vaccine efficacy, and risk of reinfection. Here, we show that B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (∼sim;2-fold), by serum samples from convalescent individuals and recipients of an mRNA vaccine (mRNA-1273, Moderna) and a protein nanoparticle vaccine (NVX-CoV2373, Novavax). A subset of monoclonal antibodies to the receptor binding domain (RBD) of spike are less effective against the variant, while others are largely unaffected. These findings indicate that variant B.1.1.7 is unlikely to be a major concern for current vaccines or for an increased risk of reinfection.
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Affiliation(s)
- Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - William Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Kevin O Sanders
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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754
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Greaney AJ, Loes AN, Gentles LE, Crawford KH, Starr TN, Malone KD, Chu HY, Bloom JD. The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.14.439844. [PMID: 33880474 PMCID: PMC8057239 DOI: 10.1101/2021.04.14.439844] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution. ONE SENTENCE SUMMARY Deep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Lauren E. Gentles
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Microbiology, University of Washington; Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Keara D. Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, Washington, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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755
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Fassy J, Lacoux C, Leroy S, Noussair L, Hubac S, Degoutte A, Vassaux G, Leclercq V, Rouquié D, Marquette CH, Rottman M, Touron P, Lemoine A, Herrmann JL, Barbry P, Nahon JL, Zaragosi LE, Mari B. Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples. PLoS One 2021; 16:e0243333. [PMID: 33852580 PMCID: PMC8046349 DOI: 10.1371/journal.pone.0243333] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
The emergence and quick spread of SARS-CoV-2 has pointed at a low capacity response for testing large populations in many countries, in line of material, technical and staff limitations. The traditional RT-qPCR diagnostic test remains the reference method and is by far the most widely used test. These assays are limited to a few probe sets, require large sample PCR reaction volumes, along with an expensive and time-consuming RNA extraction step. Here we describe a quantitative nanofluidic assay that overcomes some of these shortcomings, based on the BiomarkTM instrument from Fluidigm. This system offers the possibility of performing 4608 qPCR end-points in a single run, equivalent to 192 clinical samples combined with 12 pairs of primers/probe sets in duplicate, thus allowing the monitoring of SARS-CoV-2 including the detection of specific SARS-CoV-2 variants, as well as the detection other pathogens and/or host cellular responses (virus receptors, response markers, microRNAs). The 10 nL-range volume of BiomarkTM reactions is compatible with sensitive and reproducible reactions that can be easily and cost-effectively adapted to various RT-qPCR configurations and sets of primers/probe. Finally, we also evaluated the use of inactivating lysis buffers composed of various detergents in the presence or absence of proteinase K to assess the compatibility of these buffers with a direct reverse transcription enzymatic step and we propose several protocols, bypassing the need for RNA purification. We advocate that the combined utilization of an optimized processing buffer and a high-throughput real-time PCR device would contribute to improve the turn-around-time to deliver the test results to patients and increase the SARS-CoV-2 testing capacities.
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Affiliation(s)
- Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Sylvie Leroy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
- Département de Pneumologie, CHU-Nice, FHU-OncoAge, Université Côte d’Azur, Nice, France
| | - Latifa Noussair
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
| | - Sylvain Hubac
- Institut de Recherche Criminelle de la Gendarmerie Nationale (IRCGN), Cergy, France
| | - Aurélien Degoutte
- Département de Pneumologie, CHU-Nice, FHU-OncoAge, Université Côte d’Azur, Nice, France
| | - Georges Vassaux
- Université Côte d’Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | | | | | | | - Martin Rottman
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Patrick Touron
- Institut de Recherche Criminelle de la Gendarmerie Nationale (IRCGN), Cergy, France
| | - Antoinette Lemoine
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
| | - Jean-Louis Herrmann
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Pascal Barbry
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Jean-Louis Nahon
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d’Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
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756
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Edara VV, Norwood C, Floyd K, Lai L, Davis-Gardner ME, Hudson WH, Mantus G, Nyhoff LE, Adelman MW, Fineman R, Patel S, Byram R, Gomes DN, Michael G, Abdullahi H, Beydoun N, Panganiban B, McNair N, Hellmeister K, Pitts J, Winters J, Kleinhenz J, Usher J, O'Keefe JB, Piantadosi A, Waggoner JJ, Babiker A, Stephens DS, Anderson EJ, Edupuganti S, Rouphael N, Ahmed R, Wrammert J, Suthar MS. Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. Cell Host Microbe 2021; 29:516-521.e3. [PMID: 33798491 PMCID: PMC7980225 DOI: 10.1016/j.chom.2021.03.009] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies. We compared antibody binding and live virus neutralization of sera from naturally infected and Moderna-vaccinated individuals against two SARS-CoV-2 variants: B.1 containing the spike mutation D614G and the emerging B.1.351 variant containing additional spike mutations and deletions. Sera from acutely infected and convalescent COVID-19 patients exhibited a 3-fold reduction in binding antibody titers to the B.1.351 variant receptor-binding domain of the spike protein and a 3.5-fold reduction in neutralizing antibody titers against SARS-CoV-2 B.1.351 variant compared to the B.1 variant. Similar results were seen with sera from Moderna-vaccinated individuals. Despite reduced antibody titers against the B.1.351 variant, sera from infected and vaccinated individuals containing polyclonal antibodies to the spike protein could still neutralize SARS-CoV-2 B.1.351, suggesting that protective humoral immunity may be retained against this variant.
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Affiliation(s)
- Venkata Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Carson Norwood
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Katharine Floyd
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Lilin Lai
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - William H Hudson
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Grace Mantus
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Lindsay E Nyhoff
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Max W Adelman
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Rebecca Fineman
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Shivan Patel
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Rebecca Byram
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Dumingu Nipuni Gomes
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Garett Michael
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Hayatu Abdullahi
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nour Beydoun
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Bernadine Panganiban
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nina McNair
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Kieffer Hellmeister
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jamila Pitts
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Joy Winters
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jennifer Kleinhenz
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jacob Usher
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - James B O'Keefe
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Anne Piantadosi
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, Georgia, USA
| | - Jesse J Waggoner
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Ahmed Babiker
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, Georgia, USA
| | - David S Stephens
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Evan J Anderson
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA; Hope Clinic of Emory Vaccine Center, Emory University, Decatur, GA 30030, USA
| | - Nadine Rouphael
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA; Hope Clinic of Emory Vaccine Center, Emory University, Decatur, GA 30030, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA.
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757
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He Q, Mao Q, Zhang J, Bian L, Gao F, Wang J, Xu M, Liang Z. COVID-19 Vaccines: Current Understanding on Immunogenicity, Safety, and Further Considerations. Front Immunol 2021; 12:669339. [PMID: 33912196 PMCID: PMC8071852 DOI: 10.3389/fimmu.2021.669339] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
The world has entered the second wave of the COVID-19 pandemic, and its intensity is significantly higher than that of the first wave of early 2020. Many countries or regions have been forced to start the second round of lockdowns. To respond rapidly to this global pandemic, dozens of COVID-19 vaccine candidates have been developed and many are undergoing clinical testing. Evaluating and defining effective vaccine candidates for human use is crucial for prioritizing vaccination programs against COVID-19. In this review, we have summarized and analyzed the efficacy, immunogenicity and safety data from clinical reports on different COVID-19 vaccines. We discuss the various guidelines laid out for the development of vaccines and the importance of biological standards for comparing the performance of vaccines. Lastly, we highlight the key remaining challenges, possible strategies for addressing them and the expected improvements in the next generation of COVID-19 vaccines.
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Affiliation(s)
- Qian He
- National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- National Institutes for Food and Drug Control, Beijing, China
| | - Jialu Zhang
- National Institutes for Food and Drug Control, Beijing, China
| | - Lianlian Bian
- National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- National Institutes for Food and Drug Control, Beijing, China
| | - Junzhi Wang
- National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- National Institutes for Food and Drug Control, Beijing, China
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758
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Guo S, Liu K, Zheng J. The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Int J Biol Sci 2021; 17:1476-1485. [PMID: 33907511 PMCID: PMC8071763 DOI: 10.7150/ijbs.59137] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
The pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is far from being controlled despite the great effort that have been taken throughout the world. Herd immunity through vaccination is our major expectation to rein the virus. However, the emergence of widespread genetic variants could potentially undermine the vaccines. The evidence that some variants could evade immune responses elicited by vaccines and previous infection is growing. In this review, we summarized the current understanding on five notable genetic variants, i.e., D614G, Cluster 5, VOC 202012/01, 501Y.V2 and P.1, and discussed the potential impact of these variants on the virus transmission, pathogenesis and vaccine efficacy. We also highlight that mutations in the N-terminal domain of spike protein should be considered when evaluating the antibody neutralization abilities. Among these genetic variants, a concern of genetic variant 501Y.V2 to escape the protection by vaccines was raised. We therefore call for new vaccines targeting this variant to be developed.
