Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques

To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting neutralizing antibody responses against multiple CoVs. Because of the phylogenetic similarity to humans, rhesus macaques are an animal model of choice for many virus-challenge and vaccine-evaluation studies, including SARS-CoV-2. Here, we show that immunization of macaques with SARS-CoV-2 spike (S) protein generates potent receptor binding domain cross- neutralizing antibody (nAb) responses to both SARS-CoV-2 and SARS-CoV-1, in contrast to human infection or vaccination where responses are typically SARS-CoV-2-specific. Furthermore, the macaque nAbs are equally effective against SARS-CoV-2 variants of concern. Structural studies show that different immunodominant sites are targeted by the two primate species. Human antibodies generally target epitopes strongly overlapping the ACE2 receptor binding site (RBS), whereas the macaque antibodies recognize a relatively conserved region proximal to the RBS that represents another potential pan-SARS-related virus site rarely targeted by human antibodies. B cell repertoire differences between the two primates appear to significantly influence the vaccine response and suggest care in the use of rhesus macaques in evaluation of vaccines to SARS-related viruses intended for human use. ONE SENTENCE SUMMARY Broadly neutralizing antibodies to an unappreciated site of conservation in the RBD in SARS- related viruses can be readily induced in rhesus macaques because of distinct properties of the naïve macaque B cell repertoire that suggest prudence in the use of the macaque model in SARS vaccine evaluation and design.

[1]  Lisa E. Gralinski,et al.  Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses , 2022, Nature Immunology.

[2]  D. Burton,et al.  A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection , 2022, Science Translational Medicine.

[3]  J. Mascola,et al.  SARS-CoV-2 Omicron Variant Neutralization after mRNA-1273 Booster Vaccination , 2022, The New England journal of medicine.

[4]  D. Burton,et al.  A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection , 2022, bioRxiv.

[5]  Gregory D. Gromowski,et al.  A SARS-CoV-2 ferritin nanoparticle vaccine elicits protective immune responses in nonhuman primates , 2021, Science Translational Medicine.

[6]  J. Mascola,et al.  Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization , 2021, medRxiv.

[7]  D. Irvine,et al.  A particulate saponin/TLR agonist vaccine adjuvant alters lymph flow and modulates adaptive immunity , 2021, Science Immunology.

[8]  Aaron M. Rosenfeld,et al.  mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern , 2021, Science.

[9]  B. Pulendran,et al.  Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines , 2021, Cell.

[10]  Rommie E. Amaro,et al.  SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma , 2021, Proceedings of the National Academy of Sciences.

[11]  B. Haynes,et al.  Protective antibodies elicited by SARS-CoV-2 spike protein vaccination are boosted in the lung after challenge in nonhuman primates , 2021, Science Translational Medicine.

[12]  M. Beltramello,et al.  Broad sarbecovirus neutralization by a human monoclonal antibody , 2021, Nature.

[13]  C. Woods,et al.  In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies , 2021, Cell.

[14]  C. Rice,et al.  Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection , 2021, Nature.

[15]  X. Xie,et al.  Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines , 2021, Cell Research.

[16]  D. Burton,et al.  Cross-reactive serum and memory B-cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection , 2021, Nature Communications.

[17]  Rachel L. Spreng,et al.  Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses , 2021, Nature.

[18]  Daniel W. Kulp,et al.  Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drives rapid and potent immunogenicity capable of single-dose protection , 2021, bioRxiv.

[19]  J. Mascola,et al.  Immune Correlates of Protection by mRNA-1273 Immunization against SARS-CoV-2 Infection in Nonhuman Primates , 2021, bioRxiv.

[20]  B. Pulendran,et al.  Adjuvanting a subunit COVID-19 vaccine to induce protective immunity , 2021, Nature.

[21]  F. Krammer Correlates of protection from SARS-CoV-2 infection , 2021, The Lancet.

[22]  P. Klenerman,et al.  SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN) , 2021, The Lancet.

[23]  D. Burton,et al.  A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection , 2021, bioRxiv.

[24]  L. Stamatatos,et al.  mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection , 2021, Science.

[25]  D. Ho,et al.  Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 , 2021, Nature.

[26]  B. Haynes,et al.  Vaccination with SARS-CoV-2 Spike Protein and AS03 Adjuvant Induces Rapid Anamnestic Antibodies in the Lung and Protects Against Virus Challenge in Nonhuman Primates , 2021, bioRxiv.

