Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys.
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
09 2022
09 2022
Historique:
received:
08
06
2022
accepted:
06
07
2022
pubmed:
26
7
2022
medline:
31
8
2022
entrez:
25
7
2022
Statut:
ppublish
Résumé
The SARS-CoV-2 Omicron variant has very high levels of transmission, is resistant to neutralization by authorized therapeutic human monoclonal antibodies (mAb) and is less sensitive to vaccine-mediated immunity. To provide additional therapies against Omicron, we isolated a mAb named P2G3 from a previously infected vaccinated donor and showed that it has picomolar-range neutralizing activity against Omicron BA.1, BA.1.1, BA.2 and all other variants tested. We solved the structure of P2G3 Fab in complex with the Omicron spike using cryo-electron microscopy at 3.04 Å resolution to identify the P2G3 epitope as a Class 3 mAb that is different from mAb-binding spike epitopes reported previously. Using a SARS-CoV-2 Omicron monkey challenge model, we show that P2G3 alone, or in combination with P5C3 (a broadly active Class 1 mAb previously identified), confers complete prophylactic or therapeutic protection. Although we could select for SARS-CoV-2 mutants escaping neutralization by P2G3 or by P5C3 in vitro, they had low infectivity and 'escape' mutations are extremely rare in public sequence databases. We conclude that this combination of mAbs has potential as an anti-Omicron drug.
Identifiants
pubmed: 35879526
doi: 10.1038/s41564-022-01198-6
pii: 10.1038/s41564-022-01198-6
pmc: PMC9418005
doi:
Substances chimiques
Antibodies, Monoclonal
0
Antibodies, Viral
0
Epitopes
0
Membrane Glycoproteins
0
Spike Glycoprotein, Coronavirus
0
Viral Envelope Proteins
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1376-1389Informations de copyright
© 2022. The Author(s).
Références
Weekly Epidemiological Update on COVID-19 - 18 January 2022 (WHO, 2022).
Elbe, S. & Buckland-Merrett, G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob. Chall. 1, 33–46 (2017).
pubmed: 31565258
pmcid: 6607375
doi: 10.1002/gch2.1018
Viana, R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 603, 679–686 (2022).
pubmed: 35042229
pmcid: 8942855
doi: 10.1038/s41586-022-04411-y
Barnes, C. O. et al. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. Cell 182, 828–842.e16 (2020).
pubmed: 32645326
pmcid: 7311918
doi: 10.1016/j.cell.2020.06.025
Piccoli, L. et al. Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology. Cell 183, 1024–1042.e21 (2020).
pubmed: 32991844
pmcid: 7494283
doi: 10.1016/j.cell.2020.09.037
Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021).
pubmed: 33684923
doi: 10.1038/s41586-021-03398-2
Garcia-Beltran, W. F. et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184, 2372–2383.e79 (2021).
pubmed: 33743213
pmcid: 7953441
doi: 10.1016/j.cell.2021.03.013
Iketani, S. et al. Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature 604, 553–556 (2022).
pubmed: 35240676
pmcid: 9021018
doi: 10.1038/s41586-022-04594-4
Cao, Y. W. et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature 602, 657–663 (2022).
pubmed: 35016194
doi: 10.1038/s41586-021-04385-3
VanBlargan, L. A. et al. An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies. Nat. Med. 28, 490–495 (2022).
pubmed: 35046573
pmcid: 8767531
doi: 10.1038/s41591-021-01678-y
Liu, L. et al. Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature 602, 676–681 (2021).
pubmed: 35016198
doi: 10.1038/s41586-021-04388-0
Mannar, D. et al. SARS-CoV-2 Omicron variant: antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science 375, 760–764 (2022).
pubmed: 35050643
doi: 10.1126/science.abn7760
Planas, D. et al. Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature 602, 671–675 (2021).
pubmed: 35016199
doi: 10.1038/s41586-021-04389-z
Wang, Z. et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 592, 616–622 (2021).
pubmed: 33567448
pmcid: 8503938
doi: 10.1038/s41586-021-03324-6
Chen, R. E. et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat. Med 27, 717–726 (2021).
pubmed: 33664494
pmcid: 8058618
doi: 10.1038/s41591-021-01294-w
Fenwick, C. et al. A high-throughput cell- and virus-free assay shows reduced neutralization of SARS-CoV-2 variants by COVID-19 convalescent plasma. Sci. Transl. Med. 13, eabi8452 (2021).
pubmed: 34257144
doi: 10.1126/scitranslmed.abi8452
Baum, A. et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369, 1014–1018 (2020).
pubmed: 32540904
doi: 10.1126/science.abd0831
Dong, J. et al. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat. Microbiol. 6, 1233–1244 (2021).
pubmed: 34548634
pmcid: 8543371
doi: 10.1038/s41564-021-00972-2
Rappazzo, C. G. et al. An engineered antibody with broad protective efficacy in murine models of SARS and COVID-19. Preprint at bioRxiv https://doi.org/10.1101/2020.11.17.385500 (2020).