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Affiliation(s)
- Shuxin Guo
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Kefang Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Institute of Translational Medicine, University of Macau, Macau SAR, China
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759
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Emary KRW, Golubchik T, Aley PK, Ariani CV, Angus B, Bibi S, Blane B, Bonsall D, Cicconi P, Charlton S, Clutterbuck EA, Collins AM, Cox T, Darton TC, Dold C, Douglas AD, Duncan CJA, Ewer KJ, Flaxman AL, Faust SN, Ferreira DM, Feng S, Finn A, Folegatti PM, Fuskova M, Galiza E, Goodman AL, Green CM, Green CA, Greenland M, Hallis B, Heath PT, Hay J, Hill HC, Jenkin D, Kerridge S, Lazarus R, Libri V, Lillie PJ, Ludden C, Marchevsky NG, Minassian AM, McGregor AC, Mujadidi YF, Phillips DJ, Plested E, Pollock KM, Robinson H, Smith A, Song R, Snape MD, Sutherland RK, Thomson EC, Toshner M, Turner DPJ, Vekemans J, Villafana TL, Williams CJ, Hill AVS, Lambe T, Gilbert SC, Voysey M, Ramasamy MN, Pollard AJ. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. Lancet 2021; 397:1351-1362. [PMID: 33798499 PMCID: PMC8009612 DOI: 10.1016/s0140-6736(21)00628-0] [Citation(s) in RCA: 447] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 02/09/2023]
Abstract
BACKGROUND A new variant of SARS-CoV-2, B.1.1.7, emerged as the dominant cause of COVID-19 disease in the UK from November, 2020. We report a post-hoc analysis of the efficacy of the adenoviral vector vaccine, ChAdOx1 nCoV-19 (AZD1222), against this variant. METHODS Volunteers (aged ≥18 years) who were enrolled in phase 2/3 vaccine efficacy studies in the UK, and who were randomly assigned (1:1) to receive ChAdOx1 nCoV-19 or a meningococcal conjugate control (MenACWY) vaccine, provided upper airway swabs on a weekly basis and also if they developed symptoms of COVID-19 disease (a cough, a fever of 37·8°C or higher, shortness of breath, anosmia, or ageusia). Swabs were tested by nucleic acid amplification test (NAAT) for SARS-CoV-2 and positive samples were sequenced through the COVID-19 Genomics UK consortium. Neutralising antibody responses were measured using a live-virus microneutralisation assay against the B.1.1.7 lineage and a canonical non-B.1.1.7 lineage (Victoria). The efficacy analysis included symptomatic COVID-19 in seronegative participants with a NAAT positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to vaccine received. Vaccine efficacy was calculated as 1 - relative risk (ChAdOx1 nCoV-19 vs MenACWY groups) derived from a robust Poisson regression model. This study is continuing and is registered with ClinicalTrials.gov, NCT04400838, and ISRCTN, 15281137. FINDINGS Participants in efficacy cohorts were recruited between May 31 and Nov 13, 2020, and received booster doses between Aug 3 and Dec 30, 2020. Of 8534 participants in the primary efficacy cohort, 6636 (78%) were aged 18-55 years and 5065 (59%) were female. Between Oct 1, 2020, and Jan 14, 2021, 520 participants developed SARS-CoV-2 infection. 1466 NAAT positive nose and throat swabs were collected from these participants during the trial. Of these, 401 swabs from 311 participants were successfully sequenced. Laboratory virus neutralisation activity by vaccine-induced antibodies was lower against the B.1.1.7 variant than against the Victoria lineage (geometric mean ratio 8·9, 95% CI 7·2-11·0). Clinical vaccine efficacy against symptomatic NAAT positive infection was 70·4% (95% CI 43·6-84·5) for B.1.1.7 and 81·5% (67·9-89·4) for non-B.1.1.7 lineages. INTERPRETATION ChAdOx1 nCoV-19 showed reduced neutralisation activity against the B.1.1.7 variant compared with a non-B.1.1.7 variant in vitro, but the vaccine showed efficacy against the B.1.1.7 variant of SARS-CoV-2. FUNDING UK Research and Innovation, National Institute for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midlands NIHR Clinical Research Network, and AstraZeneca.
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Affiliation(s)
- Katherine R W Emary
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Brian Angus
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Beth Blane
- COVID-19 Genomics UK, Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paola Cicconi
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sue Charlton
- National Infection Service, Public Health England, Salisbury, UK
| | | | - Andrea M Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | | | - Thomas C Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Alexander D Douglas
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher J A Duncan
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Katie J Ewer
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amy L Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Saul N Faust
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust; Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Shuo Feng
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Adam Finn
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Pedro M Folegatti
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle Fuskova
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eva Galiza
- St George's Vaccine Institute, St George's, University of London, London, UK
| | - Anna L Goodman
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, London, UK; MRC Clinical Trials Unit, University College London, London, UK
| | - Catherine M Green
- Clinical BioManufacturing Facility, University of Oxford, Oxford, UK
| | - Christopher A Green
- NIHR/Wellcome Trust Clinical Research Facility, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Melanie Greenland
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Bassam Hallis
- National Infection Service, Public Health England, Salisbury, UK
| | - Paul T Heath
- St George's Vaccine Institute, St George's, University of London, London, UK
| | - Jodie Hay
- University of Glasgow, Glasgow, UK; Lighthouse Laboratory in Glasgow, Queen Elizabeth University Hospital, Glasgow, UK
| | - Helen C Hill
- Department of Clinical Sciences, Liverpool School of Tropical Medicine and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Kerridge
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Vincenzo Libri
- NIHR UCLH Clinical Research Facility, London, UK; NIHR UCLH Biomedical Research Centre, London, UK
| | | | - Catherine Ludden
- COVID-19 Genomics UK, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Natalie G Marchevsky
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Angela M Minassian
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Yama F Mujadidi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel J Phillips
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Katrina M Pollock
- NIHR Imperial Clinical Research Facility, London, UK; NIHR Imperial Biomedical Research Centre, London, UK
| | - Hannah Robinson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Andrew Smith
- College of Medical, Veterinary & Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, Glasgow, UK
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Rebecca K Sutherland
- Clinical Infection Research Group, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Emma C Thomson
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK; Severn Pathology, North Bristol NHS Trust, Bristol, UK; Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Mark Toshner
- Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK; NIHR Cambridge Clinical Research Facility, Cambridge, UK; Cambridge University Hospital and Royal Papworth NHS Foundation Trusts, Cambridge, UK
| | - David P J Turner
- University of Nottingham, Nottingham, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK
| | | | | | | | - Adrian V S Hill
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Maheshi N Ramasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
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760
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.08.438911. [PMID: 33851164 PMCID: PMC8043454 DOI: 10.1101/2021.04.08.438911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and viral neutralization properties, which can be strongly enhanced with oligomerization. This repertoire samples the epitope landscape of the Spike ectodomain inside and outside the receptor binding domain, recognizing a multitude of distinct epitopes and revealing multiple neutralization targets of pseudoviruses and authentic SARS-CoV-2, including in primary human airway epithelial cells. Combinatorial nanobody mixtures show highly synergistic activities, and are resistant to mutational escape and emerging viral variants of concern. These nanobodies establish an exceptional resource for superior COVID-19 prophylactics and therapeutics.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Magda Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nicolas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sarah Keegan
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
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761
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Narayanan KK, Procko E. Deep Mutational Scanning of Viral Glycoproteins and Their Host Receptors. Front Mol Biosci 2021; 8:636660. [PMID: 33898517 PMCID: PMC8062978 DOI: 10.3389/fmolb.2021.636660] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
Deep mutational scanning or deep mutagenesis is a powerful tool for understanding the sequence diversity available to viruses for adaptation in a laboratory setting. It generally involves tracking an in vitro selection of protein sequence variants with deep sequencing to map mutational effects based on changes in sequence abundance. Coupled with any of a number of selection strategies, deep mutagenesis can explore the mutational diversity available to viral glycoproteins, which mediate critical roles in cell entry and are exposed to the humoral arm of the host immune response. Mutational landscapes of viral glycoproteins for host cell attachment and membrane fusion reveal extensive epistasis and potential escape mutations to neutralizing antibodies or other therapeutics, as well as aiding in the design of optimized immunogens for eliciting broadly protective immunity. While less explored, deep mutational scans of host receptors further assist in understanding virus-host protein interactions. Critical residues on the host receptors for engaging with viral spikes are readily identified and may help with structural modeling. Furthermore, mutations may be found for engineering soluble decoy receptors as neutralizing agents that specifically bind viral targets with tight affinity and limited potential for viral escape. By untangling the complexities of how sequence contributes to viral glycoprotein and host receptor interactions, deep mutational scanning is impacting ideas and strategies at multiple levels for combatting circulating and emergent virus strains.
