1
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Benlarbi M, Ding S, Bélanger É, Tauzin A, Poujol R, Medjahed H, El Ferri O, Bo Y, Bourassa C, Hussin J, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio 2024; 15:e0090724. [PMID: 38953636 PMCID: PMC11323525 DOI: 10.1128/mbio.00907-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants' Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.IMPORTANCEThe persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants' transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.
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Affiliation(s)
- Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Étienne Bélanger
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | | | - Omar El Ferri
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
- Mila—Quebec AI institute, Montreal, Quebec, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cameron Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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2
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Li K, Liu Q, Wu Y, Wu B, Chen S, Zhang X, Jia X, Gong R, Peng Y, Zhang H, Chiu S. A bivalent Delta/BA.5 mRNA vaccine elicits broad immune responses against various lineages of SARS-CoV-2 including JN.1. Virol Sin 2024:S1995-820X(24)00117-2. [PMID: 39127113 DOI: 10.1016/j.virs.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 08/06/2024] [Indexed: 08/12/2024] Open
Affiliation(s)
- Kangyin Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Liu
- Liverna Therapeutics Inc., Zhuhai, 519000, China
| | - Yan Wu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China
| | - Bihao Wu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohong Chen
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinghai Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China
| | - Xiaoying Jia
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China
| | - Rui Gong
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China
| | - Yucai Peng
- Liverna Therapeutics Inc., Zhuhai, 519000, China.
| | - Huajun Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430062, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Department of Laboratory Medicine, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, China.
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3
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Mühlemann B, Trimpert J, Walper F, Schmidt ML, Jansen J, Schroeder S, Jeworowski LM, Beheim-Schwarzbach J, Bleicker T, Niemeyer D, Richter A, Adler JM, Vidal RM, Langner C, Vladimirova D, Wilks SH, Smith DJ, Voß M, Paltzow L, Martínez Christophersen C, Rose R, Krumbholz A, Jones TC, Corman VM, Drosten C. Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants. Proc Natl Acad Sci U S A 2024; 121:e2310917121. [PMID: 39078681 PMCID: PMC11317614 DOI: 10.1073/pnas.2310917121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Felix Walper
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Marie L. Schmidt
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jenny Jansen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Simon Schroeder
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Julia M. Adler
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | | | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Lea Paltzow
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | | | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | - Terry C. Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Victor M. Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin13353, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
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4
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Mandolesi M, Das H, de Vries L, Yang Y, Kim C, Dhinakaran M, Castro Dopico X, Fischbach J, Kim S, Guryleva MV, Àdori M, Chernyshev M, Stålmarck A, Hanke L, McInerney GM, Sheward DJ, Corcoran M, Hällberg BM, Murrell B, Karlsson Hedestam GB. Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques. Nat Commun 2024; 15:6338. [PMID: 39068149 PMCID: PMC11283548 DOI: 10.1038/s41467-024-50286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Macaca mulatta
- Antibodies, Neutralizing/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- B-Lymphocytes/immunology
- Antibodies, Viral/immunology
- Phylogeny
- Antibodies, Monoclonal/immunology
- Epitopes/immunology
- COVID-19/immunology
- COVID-19/virology
- Humans
- COVID-19 Vaccines/immunology
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/genetics
- Somatic Hypermutation, Immunoglobulin
- Immunization
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Affiliation(s)
- Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Liset de Vries
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yiqiu Yang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Manojj Dhinakaran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mariia V Guryleva
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- 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
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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5
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Lopes R, Pham K, Klaassen F, Chitwood MH, Hahn AM, Redmond S, Swartwood NA, Salomon JA, Menzies NA, Cohen T, Grubaugh ND. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Rep 2024; 43:114451. [PMID: 38970788 DOI: 10.1016/j.celrep.2024.114451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/03/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Omicron surged as a variant of concern in late 2021. Several distinct Omicron variants appeared and overtook each other. We combined variant frequencies and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population before it was replaced by BA.2. We estimate that BA.5 infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other variants-BA.2, BA.4, and XBB-together infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability and a negative correlation between the BA.1 and BA.2 attack rates. Our findings illustrate the complex interplay between viral evolution, population susceptibility, and social factors during the Omicron emergence in the US.
