Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains

Abstract

Omicron variant strains encode large numbers of changes in the spike protein compared to historical SARS-CoV-2 isolates. Although in vitro studies have suggested that several monoclonal antibody therapies lose neutralizing activity against Omicron variants, the effects in vivo remain largely unknown. Here, we report on the protective efficacy against three SARS-CoV-2 Omicron lineage strains (BA.1, BA.1.1, and BA.2) of two monoclonal antibody therapeutics (S309 [Vir Biotechnology] monotherapy and AZD7442 [AstraZeneca] combination), which correspond to ones used to treat or prevent SARS-CoV-2 infections in humans. Despite losses in neutralization potency in cell culture, S309 or AZD7442 treatments reduced BA.1, BA.1.1, and BA.2 lung infection in susceptible mice that express human ACE2 (K18-hACE2) in prophylactic and therapeutic settings. Correlation analyses between in vitro neutralizing activity and reductions in viral burden in K18-hACE2 or human FcγR transgenic mice suggest that S309 and AZD7442 have different mechanisms of protection against Omicron variants, with S309 utilizing Fc effector function interactions and AZD7442 acting principally by direct neutralization. Our data in mice demonstrate the resilience of S309 and AZD7442 mAbs against emerging SARS-CoV-2 variant strains and provide insight into the relationship between loss of antibody neutralization potency and retained protection in vivo.

Conflict of interest statement

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 Innovations, Merck, and GlaxoSmithKline, is a member of the Scientific Advisory Board of Meissa Vaccines and is founder of IDBiologics. The Crowe laboratory has received sponsored research agreements from AstraZeneca, Takeda, and IDBiologics during the conduct of the study. Vanderbilt University has applied for patents for some of the antibodies in this paper, for which J.E.C. is an inventor. B.G., M.A.S, G.S., H.V.D., H.W.V., D.C., and L.A.P. are employees of Vir Biotechnology and may hold equity in Vir Biotechnology. L.A.P. is a former employee and may hold equity in Regeneron Pharmaceuticals. H.W.V. is a founder and holds shares in PierianDx and Casma Therapeutics. Neither company provided resources to this study. Y.K. has received unrelated funding support from Daiichi Sankyo Pharmaceutical, Toyama Chemical, Tauns Laboratories, Inc., Shionogi & Co. LTD, Otsuka Pharmaceutical, KM Biologics, Kyoritsu Seiyaku, Shinya Corporation, and Fuji Rebio. K. Rosenthal, K. Ren, Y-M.L. and M.T.E. are employees of AstraZeneca and may hold stock in AstraZeneca. All other authors declare no competing interests.

© 2022. The Author(s).

Figures

Fig. 1. Neutralization of Omicron lineage strains by mAbs.

a One protomer of the SARS-CoV-2 spike trimer (PDB: 7C2L) is depicted with BA.2 variant amino acid substitutions labelled and shown as red spheres. The N-terminal domain (NTD), RBD, RBM, and S2 are colored in yellow, green, magenta, and blue, respectively. All mutated residues in the BA.2 RBD relative to WA1/2020 are indicated in b, and the BA.2 RBD bound by mAbs S309 (orange, PDB: 6WPS) (b), AZD8895 (green, PDB: 7L7D) (c), and AZD1061 (purple, PDB:7L7E) (d) are shown. BA.2 mutations in the respective epitopes of each mAb are shaded red, whereas those outside the epitope are shaded green. e Multiple sequence alignment showing the epitope footprints of each mAb on the SARS-CoV-2 RBD (orange, S309; green, AZD8895; purple, AZD1061). The WA1/2020 RBD is shown in the last row with relative variant sequence changes indicated. Red circles below the sequence alignment indicate hACE2 contact residues on the SARS-CoV-2 RBD. Structural analysis and depictions were generated using UCSF ChimeraX. f–i Neutralization curves in Vero-TMPRSS2 cells with the indicated SARS-CoV-2 strain and mAb. The average of three to four experiments performed in technical duplicate are shown. j–m Comparison of EC50 values for the indicated mAb against D614G, BA.1, BA.1.1, and BA.2 viruses. Data are the average of three experiments, error bars indicate standard error of the mean (SEM), and the dashed line indicates the upper limit of detection (one-way ANOVA with Dunnett’s test; ns, not significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). n Summary of the EC50 values for each mAb against the indicated SARS-CoV-2 strain. o Summary of the fold-change in EC50 values for each mAb against the indicated Omicron strain relative to SARS-CoV-2 D614G. Source data are provided as a Source Data file.

