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antibodies, neutralizing, sarscov, pubmed, omicron, data, fig, rbd, group, article, antibody, google, scholar, cas, mutations, mutation, extended, escape, epitope, neutralization, central, nature, groups, cell, yeast, individuals, variants, binding, site, cells, pseudovirus, ads, convalescent, wang, beijing, human, epitopes, protein, sites, sequencing, variant, ace, escaping, escaped, spike, compared, performed, science, analysis, display,

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cd20+ cd27+igm−ova−rbd-pe+rbd-apc+ live /media/jbloomlab/sars2_rbd_ab_escape_maps/main/processed_data/escape_data nature portfolio /sunneyxielab/sars-cov-2-rbd-abs-htdms privacy policy /single-cell-vdj/software/downloads/latest 3 μl pe/cyanine7 anti-igm bnt162b2-immunized sars-cov-1 survivors structure-guided high-resolution serology advertising anti-c-myc magnetic beads sars-cov-1 rbd double-positive high-throughput single-cell sequencing pan-sarbecovirus antibody-based drugs xiaoliang sunney xie vsv-based sars-cov-2 pseudovirus antigen-specific single-b-cell deep mutational scanning reprints high-efficiency yeast transformation sars-cov-2 wild type sars-cov-1 convalescent individual sars-cov-2 spike protein recent sars-cov-2 variants sars-cov-2 neutralizing antibodies17 isolate sars-cov-2 rbd sars-cov-2 convalescent individuals sars-cov-1 convalescent individuals zymo research research design knowledge-based structural classifications3 thermo fisher scientific received sars-cov-2 vaccines dimensional t-sne embeddings short-term convalescent individuals sars-cov-2 neutralizing antibodies previous sars-cov-2 infection sars-cov-2 antibody cocktail critical salt-bridge interaction dimensional t-sne plots half-maximal effective concentration sars-cov-2 rbd antibodies pan-sarbecovirus neutralizing antibodies broadly neutralizing antibodies sex-transmitted virus vaccines shorter complementarity-determining region 3 sars-cov-2 rbd mutations anti-rbd neutralizing antibodies neutralizing-antibody-based drugs aggregated antibody-antigen interface

Questions {❓}

• How bad is Omicron?

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         headline:Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
         description:The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F)—a grouping that is highly concordant with knowledge-based structural classifications3–5. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants. A high-throughput yeast display platform is used to analyse the profiles of mutations in the SARS-CoV-2 receptor-binding domain (RBD) that enable escape from antibodies, and suggests that most anti-RBD antibodies can be escaped by the Omicron variant.
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      headline:Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
      description:The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F)—a grouping that is highly concordant with knowledge-based structural classifications3–5. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants. A high-throughput yeast display platform is used to analyse the profiles of mutations in the SARS-CoV-2 receptor-binding domain (RBD) that enable escape from antibodies, and suggests that most anti-RBD antibodies can be escaped by the Omicron variant.
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      name:Xiaohua Hao
      affiliation:
            name:Capital Medical University
            address:
               name:Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      name:Fei Shao
      affiliation:
            name:Peking University
            address:
               name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      name:Ronghua Jin
      affiliation:
            name:Capital Medical University
            address:
               name:Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      name:Xiangxi Wang
      affiliation:
            name:Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Junyu Xiao
      url:http://orcid.org/0000-0003-1822-1701
      affiliation:
            name:Peking University
            address:
               name:Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
            name:Peking University
            address:
               name:School of Life Sciences, Peking University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Youchun Wang
      url:http://orcid.org/0000-0001-9769-5141
      affiliation:
            name:National Institutes for Food and Drug Control (NIFDC)
            address:
               name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Xiaoliang Sunney Xie
      url:http://orcid.org/0000-0001-9281-5239
      affiliation:
            name:Peking University
            address:
               name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
            name:Peking University
            address:
               name:Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P. R. China
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Joint Graduate Program of Peking–Tsinghua–NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Tsinghua-Peking Center for Life Sciences, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Beijing YouAn Hospital, Capital Medical University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
      name:CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
      name:Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P. R. China
      name:School of Life Sciences, Peking University, Beijing, P. R. China
      name:Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
      name:Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
      name:Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P. R. China

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