Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2

Abstract

The continued evolution of SARS-CoV-2 has led to the emergence of several new Omicron subvariants, including BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Here, we examine the neutralization resistance of these subvariants against sera from 3-dose vaccinated healthcare workers, hospitalized BA.1-wave patients, and BA.4/5-wave patients. We found enhanced neutralization resistance in all new subvariants, especially in the BQ.1 and BQ.1.1 subvariants driven by N460K and K444T mutations, as well as the BA.2.75.2 subvariant driven largely by its F486S mutation. All Omicron subvariants maintained their weakened infectivity in Calu-3 cells, with the F486S mutation driving further diminished titer for the BA.2.75.2 subvariant. Molecular modeling revealed the mechanisms of antibody-mediated immune evasion by R346T, K444T, F486S, and D1199N mutations. Altogether, these findings shed light on the evolution of newly emerging SARS-CoV-2 Omicron subvariants.

Keywords: Omicron subvariants; immune evasion; molecular modeling; mutations; neutralization.

Graphical abstract

Figure 1

Omicron subvariant-defining mutations and their impacts on pseudotyped viral infectivity in HEK293T-ACE2 and Calu-3 cells (A) Displayed is a schematic of SARS-CoV-2 Omicron subvariant evolution indicating the mutations acquired by the BA.4.6, BF.7, BQ.1, BQ.1.1, and BA.2.75.2 subvariants. (B and C) Infectivity of lentivirus pseudotyped with the indicated Omicron subvariant S constructs in HEK293T-ACE2 cells (B) (n = 3) or in Calu-3 cells (C) (n = 3). Bars represent means ± standard error. Significance relative to D614G was determined by one-way ANOVA with Bonferroni’s multiple testing correction. p values are represented as ns for p ≥ 0.05, ^∗p < 0.05, and ^∗∗∗∗p < 0.0001. (D–G) Infectivity of lentivirus pseudotyped with the indicated BA.4/5-derived mutant S constructs (D and F) (n = 3) or BA.2.75-derived mutant S constructs (E and G) (n = 3) in HEK293T-ACE2 or Calu-3 cells. Bars represent means ± standard error. Significance relative to BA.4/5 or BA.2.75 was determined by one-way ANOVA with Bonferroni’s multiple testing correction. p values are represented as ns for p ≥ 0.05, ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, and ^∗∗∗∗p < 0.0001.

Figure 2

Omicron subvariants, especially BQ.1, BQ.1.1, and BA.2.75.2, exhibit strong neutralization resistance Neutralizing antibody titers were determined against lentivirus pseudotyped with S from the Omicron subvariants and ancestral D614G variant for sera from health care workers (HCWs) (n = 15) who received a single homologous monovalent Moderna mRNA-1273 (n = 3) or Pfizer/BioNTech BNT162b2 (n = 12) mRNA booster vaccination (A); for sera from BA.1-wave hospitalized COVID-19 patients (n = 15) (B); or for sera from BA.4/5-wave SARS-CoV-2 infected Columbus, Ohio first responders and household contacts (n = 20) (C). Bars represent geometric means with 95% confidence intervals. Geometric means are displayed at the top of the plots. Significance relative to D614G was determined by one-way repeated measures ANOVA with Bonferroni’s multiple testing correction. p values are displayed as ns for p ≥ 0.05, ^∗p < 0.05, ^∗∗p < 0.01, and ^∗∗∗∗p < 0.0001.

Figure 3

Mutations N460K and F486S, and to a lesser extent, R346T and K444T, drive Omicron subvariant neutralization resistance Neutralizing antibody titers were determined against lentivirus pseudotyped with S from the BA.4/5-derived (A–C) or BA.2.75 (D–F) mutants for sera from healthcare workers (HCWs) (A and D) (n = 15) who received a single homologous monovalent Moderna mRNA-1273 (n = 3) or Pfizer/BioNTech BNT162b2 (n = 12) mRNA booster vaccination; for sera from BA.1-wave hospitalized COVID-19 patients (B and E) (n = 15); or for sera from BA.4/5-wave SARS-CoV-2 infected Columbus, Ohio first responders, and household contacts (C and F) (n = 20). Bars represent geometric means with 95% confidence intervals. Geometric means are displayed at the top of the plots. Significance relative to parental variants was determined by one-way repeated measures ANOVA with Bonferroni’s multiple testing correction. p values are displayed as ns for p ≥ 0.05, ^∗p < 0.05, ^∗∗p < 0.01, and ^∗∗∗∗p < 0.0001.

Figure 4

Homology modeling-based structural analyses of mutations essential for nAb resistance and fusogenicity (A and B) Structures of spike-antibody binding interface shown as ribbons. Spike recognition of class III neutralizing antibodies C1365 (A) and SW186 (B) are interfered by R346T and K444T mutations, where multiple hydrogen bonds and salt-bridge (shown as yellow dot lines) are abolished. (C) Structure of spike-ACE2 binding interface shown as ribbon. F486 interacts hydrophobically with M82 and Y83 on ACE2, whereas F486S impedes this interaction. (D) Structure of class I antibody (AZD8895) recognition focusing on residue F486, with multiple antibody residues forming a surrounding hydrophobic cage. The F486S mutation abolishes this interaction. (E) Structural model of HR2 region of SARS-CoV-2 S. Inset: electrostatic surface potential of HR2 membrane proximal region. D1199 contributes to the overall negative charge of this region.