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Affiliation(s)
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, United States
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762
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Wolf JM, Streck AF, Fonseca A, Ikuta N, Simon D, Lunge VR. Dissemination and evolution of SARS-CoV-2 in the early pandemic phase in South America. J Med Virol 2021; 93:4496-4507. [PMID: 33764553 PMCID: PMC8250755 DOI: 10.1002/jmv.26967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil with more than seven million cases of infection. Three major pandemic lineages/clades could be identified along with SARS-CoV-2 dissemination (G, GR, and GH) in the Americas. These clades differ according to their genomic characteristics, virulence, and spreading times. The present study describes the main clades and the respective temporal spreading analyses based on SARS-CoV-2 whole-genome sequences (WGS) from South America, obtained in the early pandemic phase (from March 1 to May 31 in 2020). SARS-CoV-2 WGSs with available information from country and year of sampling were obtained from different countries and the main clades were identified and analyzed independently with a Bayesian approach. The results demonstrated the prevalence of clades GR (n = 842; 54.6%), G (n = 529; 34.3%), and GH (n = 171; 11.1%). The frequencies of the clades were significantly different between South American countries. Clade G was the most prevalent in Ecuador, Suriname, and Uruguay, clade GR in Argentina, Brazil, and Peru, and clade GH in Colombia. The phylodynamic analysis indicated that all these main lineages increased viral spreading from February to early March and after an evolutionary stationary phase was observed. The decrease observed in the virus dissemination was directly associated to the reduction of social movement after March. In conclusion, these data demonstrated the current predominance of clades G, GR, and GH in South America because of the early dissemination of them in the first pandemic phase in South America.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - André Felipe Streck
- Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - André Fonseca
- Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Nilo Ikuta
- Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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763
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, di iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SP, Bloom JD, Corti D, Veesler D, Pizzuto MS. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.07.438818. [PMID: 33851169 PMCID: PMC8043460 DOI: 10.1101/2021.04.07.438818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2X259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2X259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2X259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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Affiliation(s)
- M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Michael A. Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | | | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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764
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Ikegame S, Siddiquey MNA, Hung CT, Haas G, Brambilla L, Oguntuyo KY, Kowdle S, Vilardo AE, Edelstein A, Perandones C, Kamil JP, Lee B. Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. RESEARCH SQUARE 2021:rs.3.rs-400230. [PMID: 33851150 PMCID: PMC8043464 DOI: 10.21203/rs.3.rs-400230/v1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The novel pandemic betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected at least 120 million people since its identification as the cause of a December 2019 viral pneumonia outbreak in Wuhan, China1,2. Despite the unprecedented pace of vaccine development, with six vaccines already in use worldwide, the emergence of SARS-CoV-2 'variants of concern' (VOC) across diverse geographic locales have prompted re-evaluation of strategies to achieve universal vaccination3. All three officially designated VOC carry Spike (S) polymorphisms thought to enable escape from neutralizing antibodies elicited during initial waves of the pandemic4-8. Here, we characterize the biological consequences of the ensemble of S mutations present in VOC lineages B.1.1.7 (501Y.V1) and B.1.351 (501Y.V2). Using a replication-competent EGFP-reporter vesicular stomatitis virus (VSV) system, rcVSV-CoV2-S, which encodes S from SARS coronavirus 2 in place of VSV-G, and coupled with a clonal HEK-293T ACE2 TMPRSS2 cell line optimized for highly efficient S-mediated infection, we determined that only 1 out of 12 serum samples from a cohort of recipients of the Gamaleya Sputnik V Ad26 / Ad5 vaccine showed effective neutralization (IC90) of rcVSV-CoV2-S: B.1.351 at full serum strength. The same set of sera efficiently neutralized S from B.1.1.7 and showed only moderately reduced activity against S carrying the E484K substitution alone. Taken together, our data suggest that control of some emergent SARS-CoV-2 variants may benefit from updated vaccines.
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Affiliation(s)
- Satoshi Ikegame
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mohammed N. A. Siddiquey
- Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA
| | - Chuan-Tien Hung
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Griffin Haas
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Luca Brambilla
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kasopefoluwa Y. Oguntuyo
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shreyas Kowdle
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariel Esteban Vilardo
- National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Alexis Edelstein
- National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Claudia Perandones
- National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA
| | - Benhur Lee
- Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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765
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Hurt AC, Wheatley AK. Neutralizing Antibody Therapeutics for COVID-19. Viruses 2021; 13:628. [PMID: 33916927 PMCID: PMC8067572 DOI: 10.3390/v13040628] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic has resulted in a significant global public health burden, leading to an urgent need for effective therapeutic strategies. In this article, we review the role of SARS-CoV-2 neutralizing antibodies (nAbs) in the clinical management of COVID-19 and provide an overview of recent randomized controlled trial data evaluating nAbs in the ambulatory, hospitalized and prophylaxis settings. Two nAb cocktails (casirivimab/imdevimab and bamlanivimab/etesevimab) and one nAb monotherapy (bamlanivimab) have been granted Emergency Use Authorization by the US Food and Drug Administration for the treatment of ambulatory patients who have a high risk of progressing to severe disease, and the European Medicines Agency has similarly recommended both cocktails and bamlanivimab monotherapy for use in COVID-19 patients who do not require supplemental oxygen and who are at high risk of progressing to severe COVID-19. Efficacy of nAbs in hospitalized patients with COVID-19 has been varied, potentially highlighting the challenges of antiviral treatment in patients who have already progressed to severe disease. However, early data suggest a promising prophylactic role for nAbs in providing effective COVID-19 protection. We also review the risk of treatment-emergent antiviral resistant "escape" mutants and strategies to minimize their occurrence, discuss the susceptibility of newly emerging SARS-COV-2 variants to nAbs, as well as explore administration challenges and ways to improve patient access.
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Affiliation(s)
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia;
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766
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Wang A, Chang SH, Kim EJ, Bessich JL, Sabari JK, Cooper B, Geraci TC, Cerfolio RJ. Dynamic Management of Lung Cancer Care During Surging COVID-19. Front Surg 2021; 8:663364. [PMID: 33898509 PMCID: PMC8059638 DOI: 10.3389/fsurg.2021.663364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 01/08/2023] Open
Abstract
Management of patients with lung cancer continues to be challenging during the COVID-19 pandemic, due to the increased risk of complications in this subset of patients. During the COVID-19 surge in New York City, New York University Langone Health adopted triage strategies to help with care for lung cancer patients, with good surgical outcomes and no transmission of COVID-19 to patients or healthcare workers. Here, we will review current recommendations regarding screening and management of lung cancer patients during both a non-surge phase and surge phase of COVID-19.
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Affiliation(s)
- Annie Wang
- Department of Surgery, New York University Langone Health, New York, NY, United States
| | - Stephanie H Chang
- Department of Cardiothoracic Surgery, New York University Langone Health, New York, NY, United States
| | - Eric J Kim
- New York University Grossman School of Medicine, New York, NY, United States
| | - Jamie L Bessich
- Department of Medicine, New York University Langone Health, New York, NY, United States
| | - Joshua K Sabari
- Department of Medicine, New York University Langone Health, New York, NY, United States
| | - Benjamin Cooper
- Department of Radiation Oncology, New York University Langone Health, New York, NY, United States
| | - Travis C Geraci
- Department of Cardiothoracic Surgery, New York University Langone Health, New York, NY, United States
| | - Robert J Cerfolio
- Department of Cardiothoracic Surgery, New York University Langone Health, New York, NY, United States
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767
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Karim SSA. Vaccines and SARS-CoV-2 variants: the urgent need for a correlate of protection. Lancet 2021; 397:1263-1264. [PMID: 33765410 PMCID: PMC7984864 DOI: 10.1016/s0140-6736(21)00468-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 01/12/2023]
Affiliation(s)
- Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban 4013, South Africa; Department of Epidemiology, Columbia University, New York, USA.