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Affiliation(s)
- Rafael Lopes
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Fayette Klaassen
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Seth Redmond
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Nicole A Swartwood
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Joshua A Salomon
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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6
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Guselnikov SV, Baranov KO, Kulemzin SV, Belovezhets TN, Chikaev AN, Murasheva SV, Volkova OY, Mechetina LV, Najakshin AM, Chikaev NA, Solodkov PP, Sergeeva MV, Smirnov AV, Serova IA, Serov OL, Markhaev AG, Kononova YV, Alekseev AY, Gulyaeva MA, Danilenko DM, Battulin NR, Shestopalov AM, Taranin AV. A potent, broadly neutralizing human monoclonal antibody that efficiently protects hACE2-transgenic mice from infection with the Wuhan, BA.5, and XBB.1.5 SARS-CoV-2 variants. Front Immunol 2024; 15:1442160. [PMID: 39100673 PMCID: PMC11294225 DOI: 10.3389/fimmu.2024.1442160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
The COVID-19 pandemic has uncovered the high genetic variability of the SARS-CoV-2 virus and its ability to evade the immune responses that were induced by earlier viral variants. Only a few monoclonal antibodies that have been reported to date are capable of neutralizing a broad spectrum of SARS-CoV-2 variants. Here, we report the isolation of a new broadly neutralizing human monoclonal antibody, iC1. The antibody was identified through sorting the SARS-CoV-1 RBD-stained individual B cells that were isolated from the blood of a vaccinated donor following a breakthrough infection. In vitro, iC1 potently neutralizes pseudoviruses expressing a wide range of SARS-CoV-2 Spike variants, including those of the XBB sublineage. In an hACE2-transgenic mouse model, iC1 provided effective protection against the Wuhan strain of the virus as well as the BA.5 and XBB.1.5 variants. Therefore, iC1 can be considered as a potential component of the broadly neutralizing antibody cocktails resisting the SARS-CoV-2 mutation escape.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- Humans
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- Mice, Transgenic
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Mice
- Antibodies, Viral/immunology
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Pandemics/prevention & control
- Betacoronavirus/immunology
- Betacoronavirus/genetics
- Broadly Neutralizing Antibodies/immunology
- Disease Models, Animal
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- Pneumonia, Viral/prevention & control
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus Infections/prevention & control
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Affiliation(s)
- Sergey V. Guselnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Konstantin O. Baranov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V. Kulemzin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana N. Belovezhets
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anton N. Chikaev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana V. Murasheva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Y. Volkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ludmila V. Mechetina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander M. Najakshin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai A. Chikaev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel P. Solodkov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maria V. Sergeeva
- Department of Vaccinology, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Alexander V. Smirnov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina A. Serova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg L. Serov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander G. Markhaev
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Yulia V. Kononova
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Alexander Y. Alekseev
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Marina A. Gulyaeva
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Daria M. Danilenko
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Nariman R. Battulin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander M. Shestopalov
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander V. Taranin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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7
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Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H. Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. iScience 2024; 27:110354. [PMID: 39071888 PMCID: PMC11277385 DOI: 10.1016/j.isci.2024.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Timothée Bruel
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Pierre Rosenbaum
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
| | - Françoise Porrot
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Delphine Planas
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Olivier Schwartz
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
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8
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Figgins MD, Asarnow D, Stewart C, Lee J, Logue J, Bedford T, Murrell B, Chu HY, Veesler D, Bloom JD. Spike deep mutational scanning helps predict success of SARS-CoV-2 clades. Nature 2024; 631:617-626. [PMID: 38961298 PMCID: PMC11254757 DOI: 10.1038/s41586-024-07636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion1 and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and cell entry2,3. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning4 to measure how more than 9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully affected ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456 and 473; however, the antigenic effects of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however, many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marlin D Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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9
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Brudenell EL, Pohare MB, Zafred D, Phipps J, Hornsby HR, Darby JF, Dai J, Liggett E, Cain KM, Barran PE, de Silva TI, Sayers JR. Efficient overexpression and purification of severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins in Escherichia coli. Biochem J 2024; 481:669-682. [PMID: 38713013 DOI: 10.1042/bcj20240019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
The fundamental biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.