Fig. 2. Antibody protection against Omicron variants in K18-hACE2 mice.

a–j Eight-week-old female K18-hACE2 mice received 200 μg (about 10 mg/kg) of the indicated mAb treatment by intraperitoneal injection one day before intranasal inoculation with 103 FFU of the indicated SARS-CoV-2 strain. Tissues were collected at six (BA.2) or seven days (all other strains) after inoculation. Viral RNA levels in the lungs (a, e), nasal turbinates (c, g), and nasal washes (d, h) were determined by RT-qPCR, and infectious virus in the lungs (b, f) was assayed by plaque assay (lines indicate median ± SEM.; n = 6–8 mice per group, two experiments; Two-tailed Mann-Whitney test between isotype and mAb treatment; ns, not significant; *P < 0.05, **P < 0.01, ***P < 0.001). i, j Heat map of cytokine and chemokine protein expression levels in lung homogenates from the indicated groups. Data are presented as log2-transformed fold-change over naive mice. Blue, reduction; red, increase. k, l, Correlation analysis. The fold-change in EC50 value of AZD7442-YTE/TM (k) and S309-LS (l) for D614G and each Omicron variant strain are plotted on the x-axis. The fold-change in lung viral RNA titer between the respective isotype or mAb-treated groups against each Omicron variant strain are plotted on the y-axis. Best-fit lines were calculated using a simple linear regression. Two-tailed Pearson correlation was used to calculate the R2 and P values indicated within each panel. Source data are provided as a Source Data file.

Fig. 3. VIR-7831 binds and instructs effector cells for ADCC and ADCP.

a Binding of S309-LS, S309-GRLR, or AZD7442-TM mAbs to hFcγRI, hFcγRIIIa, or mFcγRIV (two experiments; dotted lines indicate the limit of detection; data are presented as meanvalues ± range). b ExpiCHO-S cells were transiently transfected with plasmids encoding the indicated SARS-CoV-2 spike protein. 24 to 48 h later, cells were harvested, washed, and stained with the indicated concentrations of VIR-7831 or S2X324 mAbs to assess binding to the cell surface. Representative histograms from two or three experiments are shown. c Antibody binding curves for VIR-7831 and S2X324 using the data in b and presented as mean fluorescence intensity (MFI) versus antibody concentration. d, e ExpiCHO-S cells transiently transfected with Wuhan-1 D614, BA.1, or BA.2 spike proteins were incubated with the indicated concentrations of VIR-7831 or S309-GRLR mAb and mixed with purified NK cells isolated from healthy donors at a ratio of 1:9 (target:effector). Cell lysis was determined by a lactate dehydrogenase release assay. Data are presented as mean values ± standard deviations (SD) from one representative of four donors (d). Area under the curve (AUC) analyses from four NK donors (e) (see Supplementary Fig. 8). f, g ExpiCHO-S cells transiently transfected with Wuhan-1 D614, BA.1, or BA.2 spike proteins and fluorescently labelled with PKH67 were incubated with the indicated concentrations of VIR-7831 or S309-GRLR mAb and mixed with PBMCs labelled with CellTrace Violet from healthy donors at a ratio of 1:20 (target:PBMCs). Association of CD14+ monocytes with spike-expressing target cells (ADCP) was determined by flow cytometry. Data are presented as mean values ± SD from one representative of five donors (f). AUC analyses of VIR-7831 and S309-GRLR for each Omicron variant for five donors (g). e, g Two-tailed Mann-Whitney test between VIR-7831 and S309-GRLR for the indicated variant; *P < 0.05, **P < 0.01. Source data are provided as a Source Data file. Gating strategies are shown in Supplementary Fig. 8c.

Fig. 4. Fc-effector functions and mAb-mediated protection.

a–d Eight-week-old female K18-hACE2 mice or (e, f) 12-week-old male hFcγR Tg mice received a single 10 mg/kg or 3 mg/kg dose respectively, of isotype control, S309-LS or S309-GRLR mAb by intraperitoneal injection one day before intranasal inoculation with 103 FFU of D614G, BA.1, or BA.2 (a-c) or 105 FFU of Beta (B.1.351) (e, f). Tissues were collected at 2 (B.1.351), 4 (B.1.351), 6 (BA.2), or 7 (D614G and BA.1) dpi. Viral RNA levels in the lungs (a, e, f), nasal turbinates (b), and nasal washes (c) were determined by RT-qPCR, and infectious virus in the lungs (e, f) was measured by plaque assay. a-c, e, f lines indicate median ± SEM.; a-c and e, fn = 8 and 10 mice per group, respectively; two experiments; a-c Two-tailed Mann-Whitney test between isotype and mAb treatment; ns, not significant; **P < 0.01, ***P < 0.001 e, f one-way ANOVA with Tukey’s multiple comparisons test; ns, not significant; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). d Heat map of cytokine and chemokine protein expression levels in lung homogenates from the indicated groups. Data are presented as log2-transformed fold-change over naive mice. Blue, reduction; red, increase. S309-LS data in Fig. 2i is included for comparison. g–i Eight-week-old female K18-hACE2 mice were inoculated with 103 FFU of the indicated SARS-CoV-2 strain by intranasal administration one day before receiving a single 30 mg/kg dose of S309-LS or AZD7442-TM mAb by intraperitoneal injection. Tissues were collected at 6 (BA.2) or 7 (all other strains) dpi. Viral RNA levels in the lungs (g), nasal turbinates (h), and nasal washes (i) were determined by RT-qPCR. g–i lines indicate median ± SEM; n = 8 mice per group; two experiments; Kruskal-Wallis test between isotype control and each mAb treatment with Dunn’s multiple comparisons test; ns, not significant; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Source data are provided as a Source Data file.