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[Preprint]. 2021 Dec 27:rs.3.rs-1175516.

doi: 10.21203/rs.3.rs-1175516/v1.

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

Laura VanBlargan¹, John Errico², Peter Halfmann³, Seth Zost⁴, James Crowe⁵, Lisa Purcell⁶, Yoshihiro Kawaoka⁷, Davide Corti⁸, Daved Fremont⁹, Michael Diamond¹⁰

Affiliations

¹ Department of Medicine, Washington University School of Medicine.
² Department of Pathology & Immunology, Washington University School of Medicine.
³ Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison.
⁴ Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center.
⁵ Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center; Department of Pathology, and Microbiology and Immunology, Vanderbilt University Medical Center.
⁶ Vir Biotechnology.
⁷ Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo.
⁸ Humabs BioMed SA, a subsidiary of Vir Biotechnology.
⁹ Department of Pathology & Immunology, Washington University School of Medicine; Department of Molecular Microbiology, Washington University School of Medicine; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine.
¹⁰ Department of Medicine and Department of Pathology & Immunology and Department of Molecular Microbiology, Washington University School of Medicine; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine.

PMID: 34981042
PMCID: PMC8722605
DOI: 10.21203/rs.3.rs-1175516/v1

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

Laura VanBlargan et al. Res Sq. 2021.

[Preprint]. 2021 Dec 27:rs.3.rs-1175516.

doi: 10.21203/rs.3.rs-1175516/v1.

Authors

Laura VanBlargan¹, John Errico², Peter Halfmann³, Seth Zost⁴, James Crowe⁵, Lisa Purcell⁶, Yoshihiro Kawaoka⁷, Davide Corti⁸, Daved Fremont⁹, Michael Diamond¹⁰

Affiliations

¹ Department of Medicine, Washington University School of Medicine.
² Department of Pathology & Immunology, Washington University School of Medicine.
³ Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison.
⁴ Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center.
⁵ Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center; Department of Pathology, and Microbiology and Immunology, Vanderbilt University Medical Center.
⁶ Vir Biotechnology.
⁷ Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo.
⁸ Humabs BioMed SA, a subsidiary of Vir Biotechnology.
⁹ Department of Pathology & Immunology, Washington University School of Medicine; Department of Molecular Microbiology, Washington University School of Medicine; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine.
¹⁰ Department of Medicine and Department of Pathology & Immunology and Department of Molecular Microbiology, Washington University School of Medicine; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine.

PMID: 34981042
PMCID: PMC8722605
DOI: 10.21203/rs.3.rs-1175516/v1

Update in

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies.
VanBlargan LA, Errico JM, Halfmann PJ, Zost SJ, Crowe JE Jr, Purcell LA, Kawaoka Y, Corti D, Fremont DH, Diamond MS. VanBlargan LA, et al. Nat Med. 2022 Mar;28(3):490-495. doi: 10.1038/s41591-021-01678-y. Epub 2022 Jan 19. Nat Med. 2022. PMID: 35046573 Free PMC article.

Abstract

The emergence of the highly-transmissible B.1.1.529 Omicron variant of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is concerning for antibody countermeasure efficacy because of the number of mutations in the spike protein. Here, we tested a panel of anti-receptor binding domain monoclonal antibodies (mAbs) corresponding to those in clinical use by Vir Biotechnology (S309, the parent mAb of VIR-7831 [Sotrovimab]), AstraZeneca (COV2-2196 and COV2-2130, the parent mAbs of AZD8895 and AZD1061), Regeneron (REGN10933 and REGN10987), Lilly (LY-CoV555 and LY-CoV016), and Celltrion (CT-P59) for their ability to neutralize an infectious B.1.1.529 Omicron isolate. Several mAbs (LY-CoV555, LY-CoV016, REGN10933, REGN10987, and CT-P59) completely lost neutralizing activity against B.1.1.529 virus in both Vero-TMPRSS2 and Vero-hACE2-TMPRSS2 cells, whereas others were reduced (COV2-2196 and COV2-2130 combination, ~12-fold decrease) or minimally affected (S309). Our results suggest that several, but not all, of the antibodies in clinical use may lose efficacy against the B.1.1.529 Omicron variant.

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Conflict of interest statement

COMPETING INTERESTS

M.S.D. is a consultant for Inbios, Vir Biotechnology, Senda Biosciences, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. The Diamond laboratory has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. J.E.C. has served as a consultant for Luna Biologics and Merck Sharp & Dohme Corp., is a member of the Scientific Advisory Boards of Meissa Vaccines and is Founder of IDBiologics. The Crowe laboratory has received sponsored research agreements from Takeda Vaccines, AstraZeneca and IDBiologics. Vanderbilt University has applied for patents related to two antibodies in this paper. L.A.P. and D.C. are employees of Vir Biotechnology and may hold equity in Vir Biotechnology. L.A.P is a former employee and shareholder in Regeneron Pharmaceuticals. The remaining authors declare no competing interests.