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Affiliation(s)
- Emma L Brudenell
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Manoj B Pohare
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Domen Zafred
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Janine Phipps
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Hailey R Hornsby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - John F Darby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Junxiao Dai
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Ellen Liggett
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Kathleen M Cain
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Thushan I de Silva
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Jon R Sayers
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
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10
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Xiong D, Zhang X, Xu B, Shi M, Chen M, Dong Z, Zhong J, Gong R, Wu C, Li J, Wei H, Yu J. PHDtools: A platform for pathogen detection and multi-dimensional genetic signatures decoding to realize pathogen genomics data analyses online. Gene 2024; 909:148306. [PMID: 38408616 DOI: 10.1016/j.gene.2024.148306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
OBJECTIVES Facing the emerging diseases, rapid identification of the pathogen and multi-dimensional characterization of the genomic features at both isolate-level and population-level through high-throughput sequencing data can provide invaluable information to guide the development of antiviral agents and strategies. However, a user-friendly program is in urgent need for clinical laboratories without bioinformatics background to decode the complex big genomics data. METHODS In this study, we developed an interactive online platform named PHDtools with a total of 15 functions to analyze metagenomics data to identify the potential pathogen and decode multi-dimensional genetic signatures including intra-/inter-host variations and lineage-level variations. The platform was applied to analyze the meta-genomic data of the samples collected from the 172 imported COVID-19 cases. RESULTS According to the analytical results of mNGS, 27 patients were found to have the co-infections of SARS-CoV-2 with either influenza virus (n = 9) or human picobirnavirus (n = 19). Enough coverages of all the assembled SARS-CoV-2 genomes provided the sub-lineages of Omicron variant, and the number of mutations in the non-structural genes and M gene was increased, as well as the intra-host variations occurred in E and M gene were under positive selection (Ka/Ks > 1). These findings of increased or changed mutations in the SARS-CoV-2 genome characterized the current adaptive evolution patterns of Omicron sub-lineages, and revealed the evolution speed of these sub-lineages might increase. CONCLUSIONS Consequently, the application of PHDtools has proved that this platform is accurate, user-friendly and convenient for clinical users who are deficient in bioinformatics, and the clinical monitor of SARS-CoV-2 genomes by PHDtools also highlighted the potential evolution features of current SARS-CoV-2 and indicated that the development of anti-SARS-CoV-2 agents and new-designed vaccines should incorporate the gene variations other than S gene.
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Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bohan Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjuan Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Dong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Jie Zhong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Rui Gong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Chang Wu
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Ji Li
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Zhang X, Lam SJA, Ip JD, Fong CHY, Chu AWH, Chan WM, Lai YSY, Tsoi HW, Chan BPC, Chen LL, Meng X, Yuan S, Zhao H, Cheng VCC, Yuen JKY, Yuen KY, Zhou J, To KKW. Characterizing fitness and immune escape of SARS-CoV-2 EG.5 sublineage using elderly serum and nasal organoid. iScience 2024; 27:109706. [PMID: 38660398 PMCID: PMC11039328 DOI: 10.1016/j.isci.2024.109706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/23/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024] Open
Abstract
SARS-CoV-2 Omicron variant has evolved into sublineages. Here, we compared the neutralization susceptibility and viral fitness of EG.5.1 and XBB.1.9.1. Serum neutralization antibody titer against EG.5.1 was 1.71-fold lower than that for XBB.1.9.1. However, there was no significant difference in virus replication between EG.5.1 and XBB.1.9.1 in human nasal organoids and TMPRSS2/ACE2 over-expressing A549 cells. No significant difference was observed in competitive fitness and cytokine/chemokine response between EG.5.1 and XBB.1.9.1. Both EG.5.1 and XBB.1.9.1 replicated more robustly in the nasal organoid from a younger adult than that from an older adult. Our findings suggest that enhanced immune escape contributes to the dominance of EG.5.1 over earlier sublineages. The combination of population serum susceptibility testing and viral fitness evaluation with nasal organoids may hold promise in risk assessment of upcoming variants. Utilization of serum specimens and nasal organoid derived from older adults provides a targeted risk assessment for this vulnerable population.