Pinto, D. et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290–295 (2020).
pubmed: 32422645
doi: 10.1038/s41586-020-2349-y
Fenwick, C. et al. A highly potent antibody effective against SARS-CoV-2 variants of concern. Cell Rep. 37, 109814 (2021).
pubmed: 34599871
pmcid: 8452523
doi: 10.1016/j.celrep.2021.109814
Lempp, F. A. et al. Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Nature 598, 342–347 (2021).
pubmed: 34464958
doi: 10.1038/s41586-021-03925-1
Yamin, R. et al. Fc-engineered antibody therapeutics with improved anti-SARS-CoV-2 efficacy. Nature 599, 465–470 (2021).
pubmed: 34547765
pmcid: 9038156
doi: 10.1038/s41586-021-04017-w
Schafer, A. et al. Antibody potency, effector function, and combinations in protection and therapy for SARS-CoV-2 infection in vivo. J. Exp. Med. 218, e20201993 (2021).
pubmed: 33211088
doi: 10.1084/jem.20201993
Winkler, E. S. et al. Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection. Cell 184, 1804–1820.e16 (2021).
pubmed: 33691139
pmcid: 7879018
doi: 10.1016/j.cell.2021.02.026
Yu, Y. et al. Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Sig. Transduct. Target Ther. 6, 346 (2021).
doi: 10.1038/s41392-021-00759-1
Zalevsky, J. et al. Enhanced antibody half-life improves in vivo activity. Nat. Biotechnol. 28, 157–159 (2010).
pubmed: 20081867
pmcid: 2855492
doi: 10.1038/nbt.1601
Ni, D. et al. Structural analysis of the spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion. Preprint at bioRxiv https://doi.org/10.1101/2021.12.27.474250 (2021).
Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020).
pubmed: 32075877
pmcid: 7164637
doi: 10.1126/science.abb2507
Sztain, T. et al. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat. Chem. 13, 963–968 (2021).
pubmed: 34413500
pmcid: 8488004
doi: 10.1038/s41557-021-00758-3
Halfmann, P. J. et al. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature https://doi.org/10.1038/s41586-022-04441-6 (2022).
Abdelnabi, R. et al. The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Antivir. Res. 198, 105253 (2022).
pubmed: 35066015
doi: 10.1016/j.antiviral.2022.105253
Obeid, M. et al. Humoral responses against variants of concern by COVID-19 mRNA vaccines in immunocompromised patients. JAMA Oncol. 8, e220446 (2022).
pubmed: 35271706
pmcid: 8914885
doi: 10.1001/jamaoncol.2022.0446
Mohammed, A. H., Blebil, A., Dujaili, J. & Rasool-Hassan, B. A. The risk and impact of COVID-19 pandemic on immunosuppressed patients: cancer, HIV, and solid organ transplant recipients. AIDS Rev. 22, 151–157 (2020).
pubmed: 33118527
doi: 10.24875/AIDSRev.20000052
Fenwick, C. et al. Changes in SARS-CoV-2 spike versus nucleoprotein antibody responses impact the estimates of infections in population-based seroprevalence studies. J. Virol. 95, e01828-20 (2021).
pubmed: 33144321
pmcid: 7925109
doi: 10.1128/JVI.01828-20
Maisonnasse, P. et al. COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models. Nat. Commun. 12, 6097 (2021).
pubmed: 34671037
pmcid: 8528857
doi: 10.1038/s41467-021-26354-0
Boudewijns, R. et al. STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters. Nat. Commun. 11, 5838 (2020).
pubmed: 33203860
pmcid: 7672082
doi: 10.1038/s41467-020-19684-y
Kaptein, S. J. F. et al. Favipiravir at high doses has potent antiviral activity in SARS-CoV-2-infected hamsters, whereas hydroxychloroquine lacks activity. Proc. Natl Acad. Sci. USA 117, 26955–26965 (2020).
pubmed: 33037151
pmcid: 7604414
doi: 10.1073/pnas.2014441117
Sanchez-Felipe, L. et al. A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate. Nature 590, 320–325 (2021).
pubmed: 33260195
doi: 10.1038/s41586-020-3035-9
Richardson, S. I. et al. HIV broadly neutralizing antibodies expressed as IgG3 preserve neutralization potency and show improved Fc effector function. Front. Immunol. 12, 733958 (2021).
pubmed: 34566999
pmcid: 8462932
doi: 10.3389/fimmu.2021.733958
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Rubinstein, J. L. & Brubaker, M. A. Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192, 188–195 (2015).
pubmed: 26296328
doi: 10.1016/j.jsb.2015.08.007
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101
doi: 10.1002/pro.3943
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
doi: 10.1107/S2059798319011471