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768
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Salyer SJ, Maeda J, Sembuche S, Kebede Y, Tshangela A, Moussif M, Ihekweazu C, Mayet N, Abate E, Ouma AO, Nkengasong J. The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study. Lancet 2021; 397:1265-1275. [PMID: 33773118 PMCID: PMC8046510 DOI: 10.1016/s0140-6736(21)00632-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although the first wave of the COVID-19 pandemic progressed more slowly in Africa than the rest of the world, by December, 2020, the second wave appeared to be much more aggressive with many more cases. To date, the pandemic situation in all 55 African Union (AU) Member States has not been comprehensively reviewed. We aimed to evaluate reported COVID-19 epidemiology data to better understand the pandemic's progression in Africa. METHODS We did a cross-sectional analysis between Feb 14 and Dec 31, 2020, using COVID-19 epidemiological, testing, and mitigation strategy data reported by AU Member States to assess trends and identify the response and mitigation efforts at the country, regional, and continent levels. We did descriptive analyses on the variables of interest including cumulative and weekly incidence rates, case fatality ratios (CFRs), tests per case ratios, growth rates, and public health and social measures in place. FINDINGS As of Dec 31, 2020, African countries had reported 2 763 421 COVID-19 cases and 65 602 deaths, accounting for 3·4% of the 82 312 150 cases and 3·6% of the 1 798 994 deaths reported globally. Nine of the 55 countries accounted for more than 82·6% (2 283 613) of reported cases. 18 countries reported CFRs greater than the global CFR (2·2%). 17 countries reported test per case ratios less than the recommended ten to 30 tests per case ratio range. At the peak of the first wave in Africa in July, 2020, the mean daily number of new cases was 18 273. As of Dec 31, 2020, 40 (73%) countries had experienced or were experiencing their second wave of cases with the continent reporting a mean of 23 790 daily new cases for epidemiological week 53. 48 (96%) of 50 Member States had five or more stringent public health and social measures in place by April 15, 2020, but this number had decreased to 36 (72%) as of Dec 31, 2020, despite an increase in cases in the preceding month. INTERPRETATION Our analysis showed that the African continent had a more severe second wave of the COVID-19 pandemic than the first, and highlights the importance of examining multiple epidemiological variables down to the regional and country levels over time. These country-specific and regional results informed the implementation of continent-wide initiatives and supported equitable distribution of supplies and technical assistance. Monitoring and analysis of these data over time are essential for continued situational awareness, especially as Member States attempt to balance controlling COVID-19 transmission with ensuring stable economies and livelihoods. FUNDING None.
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Affiliation(s)
- Stephanie J Salyer
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia; Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Justin Maeda
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Senga Sembuche
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Yenew Kebede
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Akhona Tshangela
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | | | | | - Natalie Mayet
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ebba Abate
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ahmed Ogwell Ouma
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - John Nkengasong
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
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769
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Heinz FX, Stiasny K. Profiles of current COVID-19 vaccines. Wien Klin Wochenschr 2021; 133:271-283. [PMID: 33725201 PMCID: PMC7962631 DOI: 10.1007/s00508-021-01835-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Franz X Heinz
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria.
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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770
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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771
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Abstract
SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.
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772
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Cho H, Gonzales-Wartz KK, Huang D, Yuan M, Peterson M, Liang J, Beutler N, Torres JL, Cong Y, Postnikova E, Bangaru S, Talana CA, Shi W, Yang ES, Zhang Y, Leung K, Wang L, Peng L, Skinner J, Li S, Wu NC, Liu H, Dacon C, Moyer T, Cohen M, Zhao M, Lee FEH, Weinberg RS, Douagi I, Gross R, Schmaljohn C, Pegu A, Mascola JR, Holbrook M, Nemazee D, Rogers TF, Ward AB, Wilson IA, Crompton PD, Tan J. Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.01.437942. [PMID: 33821267 PMCID: PMC8020967 DOI: 10.1101/2021.04.01.437942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The emergence of SARS-CoV-2 variants that threaten the efficacy of existing vaccines and therapeutic antibodies underscores the urgent need for new antibody-based tools that potently neutralize variants by targeting multiple sites of the spike protein. We isolated 216 monoclonal antibodies targeting SARS-CoV-2 from plasmablasts and memory B cells of COVID-19 patients. The three most potent antibodies targeted distinct regions of the RBD, and all three neutralized the SARS-CoV-2 variants B.1.1.7 and B.1.351. The crystal structure of the most potent antibody, CV503, revealed that it binds to the ridge region of SARS-CoV-2 RBD, competes with the ACE2 receptor, and has limited contact with key variant residues K417, E484 and N501. We designed bispecific antibodies by combining non-overlapping specificities and identified five ultrapotent bispecific antibodies that inhibit authentic SARS-CoV-2 infection at concentrations of <1 ng/mL. Through a novel mode of action three bispecific antibodies cross-linked adjacent spike proteins using dual NTD/RBD specificities. One bispecific antibody was >100-fold more potent than a cocktail of its parent monoclonals in vitro and prevented clinical disease in a hamster model at a 2.5 mg/kg dose. Notably, six of nine bispecific antibodies neutralized B.1.1.7, B.1.351 and the wild-type virus with comparable potency, despite partial or complete loss of activity of at least one parent monoclonal antibody against B.1.351. Furthermore, a bispecific antibody that neutralized B.1.351 protected against SARS-CoV-2 expressing the crucial E484K mutation in the hamster model. Thus, bispecific antibodies represent a promising next-generation countermeasure against SARS-CoV-2 variants of concern.
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Affiliation(s)
- Hyeseon Cho
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kristina Kay Gonzales-Wartz
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Janie Liang
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Thomas Moyer
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - F. Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rona S. Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robin Gross
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- These authors jointly supervised the work
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
- These authors jointly supervised the work
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
- These authors jointly supervised the work
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773
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Eguia RT, Crawford KHD, Stevens-Ayers T, Kelnhofer-Millevolte L, Greninger AL, Englund JA, Boeckh MJ, Bloom JD. A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog 2021; 17:e1009453. [PMID: 33831132 PMCID: PMC8031418 DOI: 10.1371/journal.ppat.1009453] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these "future" viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.
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Affiliation(s)
- Rachel T. Eguia
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Katharine H. D. Crawford
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Terry Stevens-Ayers
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Alexander L. Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Michael J. Boeckh
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
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774
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Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, Planchais C, Buchrieser J, Rajah MM, Bishop E, Albert M, Donati F, Prot M, Behillil S, Enouf V, Maquart M, Smati-Lafarge M, Varon E, Schortgen F, Yahyaoui L, Gonzalez M, De Sèze J, Péré H, Veyer D, Sève A, Simon-Lorière E, Fafi-Kremer S, Stefic K, Mouquet H, Hocqueloux L, van der Werf S, Prazuck T, Schwartz O. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med 2021; 27:917-924. [PMID: 33772244 DOI: 10.1038/s41591-021-01318-5] [Citation(s) in RCA: 462] [Impact Index Per Article: 154.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 and B.1.351 variants were first identified in the United Kingdom and South Africa, respectively, and have since spread to many countries. These variants harboring diverse mutations in the gene encoding the spike protein raise important concerns about their immune evasion potential. Here, we isolated infectious B.1.1.7 and B.1.351 strains from acutely infected individuals. We examined sensitivity of the two variants to SARS-CoV-2 antibodies present in sera and nasal swabs from individuals infected with previously circulating strains or who were recently vaccinated, in comparison with a D614G reference virus. We utilized a new rapid neutralization assay, based on reporter cells that become positive for GFP after overnight infection. Sera from 58 convalescent individuals collected up to 9 months after symptoms, similarly neutralized B.1.1.7 and D614G. In contrast, after 9 months, convalescent sera had a mean sixfold reduction in neutralizing titers, and 40% of the samples lacked any activity against B.1.351. Sera from 19 individuals vaccinated twice with Pfizer Cominarty, longitudinally tested up to 6 weeks after vaccination, were similarly potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Neutralizing titers increased after the second vaccine dose, but remained 14-fold lower against B.1.351. In contrast, sera from convalescent or vaccinated individuals similarly bound the three spike proteins in a flow cytometry-based serological assay. Neutralizing antibodies were rarely detected in nasal swabs from vaccinees. Thus, faster-spreading SARS-CoV-2 variants acquired a partial resistance to neutralizing antibodies generated by natural infection or vaccination, which was most frequently detected in individuals with low antibody levels. Our results indicate that B1.351, but not B.1.1.7, may increase the risk of infection in immunized individuals.
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Affiliation(s)
- Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Ludivine Grzelak
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Florence Guivel-Benhassine
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Isabelle Staropoli
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Françoise Porrot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Julian Buchrieser
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France
| | - Maaran Michael Rajah
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Elodie Bishop
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Créteil, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Mélanie Albert
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569, Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Flora Donati
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569, Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
| | - Sylvie Behillil
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569, Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569, Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Maria Gonzalez
- CHU de Strasbourg, Service de Pathologie Professionnelle et Médecine du Travail, Strasbourg, France
| | - Jérôme De Sèze
- Centre d'investigation Clinique INSERM 1434, CHU Strasbourg, France.,CHU de Strasbourg, Service de Neurologie, Strasbourg, France
| | - Hélène Péré
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | - David Veyer
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France.,Hôpital Européen Georges Pompidou, Service de Virologie, Paris, France
| | - Aymeric Sève
- CHR d'Orléans, Service de maladies infectieuses, Orléans, France
| | | | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Karl Stefic
- INSERM U1259, Université de Tours, Tours, France.,CHRU de Tours, National Reference Center for HIV-Associated laboratory, Tours, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | | | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569, Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Thierry Prazuck
- CHR d'Orléans, Service de maladies infectieuses, Orléans, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France. .,CNRS UMR 3569, Paris, France. .,Vaccine Research Institute, Créteil, France.