[27]  John P. Moore,et al.  Immunogenicity of clinically relevant SARS-CoV-2 vaccines in nonhuman primates and humans , 2021, Science Advances.

[28]  D. Irvine,et al.  Disassembly of HIV envelope glycoprotein trimer immunogens is driven by antibodies elicited via immunization , 2021, bioRxiv.

[29]  Dapeng Zhou,et al.  Potent Neutralization Antibodies Induced by a Recombinant Trimeric Spike Protein Vaccine Candidate Containing PIKA Adjuvant for COVID-19 , 2021, bioRxiv.

[30]  D. Burton,et al.  Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants , 2021, Science.

[31]  J. Mascola,et al.  SARS-CoV-2 Viral Variants-Tackling a Moving Target. , 2021, JAMA.

[32]  M. Nussenzweig,et al.  mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants , 2021, Nature.

[33]  B. Murrell,et al.  Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles , 2021, Immunity.

[34]  M. Nussenzweig,et al.  mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants , 2021, bioRxiv.

[35]  L. Morris,et al.  SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma , 2021, bioRxiv.

[36]  N. Patel,et al.  SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice , 2021, Nature Communications.

[37]  M. Nussenzweig,et al.  Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice , 2020, Science.

[38]  W. Chiu,et al.  A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice , 2021, ACS central science.

[39]  M. Seong,et al.  Stereotypic neutralizing VH antibodies against SARS-CoV-2 spike protein receptor binding domain in patients with COVID-19 and healthy individuals , 2021, Science Translational Medicine.

[40]  C. Woods,et al.  The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates , 2021, bioRxiv.

[41]  G. B. Karlsson Hedestam,et al.  Adjuvanted SARS-CoV-2 spike protein elicits neutralizing antibodies and CD4 T cell responses after a single immunization in mice , 2020, EBioMedicine.

[42]  Rommie E. Amaro,et al.  SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma , 2020, bioRxiv.

[43]  G. Gao,et al.  Viral targets for vaccines against COVID-19 , 2020, Nature reviews. Immunology.

[44]  P. Dormitzer,et al.  Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine , 2020, The New England journal of medicine.

[45]  D. Lauffenburger,et al.  Correlates of Protection Against SARS-CoV-2 in Rhesus Macaques , 2020, Nature.

[46]  Lisa E. Gralinski,et al.  Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2 , 2020, Cell.

[47]  M. Nussenzweig,et al.  SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies , 2020, Nature.

[48]  Yong-tang Zheng,et al.  S-Trimer, a COVID-19 subunit vaccine candidate, induces protective immunity in nonhuman primates , 2020, Nature Communications.

[49]  D. Burton,et al.  Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection , 2020, bioRxiv.

[50]  F. Krammer SARS-CoV-2 vaccines in development , 2020, Nature.

[51]  M. Beltramello,et al.  Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology , 2020, Cell.

[52]  X. Xie,et al.  Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy , 2020, Cell.

[53]  W. Chiu,et al.  A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice , 2020, bioRxiv.

[54]  J. Bloom,et al.  Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate , 2020, medRxiv.

[55]  J. Mascola,et al.  Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates , 2020, The New England journal of medicine.

[56]  C. Rice,et al.  Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants , 2020, bioRxiv.

[57]  Lisa E. Gralinski,et al.  Potently neutralizing and protective human antibodies against SARS-CoV-2 , 2020, Nature.

[58]  J. Mascola,et al.  An mRNA Vaccine against SARS-CoV-2 — Preliminary Report , 2020, The New England journal of medicine.

[59]  D. Burton,et al.  Structural basis of a shared antibody response to SARS-CoV-2 , 2020, Science.

[60]  M. Nussenzweig,et al.  Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies , 2020, Cell.

[61]  J. Dye,et al.  Broad neutralization of SARS-related viruses by human monoclonal antibodies , 2020, Science.

[62]  D. Burton,et al.  Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model , 2020, Science.

[63]  R. Welsh,et al.  Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail , 2020, Science.

[64]  C. Rice,et al.  Convergent Antibody Responses to SARS-CoV-2 in Convalescent Individuals , 2020, Nature.

[65]  M. Nussenzweig,et al.  Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies , 2020, bioRxiv.

[66]  Linqi Zhang,et al.  Human neutralizing antibodies elicited by SARS-CoV-2 infection , 2020, Nature.

[67]  William J. Liu,et al.  A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2 , 2020, Nature.

[68]  Amalio Telenti,et al.  Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody , 2020, Nature.