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Affiliation(s)
- Xiaojuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Stephanie Joy-Ann Lam
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Carol Ho-Yan Fong
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yoyo Suet-Yiu Lai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Hoi-Wah Tsoi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Xinjie Meng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Hanjun Zhao
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jacqueline Kwan Yuk Yuen
- Division of Geriatric Medicine, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jie Zhou
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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12
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Feng S, Reid GE, Clark NM, Harrington A, Uprichard SL, Baker SC. Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies. Virol J 2024; 21:105. [PMID: 38715113 PMCID: PMC11075269 DOI: 10.1186/s12985-024-02378-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. RESULTS We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. CONCLUSIONS Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Gail E Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Nina M Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan L Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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13
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Ogger PP, Martín MG, Jang S, Zhou J, Brown J, Sukhova K, Furnon W, Patel AH, Cowton V, Palmarini M, Barclay WS, Johansson C. SARS-CoV-2 strains bearing Omicron BA.1 spike replicate in C57BL/6 mice. Front Immunol 2024; 15:1383612. [PMID: 38742107 PMCID: PMC11089223 DOI: 10.3389/fimmu.2024.1383612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction SARS-CoV-2, the cause of the COVID pandemic, is an RNA virus with a high propensity to mutate. Successive virus variants, including variants of concern (VOC), have emerged with increased transmission or immune escape. The original pandemic virus and early variants replicated poorly, if at all, in mice at least partly due to a mismatch between the receptor binding domain on the viral spike protein and the murine angiotensin converting enzyme 2 (ACE2). Omicron VOC emerged in late 2021 harboring > 50 new mutations, 35 of them in the spike protein. This variant resulted in a very large wave of infections, even in the face of prior immunity, albeit being inherently less severe than earlier variants. Reflecting the lower severity reported in humans, Omicron displayed attenuated infection in hamsters and also in the K18-hACE2 mouse model. K18-hACE2 mice express both the human ACE2 as well as the endogenous mouse ACE2. Methods Here we infected hACE2 knock-in mice that express only human ACE2 and no murine ACE2, or C57BL/6 wildtype mice with SARS-CoV-2 D614G (first-wave isolate), Delta or Omicron BA.1 variants and assessed infectivity and downstream innate immune responses. Results While replication of SARS-CoV-2 Omicron was lower in the lungs of hACE2 knock-in mice compared with SARS-CoV-2 D614G and VOC Delta, it replicated more efficiently than the earlier variants in C57BL/6 wildtype mice. This opens the opportunity to test the effect of host genetics on SARS-CoV-2 infections in wildtype mice. As a proof of principle, we tested Omicron infection in mice lacking expression of the interferon-alpha receptor-1 (IFNAR1). In these mice we found that loss of type I IFN receptor signaling resulted in higher viral loads in the lungs were detected. Finally, using a chimeric virus of first wave SARS-CoV-2 harboring the Omicron spike protein, we show that Omicron spike increase infection of C57BL/6 wildtype mice, but non-spike genes of Omicron confer attenuation of viral replication. Discussion Since this chimeric virus efficiently infected C57BL/6 wildtype mice, and replicated in their lungs, our findings illustrate a pathway for genetic mapping of virushost interactions during SARS-CoV-2 infection.
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Affiliation(s)
- Patricia P. Ogger
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Minerva Garcia Martín
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Soyeon Jang
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jonathan Brown
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Cecilia Johansson
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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14
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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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15
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de Rioja VL, Basile L, Perramon-Malavez A, Martínez-Solanas É, López D, Medina Maestro S, Coma E, Fina F, Prats C, Mendioroz Peña J, Alvarez-Lacalle E. Severity of Omicron Subvariants and Vaccine Impact in Catalonia, Spain. Vaccines (Basel) 2024; 12:466. [PMID: 38793717 PMCID: PMC11125683 DOI: 10.3390/vaccines12050466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
In the current COVID-19 landscape dominated by Omicron subvariants, understanding the timing and efficacy of vaccination against emergent lineages is crucial for planning future vaccination campaigns, yet detailed studies stratified by subvariant, vaccination timing, and age groups are scarce. This retrospective study analyzed COVID-19 cases from December 2021 to January 2023 in Catalonia, Spain, focusing on vulnerable populations affected by variants BA.1, BA.2, BA.5, and BQ.1 and including two national booster campaigns. Our database includes detailed information such as dates of diagnosis, hospitalization and death, last vaccination, and cause of death, among others. We evaluated the impact of vaccination on disease severity by age, variant, and vaccination status, finding that recent vaccination significantly mitigated severity across all Omicron subvariants, although efficacy waned six months post-vaccination, except for BQ.1, which showed more stable levels. Unvaccinated individuals had higher hospitalization and mortality rates. Our results highlight the importance of periodic vaccination to reduce severe outcomes, which are influenced by variant and vaccination timing. Although the seasonality of COVID-19 is uncertain, our analysis suggests the potential benefit of annual vaccination in populations >60 years old, probably in early fall, if COVID-19 eventually exhibits a major peak similar to other respiratory viruses.
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Affiliation(s)
- Víctor López de Rioja
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Luca Basile
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
| | - Aida Perramon-Malavez
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | | | - Daniel López
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Sergio Medina Maestro
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
| | - Ermengol Coma
- Primary Care Services Information System (SISAP), Institut Català de la Salut, 08007 Barcelona, Spain; (E.C.)
| | - Francesc Fina
- Primary Care Services Information System (SISAP), Institut Català de la Salut, 08007 Barcelona, Spain; (E.C.)
| | - Clara Prats
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Jacobo Mendioroz Peña
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
- University of Vic—Central University of Catalonia (UVic-UCC), 08500 Vic, Spain
| | - Enric Alvarez-Lacalle
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
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16
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Tonon E, Cecchetto R, Diani E, Medaina N, Turri G, Lagni A, Lotti V, Gibellini D. Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy. Microorganisms 2024; 12:846. [PMID: 38792676 PMCID: PMC11124265 DOI: 10.3390/microorganisms12050846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.