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775
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Stamatatos L, Czartoski J, Wan YH, Homad LJ, Rubin V, Glantz H, Neradilek M, Seydoux E, Jennewein MF, MacCamy AJ, Feng J, Mize G, De Rosa SC, Finzi A, Lemos MP, Cohen KW, Moodie Z, McElrath MJ, McGuire AT. mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. Science 2021; 372:eabg9175. [PMID: 33766944 PMCID: PMC8139425 DOI: 10.1126/science.abg9175] [Citation(s) in RCA: 381] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022]
Abstract
Emerging SARS-CoV-2 variants have raised concerns about resistance to neutralizing antibodies elicited by previous infection or vaccination. We examined whether sera from recovered and naïve donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization. Immunization of naïve donors also elicited cross-neutralizing responses, but at lower titers. Our study highlights the importance of vaccinating both uninfected and previously infected persons to elicit cross-variant neutralizing antibodies.
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Affiliation(s)
- Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Julie Czartoski
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Vanessa Rubin
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Hayley Glantz
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Moni Neradilek
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Gregory Mize
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Stephen C De Rosa
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Maria P Lemos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Kristen W Cohen
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Zoe Moodie
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - M Juliana McElrath
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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776
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Zhou H, Dcosta BM, Samanovic MI, Mulligan MJ, Landau NR, Tada T. B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33791698 DOI: 10.1101/2021.03.24.436620] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA sequence analysis recently identified the novel SARS-CoV-2 variant B.1.526 that is spreading at an alarming rate in the New York City area. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein together with four novel point mutations and with an E484K or S477N mutation in the receptor binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. We report that convalescent sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer as compared to D614G. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody but the combination cocktail with REGN10987 was fully active. The findings suggest that current vaccines and therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of wide-spread vaccination.
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777
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Rees-Spear C, Muir L, Griffith SA, Heaney J, Aldon Y, Snitselaar JL, Thomas P, Graham C, Seow J, Lee N, Rosa A, Roustan C, Houlihan CF, Sanders RW, Gupta RK, Cherepanov P, Stauss HJ, Nastouli E, Doores KJ, van Gils MJ, McCoy LE. The effect of spike mutations on SARS-CoV-2 neutralization. Cell Rep 2021; 34:108890. [PMID: 33713594 PMCID: PMC7936541 DOI: 10.1016/j.celrep.2021.108890] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines show protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, spike. Because new SARS-CoV-2 variants are emerging rapidly, as exemplified by the B.1.1.7, B.1.351, and P.1 lineages, it is critical to understand whether antibody responses induced by infection with the original SARS-CoV-2 virus or current vaccines remain effective. In this study, we evaluate neutralization of a series of mutated spike pseudotypes based on divergence from SARS-CoV and then compare neutralization of the B.1.1.7 spike pseudotype and individual mutations. Spike-specific monoclonal antibody neutralization is reduced dramatically; in contrast, polyclonal antibodies from individuals infected in early 2020 remain active against most mutated spike pseudotypes, but potency is reduced in a minority of samples. This work highlights that changes in SARS-CoV-2 spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their effect on vaccine efficacy.
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Affiliation(s)
- Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Sarah A Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Judith Heaney
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK
| | - Yoann Aldon
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Peter Thomas
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Carl Graham
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Jeffrey Seow
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Nayung Lee
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | | | | | - Catherine F Houlihan
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; Research Department of Infection, Division of Infection and Immunity, University College London, London WC1 6BT, UK
| | - Rogier W Sanders
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Hans J Stauss
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Eleni Nastouli
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; The Francis Crick Institute, London NW1 1AT, UK; Great Ormond Street Institute for Child Health, Infection, Immunity and Inflammation, University College London, London WC1N 1EH, UK
| | - Katie J Doores
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Marit J van Gils
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK.
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778
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Abstract
In the year since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and with understanding of the etiology of the coronavirus disease 2019 (COVID-19) pandemic, it has become clear that most infected individuals achieve some form of immunity against the virus with relatively few reported reinfections. A number of vaccines have already achieved emergency use authorization based on data from large phase 3 field efficacy clinical trials. However, our knowledge about the extent and durability of this immunity, and the breadth of vaccine coverage against SARS-CoV-2 variants is still evolving. In this narrative review, we summarize the latest and rapidly developing understanding of immunity to SARS-CoV-2 infection, including what we have learned about the key antigens of SARS-CoV-2 (i.e., the spike protein and its receptor-binding domain), their importance in vaccine development, the immediate immune response to SARS-CoV-2, breadth of coverage of emerging SARS-CoV-2 variants, contributions of preexisting immunity to related coronaviruses, and duration of immunity. We also discuss lessons from newer approaches, such as systems serology, that provide insights into molecular and cellular immune responses elicited and how they relate to the trajectory of infection, and potentially inform immune correlates of protection. We also briefly examine the limited research literature on immune responses in special populations, such as pregnant women and children.
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Affiliation(s)
- Jaime Fergie
- Department of Pediatric Infectious Diseases, Driscoll Children's Hospital, Corpus Christi, TX, United States
| | - Amit Srivastava
- Vaccine Medical Development, Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, United States
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779
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Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, Gaebler C, Cho A, Agudelo M, Finkin S, Wang Z, Poston D, Muecksch F, Hatziioannou T, Bieniasz PD, Robbiani DF, Nussenzweig MC, Bjorkman PJ, Bloom JD. Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.17.435863. [PMID: 33758856 PMCID: PMC7987015 DOI: 10.1101/2021.03.17.435863] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasma, including plasma from individuals from whom some of the antibodies were isolated. The plasma-escape maps most closely resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is dominated by a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D. Bieniasz
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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780
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Alrubayyi A, Gea-Mallorquí E, Touizer E, Hameiri-Bowen D, Kopycinski J, Charlton B, Fisher-Pearson N, Muir L, Rosa A, Roustan C, Earl C, Cherepanov P, Pellegrino P, Waters L, Burns F, Kinloch S, Dong T, Dorrell L, Rowland-Jones S, McCoy LE, Peppa D. Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV. RESEARCH SQUARE 2021:rs.3.rs-309746. [PMID: 33758833 PMCID: PMC7987102 DOI: 10.21203/rs.3.rs-309746/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
There is an urgent need to understand the nature of immune responses against SARS-CoV-2, to inform risk-mitigation strategies for people living with HIV (PLWH). We show that the majority of PLWH, controlled on ART, mount a functional adaptive immune response to SARS-CoV-2. Humoral and SARS-CoV-2-specific T cell responses are comparable between HIV-positive and negative subjects and persist 5-7 months following predominately mild COVID-19 disease. T cell responses against Spike, Membrane and Nucleocapsid are the most prominent, with SARS-CoV-2-specific CD4 T cells outnumbering CD8 T cells. We further show that the overall magnitude of SARS-CoV-2-specific T cell responses relates to the size of the naive CD4 T cell pool and the CD4:CD8 ratio in PLWH, in whom disparate antibody and T cell responses are observed. These findings suggest that inadequate immune reconstitution on ART, could hinder immune responses to SARS-CoV-2 with implications for the individual management and vaccine effectiveness in PLWH.