[69]  X. Xie,et al.  Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells , 2020, Cell.

[70]  M. V. van Breemen,et al.  Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability , 2020, Science.

[71]  F. Gao,et al.  A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2 , 2020, Science.

[72]  I. Wilson,et al.  A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV , 2020, Science.

[73]  F. Krammer,et al.  SARS-CoV-2 Vaccines: Status Report , 2020, Immunity.

[74]  Linqi Zhang,et al.  Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor , 2020, Nature.

[75]  Lei Liu,et al.  Potent human neutralizing antibodies elicited by SARS-CoV-2 infection , 2020, bioRxiv.

[76]  Nicholas C. Wu,et al.  Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections , 2020, bioRxiv.

[77]  Nicholas C. Wu,et al.  A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV , 2020, Science.

[78]  K. Eric Wommack,et al.  Iroki: automatic customization and visualization of phylogenetic trees , 2020, PeerJ.

[79]  M. Letko,et al.  Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses , 2020, Nature Microbiology.

[80]  B. Graham,et al.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.

[81]  Daniel W. Kulp,et al.  Engineered immunogen binding to alum adjuvant enhances humoral immunity , 2020, Nature Medicine.

[82]  Matthew R. McKay,et al.  Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies , 2020, bioRxiv.

[83]  Gavin J. D. Smith,et al.  Lack of cross-neutralization by SARS patient sera towards SARS-CoV-2 , 2020, Emerging microbes & infections.

[84]  Daniel W. Kulp,et al.  Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance , 2018, Cell.

[85]  Chaim A. Schramm,et al.  Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields. , 2019, Immunity.

[86]  Dimitri Schritt,et al.  Modeling of stimuli-responsive nanoreactors: rational rate control towards the design of colloidal enzymes , 2019, Molecular Systems Design & Engineering.

[87]  Daniel W. Kulp,et al.  Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance , 2018, Cell.

[88]  D. Burton,et al.  Commonality despite exceptional diversity in the baseline human antibody repertoire , 2018, Nature.

[89]  F. Alt,et al.  Glycan Masking Focuses Immune Responses to the HIV‐1 CD4‐Binding Site and Enhances Elicitation of VRC01‐Class Precursor Antibodies , 2018, Immunity.

[90]  Yana Safonova,et al.  Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads , 2017, The Journal of Immunology.

[91]  Matthew Angel,et al.  Defining B Cell Immunodominance to Viruses , 2017, Nature Immunology.

[92]  F. Alt,et al.  Human Ig knockin mice to study the development and regulation of HIV‐1 broadly neutralizing antibodies , 2017, Immunological reviews.

[93]  Daniel G. Anderson,et al.  Sustained antigen availability during germinal center initiation enhances antibody responses to vaccination , 2016, Proceedings of the National Academy of Sciences.

[94]  F. Alt,et al.  Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires , 2016, Cell.

[95]  David Nemazee,et al.  Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies , 2016, Cell.

[96]  Barney S. Graham,et al.  Pre-fusion structure of a human coronavirus spike protein , 2016, Nature.

[97]  John P. Moore,et al.  Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-neutralizing Epitopes , 2015, Cell.

[98]  Lisa E. Gralinski,et al.  A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence , 2015, Nature Medicine.

[99]  David Nemazee,et al.  Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen , 2015, Science.

[100]  John P. Moore,et al.  Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex , 2014, Proceedings of the National Academy of Sciences.

[101]  L. Macdonald,et al.  Mice with megabase humanization of their immunoglobulin genes generate antibodies as efficiently as normal mice , 2014, Proceedings of the National Academy of Sciences.

[102]  Anneliese O. Speak,et al.  Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery , 2014, Nature Biotechnology.

[103]  Michael J. Osborn,et al.  High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Igκ/Igλ Loci Bearing the Rat CH Region , 2013, The Journal of Immunology.

[104]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[105]  Martin H. Koldijk,et al.  A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses , 2011, Science.

[106]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[107]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[108]  Wolfgang Kabsch,et al.  Integration, scaling, space-group assignment and post-refinement , 2010, Acta crystallographica. Section D, Biological crystallography.

[109]  M Radermacher,et al.  DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. , 2009, Journal of structural biology.

[110]  Michel C Nussenzweig,et al.  Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. , 2008, Journal of immunological methods.

[111]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[112]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[113]  Jaap Goudsmit,et al.  Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants , 2006, PLoS medicine.

[114]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[115]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[116]  D. Roote,et al.  Status Report , 2006, Journal of periodontology.