Figures

**Figure 1. Neutralizing mAb epitopes on B.1.1.529.**
**a-b**, SARS-CoV-2 spike trimer (PDB: 7C2L and PDB: 6W41). One spike protomer is highlighted, showing the NTD in orange, RBD in green, RBM in magenta, and S2 portion of the molecule in blue (a). Close-up view of the RBD with the RBM outlined in magenta (b). Amino acids that are changed in B.1.1.529 compared to WA1/2020 are indicated in light green (**a-b**), with the exception of N679K and P681H, which were not modeled in the structures used. **c-k,** SARS-CoV-2 RBD bound by EUA mAbs COV2–2196 (c, PDB: 7L7D); COV2–2130 (d, PDB: 7L7E); S309 (e, PDB: 6WPS); REGN-10987 (f, PDB: 6XDG); REGN-10933 (g, PDB: 6XDG)); LY-CoV555 (h, PDB: 7KMG) LY-CoV016 (i, PDB: 7C01); CT-P59 (j PDB: 7CM4) and SARS2–38 (k, PDB: 7MKM). Residues mutated in the B.1.1.529 RBD and contained in these mAbs respective epitopes are shaded red, whereas those outside the epitope are shaded green. l, multiple sequence alignment showing the epitope footprints of each EUA mAb on the SARS-CoV-2 RBD highlighted in cyan. B.1.1.529 RBD is shown in the last row, with sequence changes relative to the WT RBD highlighted red. A green diamond indicates the location of the N-linked glycan at residue 343. Stars below the alignment indicate hACE2 contact residues on the SARS-CoV-2 RBD40.

**Figure 2. Neutralization of SARS-CoV-2 B.1.1.529 Omicron strain by mAbs in Vero-TMPRSS2 cells.**
**a-f,** Neutralization curves in Vero-TMPRSS2 cells comparing the sensitivity of SARS-CoV-2 strains with the indicated mAbs (COV2–2196, COV2–2130; REGN10933, REGN10987, LY-CoV555, LY-CoV016, S309, CT-P59, and SARS2–38) with WA1/2020 D614G and B.1.1.529. Also shown are the neutralization curves for antibody cocktails (COV2–2196/COV2–2130, REGN10933/REGN10987, or LY-CoV555/LY-CoV016). For data with mAb combinations, the x-axis represents the total concentration of mAb used. One representative experiment of three performed in technical duplicate is shown. Error bars indicate range of technical replicates. Data (% relative infection) are normalized to a no mAb control. g, Summary of EC₅₀ values (ng/ml) of neutralization of SARS-CoV-2 viruses (WA1/2020 D614G and B.1.1.529) performed in Vero-TMPRSS2 cells. Data is the geometric mean of 3 experiments. Blue shading: light, EC₅₀ > 5,000 ng/mL; dark, EC₅₀ > 10,000 ng/mL. h, Comparison of EC₅₀ values by mAbs against WA1/2020 D614G and B.1.1.529 (3 experiments, ns, not significant; ****, P < 0.0001; two-way ANOVA with Sidak’s post-test). Each symbol represents neutralization data from an individual experiment. Bars indicate mean values. The dotted line indicates the upper limit of dosing of the assay.

**Figure 3. Neutralization of SARS-CoV-2 B.1.1.529 Omicron strain by mAbs in Vero-hACE2-TMPRSS2 cells.**
**a-f**, Neutralization curves in Vero-hACE2-TMPRSS2 cells comparing the sensitivity of SARS-CoV-2 strains with the indicated mAbs (S309, COV2–2196, COV2–2130; REGN10933, REGN10987, LY-CoV555, LY-CoV016, CT-P59, and SARS2–38) with WA1/2020 D614G and B.1.1.529. Also shown are the neutralization curves for antibody cocktails (COV2–2196/COV2–2130, REGN10933/REGN10987, or LY-CoV555/LY-CoV016). For data with mAb combinations, the x-axis represents the total concentration of mAb used. One representative experiment of three performed in technical duplicate is shown. Error bars indicate range of technical replicates. Data (% relative infection) are normalized to a no mAb control. g, Summary of EC₅₀ values (ng/ml) of neutralization of SARS-CoV-2 viruses (WA1/2020 D614G and B.1.1.529) performed in Vero-hACE2-TMPRSS2 cells. Data is the geometric mean of 3 experiments. Blue shading: light, EC₅₀ > 5,000 ng/mL; dark, EC₅₀ > 10,000 ng/mL. h, Comparison of EC₅₀ values by mAbs against WA1/2020 D614G and B.1.1.529. **i-j**, Neutralization curves in Vero-hACE2-TMPRSS2 cells comparing WA1/2020 D614G and B.1.1.529 infection in the presence of AZD1061, AZD8895, and the combination AZD7442. h and j. 3 experiments, ns, not significant; ****, P < 0.0001; two-way ANOVA with Sidak’s post-test. Each symbol represents neutralization data from an individual experiment. Bars indicate mean values. The dotted line indicates the upper limit of dosing of the assay.

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References

Main References

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This is a preprint.

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

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An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

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