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Affiliation(s)
| | | | - Emma Touizer
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Dan Hameiri-Bowen
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
| | - Jakub Kopycinski
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
| | - Bethany Charlton
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
| | | | - Luke Muir
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Chloe Roustan
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Christopher Earl
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Pierre Pellegrino
- Mortimer Market Centre, Department of HIV, CNWL NHS Trust, London, United Kingdom
| | - Laura Waters
- Mortimer Market Centre, Department of HIV, CNWL NHS Trust, London, United Kingdom
| | - Fiona Burns
- Institute for Global Health UCL, London, United Kingdom
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sabine Kinloch
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Tao Dong
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
| | - Lucy Dorrell
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
| | | | - Laura E. McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Dimitra Peppa
- Nuffield Dept of Clinical Medicine, University of Oxford, United Kingdom
- Mortimer Market Centre, Department of HIV, CNWL NHS Trust, London, United Kingdom
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781
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Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, O'Hagan DT, Van Der Most R, Van Voorhis WC, McLellan JS, Kleanthous H, Sheahan TP, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric R, King N, Veesler D. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.15.435528. [PMID: 33758839 PMCID: PMC7986998 DOI: 10.1101/2021.03.15.435528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the ability of SARS-CoV-2 vaccine-elicited antibodies to neutralize and protect against emerging variants of concern and other sarbecoviruses is key for guiding vaccine development decisions and public health policies. We show that a clinical stage multivalent SARS-CoV-2 receptor-binding domain nanoparticle vaccine (SARS-CoV-2 RBD-NP) protects mice from SARS-CoV-2-induced disease after a single shot, indicating that the vaccine could allow dose-sparing. SARS-CoV-2 RBD-NP elicits high antibody titers in two non-human primate (NHP) models against multiple distinct RBD antigenic sites known to be recognized by neutralizing antibodies. We benchmarked NHP serum neutralizing activity elicited by RBD-NP against a lead prefusion-stabilized SARS-CoV-2 spike immunogen using a panel of single-residue spike mutants detected in clinical isolates as well as the B.1.1.7 and B.1.351 variants of concern. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. We demonstrate that mosaic and cocktail sarbecovirus RBD-NPs elicit broad sarbecovirus neutralizing activity, including against the SARS-CoV-2 B.1.351 variant, and protect mice against severe SARS-CoV challenge even in the absence of the SARS-CoV RBD in the vaccine. This study provides proof of principle that sarbecovirus RBD-NPs induce heterotypic protection and enables advancement of broadly protective sarbecovirus vaccines to the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Allison Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Megan A O'Connor
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lisa Shireff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Douglas E Ferrell
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tyler Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | - Wesley C Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Deborah H Fuller
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Jesse Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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782
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Gómez CE, Perdiguero B, Esteban M. Emerging SARS-CoV-2 Variants and Impact in Global Vaccination Programs against SARS-CoV-2/COVID-19. Vaccines (Basel) 2021; 9:243. [PMID: 33799505 PMCID: PMC7999234 DOI: 10.3390/vaccines9030243] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in different continents is causing a major concern in human global health. These variants have in common a higher transmissibility, becoming dominant within populations in a short time, and an accumulation of a high number of mutations in the spike (S) protein, especially within the amino terminal domain (NTD) and the receptor binding domain (RBD). These mutations have direct implications on virus infection rates through higher affinity of S RBD for the cellular angiotensin-converting enzyme-2 (ACE-2) receptor. There are also signs of enhanced virulence, re-infection frequency, and increased resistance to the action of monoclonal and polyclonal antibodies from convalescence sera and in vaccinated individuals in regions where the variants spread dominantly. In this review, we describe the different SARS-CoV-2 variants that have thus far been identified in various parts of the world with mutational changes and biological properties as well as their impact in medical countermeasures and human health.
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Affiliation(s)
- Carmen Elena Gómez
- Centro Nacional de Biotecnología, Department of Molecular and Cellular Biology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | | | - Mariano Esteban
- Centro Nacional de Biotecnología, Department of Molecular and Cellular Biology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
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783
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Sun D, Sang Z, Kim YJ, Xiang Y, Cohen T, Belford AK, Huet A, Conway JF, Sun J, Taylor DJ, Schneidman-Duhovny D, Zhang C, Huang W, Shi Y. Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.09.434592. [PMID: 33758850 PMCID: PMC7987009 DOI: 10.1101/2021.03.09.434592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.
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Affiliation(s)
- Dapeng Sun
- Department of Pharmacology and Chemical Biology, University of Pittsburgh
| | - Zhe Sang
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, PA, USA
| | - Yong Joon Kim
- Department of Cell Biology, University of Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, PA, USA
| | - Tomer Cohen
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh
| | | | - Ji Sun
- Department of Structure Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Derek J. Taylor
- Department of Pharmacology, Case Western Reserve University, Clevaland, OH, USA
- Department of Biochemistry, Case Western Reserve University, Clevaland, OH, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Clevaland, OH, USA
| | - Yi Shi
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
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784
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Stamatatos L, Czartoski J, Wan YH, Homad LJ, Rubin V, Glantz H, Neradilek M, Seydoux E, Jennewein MF, MacCamy AJ, Feng J, Mize G, De Rosa SC, Finzi A, Lemos MP, Cohen KW, Moodie Z, McElrath MJ, McGuire AT. A single mRNA immunization boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.05.21251182. [PMID: 33758873 PMCID: PMC7987032 DOI: 10.1101/2021.02.05.21251182] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging SARS-CoV-2 variants have raised concerns about resistance to neutralizing antibodies elicited by previous infection or vaccination. We examined whether sera from recovered and naive donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization. Immunization of naïve donors also elicited cross-neutralizing responses, but at lower titers. Our study highlights the importance of vaccinating both uninfected and previously infected persons to elicit cross-variant neutralizing antibodies.
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Affiliation(s)
- Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Julie Czartoski
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J. Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Vanessa Rubin
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Hayley Glantz
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Moni Neradilek
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F. Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J. MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Gregory Mize
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Stephen C. De Rosa
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Maria P. Lemos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Kristen W. Cohen
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Zoe Moodie
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - M. Juliana McElrath
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew T. McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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785
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Santiago L, Uranga-Murillo I, Arias M, González-Ramírez AM, Macías-León J, Moreo E, Redrado S, García-García A, Taleb V, Lira-Navarrete E, Hurtado-Guerrero R, Aguilo N, del Mar Encabo-Berzosa M, Hidalgo S, Galvez EM, Ramirez-Labrada A, de Miguel D, Benito R, Miranda P, Fernández A, Domingo JM, Serrano L, Yuste C, Villanueva-Saz S, Paño-Pardo JR, Pardo J. Determination of the Concentration of IgG against the Spike Receptor-Binding Domain That Predicts the Viral Neutralizing Activity of Convalescent Plasma and Serum against SARS-CoV-2. BIOLOGY 2021; 10:208. [PMID: 33801808 PMCID: PMC8001978 DOI: 10.3390/biology10030208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/01/2021] [Accepted: 03/06/2021] [Indexed: 12/22/2022]
Abstract
Several hundred millions of people have been diagnosed of coronavirus disease 2019 (COVID-19), causing millions of deaths and a high socioeconomic burden. SARS-CoV-2, the causative agent of COVID-19, induces both specific T- and B-cell responses, being antibodies against the virus detected a few days after infection. Passive immunization with hyperimmune plasma from convalescent patients has been proposed as a potentially useful treatment for COVID-19. Using an in-house quantitative ELISA test, we found that plasma from 177 convalescent donors contained IgG antibodies specific to the spike receptor-binding domain (RBD) of SARS-CoV-2, although at very different concentrations which correlated with previous disease severity and gender. Anti-RBD IgG plasma concentrations significantly correlated with the plasma viral neutralizing activity (VN) against SARS-CoV-2 in vitro. Similar results were found using an independent cohort of serum from 168 convalescent health workers. These results validate an in-house RBD IgG ELISA test in a large cohort of COVID-19 convalescent patients and indicate that plasma from all convalescent donors does not contain a high enough amount of anti-SARS-CoV-2-RBD neutralizing IgG to prevent SARS-CoV-2 infection in vitro. The use of quantitative anti-RBD IgG detection systems might help to predict the efficacy of the passive immunization using plasma from patients recovered from SARS-CoV-2.
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Affiliation(s)
- Llipsy Santiago
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Iratxe Uranga-Murillo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Maykel Arias
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Andrés Manuel González-Ramírez
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Javier Macías-León
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Eduardo Moreo
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
| | - Sergio Redrado
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Ana García-García
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Víctor Taleb
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Erandi Lira-Navarrete
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
| | - Ramón Hurtado-Guerrero
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain; (A.M.G.-R.); (J.M.-L.); (A.G.-G.); (V.T.); (E.L.-N.); (R.H.-G.)
- Aragon I+D Foundation (ARAID), 50018 Zaragoza, Spain
- Laboratorio de Microscopías Avanzada (LMA), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Nacho Aguilo
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
| | | | - Sandra Hidalgo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Eva M. Galvez
- Instituto de Carboquímica (ICB), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain; (M.A.); (S.R.); (E.M.G.)
| | - Ariel Ramirez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain;
| | - Diego de Miguel
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
| | - Rafael Benito
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
- Servicio de Microbiología, Hospital Clinico Universitario Lozano Blesa, 50009 Zaragoza, Spain
| | - Patricia Miranda
- Banco de Sangre y Tejidos de Aragón, 50009 Zaragoza, Spain; (P.M.); (J.M.D.)
| | - Antonio Fernández
- Department Animal Pathology, University of Zaragoza, 50013 Zaragoza, Spain;
| | - José María Domingo
- Banco de Sangre y Tejidos de Aragón, 50009 Zaragoza, Spain; (P.M.); (J.M.D.)
| | - Laura Serrano
- Servicio de Prevención de Riesgos Laborales, Hospital Clínico Universitario Lozano Blesa, 50009 Zaragoza, Spain; (L.S.); (C.Y.)
| | - Cristina Yuste
- Servicio de Prevención de Riesgos Laborales, Hospital Clínico Universitario Lozano Blesa, 50009 Zaragoza, Spain; (L.S.); (C.Y.)
| | - Sergio Villanueva-Saz
- Department Pharmacology and Physiology, University of Zaragoza, 50013 Zaragoza, Spain;
| | - José Ramón Paño-Pardo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Servicio de Enfermedades Infecciosas, Hospital Clinico Universitario Lozano Blesa, 50009 Zaragoza, Spain
| | - Julián Pardo
- Biomedical Research Centre of Aragón (CIBA), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; (L.S.); (I.U.-M.); (S.H.); (D.d.M.); (R.B.)