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Affiliation(s)
- Emil Tonon
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Riccardo Cecchetto
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Erica Diani
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Nicoletta Medaina
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Giona Turri
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Anna Lagni
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
| | - Virginia Lotti
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
| | - Davide Gibellini
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
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17
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Rusi E, Pennacchia F, Ruqa WA, Zingaropoli MA, Pasculli P, Talarico G, Bruno G, Barbato C, Minni A, Tarani L, Galardo G, Pugliese F, Lucarelli M, Ciardi MR, Meucci L, Ferraguti G, Fiore M. Blood Count and Renal Functionality Assessments in the Emergency Section Disclose Morbidity and Mortality in Omicron COVID-19 Patients: A Retrospective Study. Clin Pract 2024; 14:685-702. [PMID: 38804387 PMCID: PMC11130961 DOI: 10.3390/clinpract14030055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/09/2024] [Accepted: 04/21/2024] [Indexed: 05/29/2024] Open
Abstract
Background: SARS-CoV-2 is the coronavirus responsible for the COVID-19 pandemic. Even though we are no longer in a pandemic situation, people are still getting infected, some of them need hospitalization and a few of them die. Methods: We conducted a retrospective study including 445 patients who accessed the Emergency Section of Policlinico Umberto I, Rome, Italy, where they had routine blood exams. In this study, we focused on the complete blood count, serum creatinine and azotemia. The data were analyzed using ANOVA, Spearman correlation and ROC analyses. They were divided into four groups based on their clinical outcomes: (1) the emergency group (patients who had mild forms and were quickly discharged); (2) the hospital ward group (patients who were admitted to the emergency section and were then hospitalized in a COVID-19 ward); (3) the intensive care unit (ICU) group (patients who required intensive assistance after the admission in the emergency section); (4) the deceased group (patients who had a fatal outcome after admission to the emergency section). Results: We found significant changes for creatinine, azotemia, hematocrit, mean corpuscular hemoglobin concentration, basophils, monocytes, red blood cell distribution width, hemoglobin, hematocrit and red blood cell numbers using ANOVA according to their clinical outcomes, particularly for the deceased group. Also, we found linear correlations of clinical outcomes with eosinophils, hemoglobin, hematocrit, mean corpuscular hemoglobin concentration, lymphocyte, neutrophil, platelet and red blood cell number and red blood cell distribution width. Conclusions: This study discloses an early association between "classical" routine blood biomarkers and the severity of clinical outcomes in Omicron patients.
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Affiliation(s)
- Eqrem Rusi
- Department of Human Neuroscience, Sapienza University of Rome, 00185 Rome, Italy
| | - Fiorenza Pennacchia
- Department of Sensory Organs, Sapienza University of Rome, 00185 Rome, Italy
| | - Wael Abu Ruqa
- Department of Sensory Organs, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Patrizia Pasculli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Giuseppina Talarico
- Department of Human Neuroscience, Sapienza University of Rome, 00185 Rome, Italy
| | - Giuseppe Bruno
- Department of Human Neuroscience, Sapienza University of Rome, 00185 Rome, Italy
| | - Christian Barbato
- Institute of Biochemistry and Cell Biology (IBBC-CNR), c/o Department of Sensory Organs, Sapienza University of Rome, 00185 Rome, Italy
| | - Antonio Minni
- Department of Sensory Organs, Sapienza University of Rome, 00185 Rome, Italy
- Division of Otolaryngology-Head and Neck Surgery, ASL Rieti-Sapienza University, Ospedale San Camillo de Lellis, 02100 Rieti, Italy
| | - Luigi Tarani
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Francesco Pugliese
- Department of Anesthesiology Critical Care Medicine and Pain Therapy, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Maria Rosa Ciardi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Luigi Meucci
- Directorate Social and Welfare Statistics, ISTAT, 00184 Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Fiore
- Institute of Biochemistry and Cell Biology (IBBC-CNR), c/o Department of Sensory Organs, Sapienza University of Rome, 00185 Rome, Italy
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18
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Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun 2024; 15:3284. [PMID: 38627386 PMCID: PMC11021415 DOI: 10.1038/s41467-024-47393-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Raksha Das
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Alexander J Mentzer
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
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19
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Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. Int J Mol Sci 2024; 25:4281. [PMID: 38673865 PMCID: PMC11049863 DOI: 10.3390/ijms25084281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we performed a computational study of binding mechanisms for the SARS-CoV-2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class one antibodies. The central objective of this investigation was to examine the molecular factors underlying epistatic couplings among convergent evolution hotspots that enable optimal balancing of ACE2 binding and antibody evasion for Omicron variants BA.1, BA2, BA.3, BA.4/BA.5, BQ.1.1, XBB.1, XBB.1.5, and XBB.1.5 + L455F/F456L. By combining evolutionary analysis, molecular dynamics simulations, and ensemble-based mutational scanning of spike protein residues in complexes with ACE2, we identified structural stability and binding affinity hotspots that are consistent with the results of biochemical studies. In agreement with the results of deep mutational scanning experiments, our quantitative analysis correctly reproduced strong and variant-specific epistatic effects in the XBB.1.5 and BA.2 variants. It was shown that Y453W and F456L mutations can enhance ACE2 