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      Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques

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          Abstract

          Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses resemble the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in convalescent humans, convalescent (re-infected) rhesus macaques, mRNA-vaccinated humans, and repRNA-vaccinated pigtail macaques. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques. Differences in macaque species and exposure type may also contribute to these findings.

          Author summary

          Non-human primates, including macaques, are considered the best animal model for studying infectious diseases that infect humans. Vaccine candidates for SARS-CoV-2 are first tested in macaques to assess immune responses prior to advancing to human trials, and macaques are also used to model the human immune response to SARS-CoV-2 infection. However, there may be differences in how macaque and human antibodies recognize the SARS-CoV-2 entry protein, Spike. Here we characterized the locations on Spike that are recognized by antibodies from vaccinated or infected macaques and humans. We also made mutations to the viral sequence and assessed how these affected antibody binding, enabling a comparison of antibody binding requirements between macaques and humans at a very precise level. We found that macaques and humans share some responses, but also recognize distinct regions of Spike. We also found that in general, antibodies from different individuals had unique responses to viral mutations, regardless of species. These results will yield a better understanding of how macaque data can be used to inform human immunity to SARS-CoV-2.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            A new coronavirus associated with human respiratory disease in China

            Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
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              Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

              Structure of the nCoV trimeric spike The World Health Organization has declared the outbreak of a novel coronavirus (2019-nCoV) to be a public health emergency of international concern. The virus binds to host cells through its trimeric spike glycoprotein, making this protein a key target for potential therapies and diagnostics. Wrapp et al. determined a 3.5-angstrom-resolution structure of the 2019-nCoV trimeric spike protein by cryo–electron microscopy. Using biophysical assays, the authors show that this protein binds at least 10 times more tightly than the corresponding spike protein of severe acute respiratory syndrome (SARS)–CoV to their common host cell receptor. They also tested three antibodies known to bind to the SARS-CoV spike protein but did not detect binding to the 2019-nCoV spike protein. These studies provide valuable information to guide the development of medical counter-measures for 2019-nCoV. Science, this issue p. 1260
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: SoftwareRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                11 April 2022
                April 2022
                : 18
                : 4
                : e1010155
                Affiliations
                [1 ] Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
                [2 ] Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
                [3 ] Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
                [4 ] Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
                [5 ] Department of Microbiology, University of Washington, Seattle, Washington, United States of America
                [6 ] HDT Bio, Seattle, Washington, United States of America
                [7 ] Department of Medicine, University of Washington, Seattle, Washington, United States of America
                [8 ] Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
                [9 ] Laboratory of Persistent Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
                [10 ] Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, Washington, United States of America
                [11 ] Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, United States of America
                Chang Gung University, TAIWAN
                Author notes

                I have read the journal’s policy and the authors of this manuscript have the following competing interests: J.H.E. has equity interest in HDT Bio. J.H.E. is a consultant for InBios. D.H.F. is a consultant for Gerson Lehrman Group, Orlance, Abacus Bioscience, HDT Bio, Immusoft, and GE Global Health. J.H.E. is a co-inventor on U.S. patent application no. 62/993,307 “Compositions and methods for delivery of RNA” pertaining to the LION formulation. H.Y.C. reported consulting with Ellume, Pfizer, The Bill and Melinda Gates Foundation, Glaxo Smith Kline, and Merck. She has received research funding from Gates Ventures, Sanofi Pasteur, and support and reagents from Ellume and Cepheid outside of the submitted work.

                Author information
                https://orcid.org/0000-0001-6037-6841
                https://orcid.org/0000-0002-0239-9444
                Article
                PPATHOGENS-D-21-02407
                10.1371/journal.ppat.1010155
                9022802
                35404959
                8d3b4b29-e15c-43ef-8bb4-519173fe7224

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 30 November 2021
                : 21 March 2022
                Page count
                Figures: 5, Tables: 1, Pages: 22
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01 AI138709
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01 AI146028
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: P51 OD010425-51
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: 27220140006C
                Award Recipient :
                Funded by: HDT Bio Corp
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100006492, Division of Intramural Research, National Institute of Allergy and Infectious Diseases;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100006492, Division of Intramural Research, National Institute of Allergy and Infectious Diseases;
                Award Recipient :
                Funded by: Howard Hughes Medical Institute and Simons Foundation
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10OD028685
                This work was supported by NIH grants R01 AI138709 (awarded to J.O.) and R01 AI146028 (awarded to F.A.M. IV). Macaque studies were supported by NIH/ORIP center grant P51 OD010425-51 (WaNPRC, PI Sullivan, D.H.F. Co-I), a supplement to the NIH/NIAID Centers for Excellence for Influenza Research and Surveillance contract 27220140006C (center grant PI Richard Webby, supplement PI J.H.E.), and HDT Bio Corp internal funds (J.H.E.) (Seattle, WA). Funding was partially provided by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases (D.W.H., K.J.H.). The research of F.A.M. IV was supported in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation, and he is an investigator of the Howard Hughes Medical Institute. Scientific Computing Infrastructure at Fred Hutch was funded by NIH/ORIP grant S10OD028685. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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                Custom metadata
                vor-update-to-uncorrected-proof
                2022-04-21
                All data files and the code required to run the analysis are located in the following github repository: https://github.com/matsengrp/phage-dms-nhp-analysis.
                COVID-19

                Infectious disease & Microbiology
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