- Department Microbiology, Preventive Medicine and Public Health, University of Zaragoza, 50009 Zaragoza, Spain; (E.M.); (N.A.)
- Aragon I+D Foundation (ARAID), 50018 Zaragoza, Spain
- Centro de Investigación Biomédicaen Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 50018 Madrid, Spain
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786
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van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.09.434529. [PMID: 33758859 PMCID: PMC7987018 DOI: 10.1101/2021.03.09.434529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.
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Affiliation(s)
- Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Sara E Vazquez
- Medical Scientist Training Program, University of California. San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - George C Hartoularos
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tianna Grant
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Raymund Bueno
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - David S Lee
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
| | - John R Greenland
- Department of Medicine, San Francisco VA Health Care System, University of California, San Francisco, CA, USA
| | - Yang Sun
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anton Ogorodnikov
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Alyssa Ward
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kara L Lynch
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Cassandra Yun
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Diane V Havlir
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Carina Marquez
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Philip J Norris
- Zuckerberg San Francisco General, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Larry J Dumont
- Vitalant Research Institute, Denver, CO, USA
- University of Colorado School of Medicine, Aurora, CO, USA
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | | | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tom Le Voyer
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Alexander Whatley
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Yichen Si
- Department of Biostaticstics, University of Michigan
| | | | - Alexis J Combes
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Arjun Arkal Rao
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Yun S Song
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Gabriela K Fragiadakis
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Kirsten Kangelaris
- Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - David J Erle
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Carolyn Hendrickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Matthew F Krummel
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G Woodruff
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Joseph L Derisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, CA, USA
- Endocrine Division, Department of Medicine, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Departments of Epidemiology and Biostatistics, Bioengineering and Therapeutic Sciences
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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787
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Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 2021; 29:463-476.e6. [PMID: 33592168 PMCID: PMC7869748 DOI: 10.1016/j.chom.2021.02.003] [Citation(s) in RCA: 809] [Impact Index Per Article: 269.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent plasma antibodies are impacted by all mutations to the spike's receptor-binding domain (RBD), the main target of plasma neutralizing activity. Binding by polyclonal plasma antibodies is affected by mutations in three main epitopes in the RBD, but longitudinal samples reveal that the impact of these mutations on antibody binding varies substantially both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD's receptor-binding motif. The most important site is E484, where neutralization by some plasma is reduced >10-fold by several mutations, including one in the emerging 20H/501Y.V2 and 20J/501Y.V3 SARS-CoV-2 lineages. Going forward, these plasma escape maps can inform surveillance of SARS-CoV-2 evolution.
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MESH Headings
- Adult
- Aged
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Binding Sites
- COVID-19/virology
- Cell Line
- Female
- Humans
- Male
- Middle Aged
- Mutation
- Prospective Studies
- Protein Binding
- Protein Domains
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Young Adult
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Keara D Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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788
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Singh J, Samal J, Kumar V, Sharma J, Agrawal U, Ehtesham NZ, Sundar D, Rahman SA, Hira S, Hasnain SE. Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Viruses 2021; 13:439. [PMID: 33803400 PMCID: PMC8000172 DOI: 10.3390/v13030439] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.
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Affiliation(s)
- Jasdeep Singh
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India;
| | - Jasmine Samal
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
| | - Jyoti Sharma
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Usha Agrawal
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Nasreen Z. Ehtesham
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
| | - Syed Asad Rahman
- BioInception Pvt. Ltd., Swift House Ground Floor, 18 Hoffmanns Way, Chelmsford, Essex CM1 1GU, UK
| | - Subhash Hira
- Department of Global Health, University of Washington-Seattle, Seattle, WA 98195, USA
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
- Dr Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500049, India
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789
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Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 2021; 592:438-443. [PMID: 33690265 DOI: 10.1038/s41586-021-03402-9] [Citation(s) in RCA: 1083] [Impact Index Per Article: 361.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.
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790
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Kumar GR, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Lareau LF, Frankino PA, Shivram H, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.07.21252647. [PMID: 33758899 PMCID: PMC7987058 DOI: 10.1101/2021.03.07.21252647] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Mir M Khalid
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Mary Kate Morris
- California Department of Public Health, Richmond, California, USA
| | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California San Francisco, California, USA
| | - Jing Cheng
- Department of Medicine, University of California San Francisco, California, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - G Renuka Kumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Taha Y Taha
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Jennifer Hayashi
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Camille R Simoneau
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Sarah McMahon
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Nicole M Green
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, California, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, California, USA
| | - Monica Haw
- California Department of Public Health, Richmond, California, USA
| | - John Bell
- California Department of Public Health, Richmond, California, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, California, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, California, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, California, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, California, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, California, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
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791
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Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ 2021; 372:n579. [PMID: 33687922 PMCID: PMC7941603 DOI: 10.1136/bmj.n579] [Citation(s) in RCA: 464] [Impact Index Per Article: 154.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To establish whether there is any change in mortality from infection with a new variant of SARS-CoV-2, designated a variant of concern (VOC-202012/1) in December 2020, compared with circulating SARS-CoV-2 variants. DESIGN Matched cohort study. SETTING Community based (pillar 2) covid-19 testing centres in the UK using the TaqPath assay (a proxy measure of VOC-202012/1 infection). PARTICIPANTS 54 906 matched pairs of participants who tested positive for SARS-CoV-2 in pillar 2 between 1 October 2020 and 29 January 2021, followed-up until 12 February 2021. Participants were matched on age, sex, ethnicity, index of multiple deprivation, lower tier local authority region, and sample date of positive specimens, and differed only by detectability of the spike protein gene using the TaqPath assay. MAIN OUTCOME MEASURE Death within 28 days of the first positive SARS-CoV-2 test result. RESULTS The mortality hazard ratio associated with infection with VOC-202012/1 compared with infection with previously circulating variants was 1.64 (95% confidence interval 1.32 to 2.04) in patients who tested positive for covid-19 in the community. In this comparatively low risk group, this represents an increase in deaths from 2.5 to 4.1 per 1000 detected cases. CONCLUSIONS The probability that the risk of mortality is increased by infection with VOC-202012/01 is high. If this finding is generalisable to other populations, infection with VOC-202012/1 has the potential to cause substantial additional mortality compared with previously circulating variants. Healthcare capacity planning and national and international control policies are all impacted by this finding, with increased mortality lending weight to the argument that further coordinated and stringent measures are justified to reduce deaths from SARS-CoV-2.