binding when coupled with Q493 in XBB.1.5, while these mutations become destabilized when coupled with the R493 position in the BA.2 variant. The results provided a molecular rationale of the epistatic mechanism in Omicron variants, showing a central role of the Q493/R493 hotspot in modulating epistatic couplings between convergent mutational sites L455F and F456L in XBB lineages. The results of mutational scanning and binding analysis of the Omicron XBB spike variants with ACE2 receptors and a panel of class one antibodies provide a quantitative rationale for the experimental evidence that epistatic interactions of the physically proximal binding hotspots Y501, R498, Q493, L455F, and F456L can determine strong ACE2 binding, while convergent mutational sites F456L and F486P are instrumental in mediating broad antibody resistance. The study supports a mechanism in which the impact on ACE2 binding affinity is mediated through a small group of universal binding hotspots, while the effect of immune evasion could be more variant-dependent and modulated by convergent mutational sites in the conformationally adaptable spike regions.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. J Chem Inf Model 2024; 64:1657-1681. [PMID: 38373700 DOI: 10.1021/acs.jcim.3c01857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The latest wave of SARS-CoV-2 Omicron variants displayed a growth advantage and increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with atomistic simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both the structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that the AlphaFold2-predicted structural ensemble of the BA.2.86 spike protein complex with ACE2 can accurately capture the main conformational states of the Omicron variant. Complementary to AlphaFold2 structural predictions, microsecond molecular dynamics simulations reveal the details of the conformational landscape and produced equilibrium ensembles of the BA.2.86 structures that are used to perform mutational scanning of spike residues and characterize structural stability and binding energy hotspots. The ensemble-based mutational profiling of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 revealed a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 convergent mutational hotspots R403K, F486P, and R493Q. To examine the immune evasion properties of BA.2.86 in atomistic detail, we performed structure-based mutational profiling of the spike protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against the BA.2.86 variant. The results revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have evolved to outcompete other Omicron subvariants by improving immune evasion while preserving binding affinity with ACE2 via through a compensatory effect of R493Q and F486P convergent mutational hotspots. This study demonstrated that an integrative approach combining AlphaFold2 predictions with complementary atomistic molecular dynamics simulations and robust ensemble-based mutational profiling of spike residues can enable accurate and comprehensive characterization of structure, dynamics, and binding mechanisms of newly emerging Omicron variants.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States of America
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Liu P, Cai J, Tian H, Li J, Lu L, Xu M, Zhu X, Zhong H, Jia R, Fu X, Wang X, Ge Y, Zhu Y, Zeng M, Xu J. Intra-host genetic diversity of SARS-CoV-2 Omicron variants in children. J Infect 2024; 88:106132. [PMID: 38431154 DOI: 10.1016/j.jinf.2024.106132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Affiliation(s)
- Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Jiehao Cai
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - He Tian
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Jingjing Li
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xunhua Zhu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xiaomin Fu
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xiangshi Wang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yanling Ge
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yanfeng Zhu
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Mei Zeng
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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Powers JM, Leist SR, Mallory ML, Yount BL, Gully KL, Zweigart MR, Bailey AB, Sheahan TP, Harkema JR, Baric RS. Divergent pathogenetic outcomes in BALB/c mice following Omicron subvariant infection. Virus Res 2024; 341:199319. [PMID: 38224840 PMCID: PMC10835285 DOI: 10.1016/j.virusres.2024.199319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Following the emergence of B.1.1.529 Omicron, the SARS-CoV-2 virus evolved into a significant number of sublineage variants that possessed numerous mutations throughout the genome, but particularly within the spike glycoprotein (S) gene. For example, the BQ.1.1 and the XBB.1 and XBB.1.5 subvariants contained 34 and 41 mutations in S, respectively. However, these variants elicited largely replication only or mild disease phenotypes in mice. To better model pathogenic outcomes and measure countermeasure performance, we developed mouse adapted versions (BQ.1.1 MA; XBB.1 MA; XBB.1.5 MA) that reflect more pathogenic acute phase pulmonary disease symptoms of SARS-CoV-2, as well as derivative strains expressing nano-luciferase (nLuc) in place of ORF7 (BQ.1.1 nLuc; XBB.1 nLuc; XBB.1.5 nLuc). Amongst the mouse adapted (MA) viruses, a wide range of disease outcomes were observed including mortality, weight loss, lung dysfunction, and tissue viral loads in the lung and nasal turbinates. Intriguingly, XBB.1 MA and XBB.1.5 MA strains, which contained identical mutations throughout except at position F486S/P in S, exhibited divergent disease outcomes in mice (Ao et al., 2023). XBB.1.5 MA infection was associated with significant weight loss and ∼45 % mortality across two independent studies, while XBB.1 MA infected animals suffered from mild weight loss and only 10 % mortality across the same two independent studies. Additionally, the development and use of nanoluciferase expressing strains provided moderate throughput for live virus neutralization assays. The availability of small animal models for the assessment of Omicron VOC disease potential will enable refined capacity to evaluate the efficacy of on market and pre-clinical therapeutics and interventions.
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Affiliation(s)
- John M Powers
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Sarah R Leist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael L Mallory
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Boyd L Yount
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kendra L Gully
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark R Zweigart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alexis B Bailey
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy P Sheahan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jack R Harkema
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Nesamari R, Omondi MA, Baguma R, Höft MA, Ngomti A, Nkayi AA, Besethi AS, Magugu SFJ, Mosala P, Walters A, Clark GM, Mennen M, Skelem S, Adriaanse M, Grifoni A, Sette A, Keeton RS, Ntusi NAB, Riou C, Burgers WA. Post-pandemic memory T cell response to SARS-CoV-2 is durable, broadly targeted, and cross-reactive to the hypermutated BA.2.86 variant. Cell Host Microbe 2024; 32:162-169.e3. [PMID: 38211583 PMCID: PMC10901529 DOI: 10.1016/j.chom.2023.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has given rise to recombinant Omicron lineages that dominate globally (XBB.1), as well as the emergence of hypermutated variants (BA.2.86). In this context, durable and cross-reactive T cell immune memory is critical for continued protection against severe COVID-19. We examined T cell responses to SARS-CoV-2 approximately 1.5 years since Omicron first emerged. We describe sustained CD4+ and CD8+ spike-specific T cell memory responses in healthcare workers in South Africa (n = 39) who were vaccinated and experienced at least one SARS-CoV-2 infection. Spike-specific T cells are highly cross-reactive with all Omicron variants tested, including BA.2.86. Abundant nucleocapsid and membrane-specific T cells are detectable in most participants. The bulk of SARS-CoV-2-specific T cell responses have an early-differentiated phenotype, explaining their persistent nature. Overall, hybrid immunity leads to the accumulation of spike and non-spike T cells evident 3.5 years after the start of the pandemic, with preserved recognition of highly mutated SARS-CoV-2 variants.
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Affiliation(s)
- Rofhiwa Nesamari
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Millicent A Omondi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Anathi A Nkayi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Asiphe S Besethi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Siyabulela F J Magugu
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Paballo Mosala
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gesina M Clark
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Alba Grifoni
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A B Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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24
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Gupta DL, Meher J, Giri AK, Shukla AK, Mohapatra E, Ruikar MM, Rao DN. RBD mutations at the residues K417, E484, N501 reduced immunoreactivity with antisera from vaccinated and COVID-19 recovered patients. Drug Target Insights 2024; 18:20-26. [PMID: 38860262 PMCID: PMC11163369 DOI: 10.33393/dti.2024.3059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
Introduction It is unclear whether induced spike protein-specific antibodies due to infections with SARS-CoV-2 or to the prototypic Wuhan isolate-based vaccination can immune-react with the emerging variants of SARS-CoV-2. Aim/objectives The main objective of the study was to measure the immunoreactivity of induced antibodies postvaccination with Covishield™ (ChAdOx1 nCoV-19 coronavirus vaccines) or infections with SARS-CoV-2 by using selected peptides of the spike protein of wild type and variants of SARS-CoV-2. Methodology Thirty patients who had recovered from SARS-CoV-2 infections and 30 individuals vaccinated with both doses of Covishield™ were recruited for the study. Venous blood samples (5 mL) were collected at a single time point from patients within 3-4 weeks of recovery from SARS-CoV-2 infections or receiving both doses of Covishield™ vaccines. The serum levels of total immunoglobulin were measured in both study groups. A total of 12 peptides of 10 to 24 amino acids length spanning to the receptor-binding domain (RBD) of wild type of SARS-CoV-2 and their variants were synthesized. The serum levels of immune-reactive antibodies were measured using these peptides. Results The serum levels of total antibodies were found to be significantly (p<0.001) higher in the vaccinated individuals as compared to COVID-19 recovered patients. Our study reported that the mutations in the RBD at the residues K417, E484, and N501 have been associated with reduced immunoreactivity with anti-sera of vaccinated people and COVID-19 recovered patients. Conclusion The amino acid substitutions at the RBD of SARS-CoV-2 have been associated with a higher potential to escape the humoral immune response.