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Affiliation(s)
- Robert Challen
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- Somerset NHS Foundation Trust, Taunton, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
| | - Ellen Brooks-Pollock
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- University of Bristol, Bristol Veterinary School, Langford, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Jonathan M Read
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- Lancaster Medical School, Lancaster University, Bailrigg, Lancaster, UK
| | - Louise Dyson
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry, UK
| | - Krasimira Tsaneva-Atanasova
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- The Alan Turing Institute, British Library, London, UK
| | - Leon Danon
- Joint Universities Pandemic and Epidemiological Research (JUNIPER consortium)
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- The Alan Turing Institute, British Library, London, UK
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
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792
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Muecksch F, Weisblum Y, Barnes CO, Schmidt F, Schaefer-Babajew D, Lorenzi JCC, Flyak AI, DeLaitsch AT, Huey-Tubman KE, Hou S, Schiffer CA, Gaebler C, Wang Z, Da Silva J, Poston D, Finkin S, Cho A, Cipolla M, Oliveira TY, Millard KG, Ramos V, Gazumyan A, Rutkowska M, Caskey M, Nussenzweig MC, Bjorkman PJ, Hatziioannou T, Bieniasz PD. Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.07.434227. [PMID: 33758864 PMCID: PMC7987023 DOI: 10.1101/2021.03.07.434227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G. Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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793
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Human Vaccines & Immunotherapeutics: news. Hum Vaccin Immunother 2021; 17:618-619. [PMID: 33734943 DOI: 10.1080/21645515.2021.1894892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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794
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S. Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.26.21252554. [PMID: 33688664 PMCID: PMC7941639 DOI: 10.1101/2021.02.26.21252554] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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Affiliation(s)
- Nuno R. Faria
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Thomas A. Mellan
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Charles Whittaker
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S. Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Swapnil Mishra
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C. Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucas A. M. Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S. Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M. Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A. M. Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S. Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M. Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M. de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C. de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J. T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J. Laydon
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | | | | | | | | | | | | | - Renato S. Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L. P. Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A. Hay
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Melodie Monod
- Department of Mathematics, Imperial College London, UK
| | | | - Helen Coupland
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Raphael Sonabend
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Michaela Vollmer
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, UK
| | - Marc A. Suchard
- Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergei L. K. Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | | | - Neil M. Ferguson
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | - Nick J. Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A. Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P. S. S. Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Samir Bhatt
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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795
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Grabowski F, Preibisch G, Giziński S, Kochańczyk M, Lipniacki T. SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Viruses 2021; 13:392. [PMID: 33804556 PMCID: PMC8000749 DOI: 10.3390/v13030392] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/24/2022] Open
Abstract
The novel SARS-CoV-2 Variant of Concern (VOC)-202012/01 (also known as B.1.1.7), first collected in United Kingdom on 20 September 2020, is a rapidly growing lineage that in January 2021 constituted 86% of all SARS-CoV-2 genomes sequenced in England. The VOC has been detected in 40 out of 46 countries that reported at least 50 genomes in January 2021. We have estimated that the replicative advantage of the VOC is in the range 1.83-2.18 [95% CI: 1.71-2.40] with respect to the 20A.EU1 variant that dominated in England in November 2020, and in range 1.65-1.72 [95% CI: 1.46-2.04] in Wales, Scotland, Denmark, and USA. As the VOC strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. We have estimated growth rates of expanding mutations acquired by the VOC lineage to find that the L18F substitution in spike has initiated a fast growing VOC substrain. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies. Of concern are immune escape mutations acquired by the VOC: E484K, F490S, S494P (in the receptor binding motif of spike) and Q677H, Q675H (in the proximity of the polybasic cleavage site at the S1/S2 boundary). These mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence.
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Affiliation(s)
- Frederic Grabowski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Grzegorz Preibisch
- Inter-Faculty Individual Studies in Mathematics and Natural Sciences, The MISMaP College, University of Warsaw, 02-097 Warsaw, Poland;
| | - Stanisław Giziński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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796
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Wang L, Zhou T, Zhang Y, Yang ES, Schramm CA, Shi W, Pegu A, Oloninyi OK, Ransier A, Darko S, Narpala SR, Hatcher C, Martinez DR, Tsybovsky Y, Phung E, Abiona OM, Cale EM, Chang LA, Corbett KS, DiPiazza AT, Gordon IJ, Leung K, Liu T, Mason RD, Nazzari A, Novik L, Olia AS, Doria-Rose NA, Stephens T, Stringham CD, Talana CA, Teng IT, Wagner D, Widge AT, Zhang B, Roederer M, Ledgerwood JE, Ruckwardt TJ, Gaudinski MR, Baric RS, Graham BS, McDermott AB, Douek DC, Kwong PD, Mascola JR, Sullivan NJ, Misasi J. Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.25.432969. [PMID: 33655252 PMCID: PMC7924272 DOI: 10.1101/2021.02.25.432969] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 μ g/mL; IC80 < 0.0006 to 0.0251 μ g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.
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Affiliation(s)
- Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olamide K. Oloninyi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep R. Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Hatcher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R. Martinez
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olubukola M. Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan M. Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren A. Chang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S. Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony T. DiPiazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosemarie D. Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alicia T. Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie E. Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ralph S. Baric
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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797
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Tarke A, Sidney J, Methot N, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, da Silva Antunes R, Frazier A, Rawlings SA, Smith DM, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. Negligible impact of SARS-CoV-2 variants on CD4 + and CD8 + T cell reactivity in COVID-19 exposed donors and vaccinees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.27.433180. [PMID: 33688655 PMCID: PMC7941626 DOI: 10.1101/2021.02.27.433180] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of SARS-CoV-2 variants highlighted the need to better understand adaptive immune responses to this virus. It is important to address whether also CD4+ and CD8+ T cell responses are affected, because of the role they play in disease resolution and modulation of COVID-19 disease severity. Here we performed a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. Similarly, we demonstrate that the sequences of the vast majority of SARS-CoV-2 T cell epitopes are not affected by the mutations found in the variants analyzed. Overall, the results demonstrate that CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations found in the SARS-CoV-2 variants.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California, San Diego, CA 92093
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
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798
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Case JB, Chen RE, Cao L, Ying B, Winkler ES, Goreshnik I, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS. Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.01.433110. [PMID: 33688650 PMCID: PMC7941621 DOI: 10.1101/2021.03.01.433110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite the introduction of public health measures and spike protein-based vaccines to mitigate the COVID-19 pandemic, SARS-CoV-2 infections and deaths continue to rise. Previously, we used a structural design approach to develop picomolar range miniproteins targeting the SARS-CoV-2 receptor binding domain. Here, we investigated the capacity of modified versions of one lead binder, LCB1, to protect against SARS-CoV-2-mediated lung disease in human ACE2-expressing transgenic mice. Systemic administration of LCB1-Fc reduced viral burden, diminished immune cell infiltration and inflammation, and completely prevented lung disease and pathology. A single intranasal dose of LCB1v1.3 reduced SARS-CoV-2 infection in the lung even when given as many as five days before or two days after virus inoculation. Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions. These data support development of LCB1v1.3 for prevention or treatment of SARS-CoV-2 infection.
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Emma S. Winkler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
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799
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Richman DD. COVID-19 vaccines: implementation, limitations and opportunities. Glob Health Med 2021; 3:1-5. [PMID: 33688588 PMCID: PMC7936373 DOI: 10.35772/ghm.2021.01010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
The speed of development and the magnitude of efficacy of recently developed vaccines directed against SARS-CoV-2 has been truly remarkable. This editorial will not summarize the highly publicized and reviewed information about the design and clinical trial results of these vaccines. Rather, I will speculate about several issues regarding i) considerations of the rollout and implementation of the multiple vaccines, ii) the use of the vaccines in ways different from those used in the registrational phase 3 studies, iii) the future both of SARS-CoV-2 in the human population and of "normal" human life returning after widespread vaccination, and iv) the implications of the success of these SARS-CoV-2 vaccines for vaccine development against other pathogens.
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Affiliation(s)
- Douglas D. Richman
- University of California San Diego, Distinguished Professor of Pathology and Medicine (Active Emeritus); Director, The HIV Institute; Co- Director, San Diego Center for AIDS Research; Florence Seeley Riford Emeritus Chair in AIDS Research, CA, USA
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800
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Sakharkar M, Rappazzo CG, Wieland-Alter WF, Hsieh CL, Wrapp D, Esterman ES, Kaku CI, Wec AZ, Geoghegan JC, McLellan JS, Connor RI, Wright PF, Walker LM. Prolonged evolution of the human B cell response to SARS-CoV-2 infection. Sci Immunol 2021; 6:eabg6916. [PMID: 33622975 PMCID: PMC8128290 DOI: 10.1126/sciimmunol.abg6916] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/11/2022]
Abstract
A comprehensive understanding of the kinetics and evolution of the human B cell response to SARS-CoV-2 infection will facilitate the development of next-generation vaccines and therapies. Here, we longitudinally profiled this response in mild and severe COVID-19 patients over a period of five months. Serum neutralizing antibody (nAb) responses waned rapidly but spike (S)-specific IgG+ memory B cells (MBCs) remained stable or increased over time. Analysis of 1,213 monoclonal antibodies (mAbs) isolated from S-specific MBCs revealed a primarily de novo response that displayed increased somatic hypermutation, binding affinity, and neutralization potency over time, providing evidence for prolonged antibody affinity maturation. B cell immunodominance hierarchies were similar across donor repertoires and remained relatively stable as the immune response progressed. Cross-reactive B cell populations, likely re-called from prior endemic beta-coronavirus exposures, comprised a small but stable fraction of the repertoires and did not contribute to the neutralizing response. The neutralizing antibody response was dominated by public clonotypes that displayed significantly reduced activity against SARS-CoV-2 variants emerging in Brazil and South Africa that harbor mutations at positions 501, 484 and 417 in the S protein. Overall, the results provide insight into the dynamics, durability, and functional properties of the human B cell response to SARS-CoV-2 infection and have implications for the design of immunogens that preferentially stimulate protective B cell responses.
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Affiliation(s)
| | | | - Wendy F Wieland-Alter
- Division of Infectious Disease and International Health, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ruth I Connor
- Division of Infectious Disease and International Health, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Peter F Wright
- Division of Infectious Disease and International Health, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Laura M Walker
- Adimab LLC, Lebanon, NH 03766, USA.
- Adagio Therapeutics, Inc., Waltham, MA 02451, USA
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