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Affiliation(s)
- Dablu Lal Gupta
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - Jhasketan Meher
- Department of General Medicine, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - Anjan Kumar Giri
- Department of Community and Family Medicine, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - Arvind K Shukla
- Department of Community Medicine, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - Eli Mohapatra
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - Manisha M Ruikar
- Department of Community Medicine, All India Institute of Medical Sciences (AIIMS), Raipur, Chhattisgarh - India
| | - DN Rao
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi - India
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25
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Jeworowski LM, Mühlemann B, Walper F, Schmidt ML, Jansen J, Krumbholz A, Simon-Lorière E, Jones TC, Corman VM, Drosten C. Humoral immune escape by current SARS-CoV-2 variants BA.2.86 and JN.1, December 2023. Euro Surveill 2024; 29:2300740. [PMID: 38214083 PMCID: PMC10785204 DOI: 10.2807/1560-7917.es.2024.29.2.2300740] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
Variant BA.2.86 and its descendant, JN.1, of SARS-CoV-2 are rising in incidence across Europe and globally. We isolated recent JN.1, BA.2.86, EG.5, XBB.1.5 and earlier variants. We tested live virus neutralisation of sera taken in September 2023 from vaccinated and exposed healthy persons (n = 39). We found clear neutralisation escape against recent variants but no specific pronounced escape for BA.2.86 or JN.1. Neutralisation escape corresponds to recent variant predominance but may not be causative of the recent upsurge in JN.1 incidence.
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Affiliation(s)
- Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- These authors contributed equally to the work and share the first authorship
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, Berlin, Germany
- These authors contributed equally to the work and share the first authorship
| | - Felix Walper
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Marie L Schmidt
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Laboratory Dr. Krause und Kollegen MVZ GmbH, Kiel, Germany
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
- National Reference Center for Viruses of Respiratory Infections, Institut Pasteur, Paris, France
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- These authors contributed equally to the work and share the last authorship
- German Centre for Infection Research (DZIF), partner site Charité, Berlin, Germany
- Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- These authors contributed equally to the work and share the last authorship
- German Centre for Infection Research (DZIF), partner site Charité, Berlin, Germany
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26
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571185. [PMID: 38168257 PMCID: PMC10760024 DOI: 10.1101/2023.12.11.571185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In this study, we combined AI-based atomistic structural modeling and microsecond molecular simulations of the SARS-CoV-2 Spike complexes with the host receptor ACE2 for XBB.1.5+L455F, XBB.1.5+F456L(EG.5) and XBB.1.5+L455F/F456L (FLip) lineages to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and physics-based rigorous computations of binding affinities, we identified binding energy hotspots and characterized molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of Q493 hotspot in synchronization of epistatic couplings between L455F and F456L mutations providing a quantitative insight into the mechanism underlying differences between XBB lineages. Mutational profiling is combined with network-based model of epistatic couplings showing that the Q493, L455 and F456 sites mediate stable communities at the binding interface with ACE2 and can serve as stable mediators of non-additive couplings. Structure-based mutational analysis of Spike protein binding with the class 1 antibodies quantified the critical role of F456L and F486P mutations in eliciting strong immune evasion response. The results of this analysis support a mechanism in which the emergence of EG.5 and FLip variants may have been dictated by leveraging strong epistatic effects between several convergent revolutionary hotspots that provide synergy between the improved ACE2 binding and broad neutralization resistance. This interpretation is consistent with the notion that functionally balanced substitutions which simultaneously optimize immune evasion and high ACE2 affinity may continue to emerge through lineages with beneficial pair or triplet combinations of RBD mutations involving mediators of epistatic couplings and sites in highly adaptable RBD regions.
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27
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Asarnow D, Stewart C, Logue J, Murrell B, Chu HY, Veesler D, Bloom JD. Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566961. [PMID: 38014024 PMCID: PMC10680755 DOI: 10.1101/2023.11.13.566961] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact other properties that contribute to viral fitness such as ACE2 receptor binding and cell entry. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning to measure how >9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry, or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully impacted ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456, and 473-however, the antigenic impacts of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y. Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98195, USA
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