Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

Abstract

The emergence of the SARS-CoV-2 variant of concern Omicron (Pango lineage B.1.1.529), first identified in Botswana and South Africa, may compromise vaccine effectiveness and lead to re-infections¹. Here we investigated Omicron escape from neutralization by antibodies from South African individuals vaccinated with Pfizer BNT162b2. We used blood samples taken soon after vaccination from individuals who were vaccinated and previously infected with SARS-CoV-2 or vaccinated with no evidence of previous infection. We isolated and sequence-confirmed live Omicron virus from an infected person and observed that Omicron requires the angiotensin-converting enzyme 2 (ACE2) receptor to infect cells. We compared plasma neutralization of Omicron relative to an ancestral SARS-CoV-2 strain and found that neutralization of ancestral virus was much higher in infected and vaccinated individuals compared with the vaccinated-only participants. However, both groups showed a 22-fold reduction in vaccine-elicited neutralization by the Omicron variant. Participants who were vaccinated and had previously been infected exhibited residual neutralization of Omicron similar to the level of neutralization of the ancestral virus observed in the vaccination-only group. These data support the notion that reasonable protection against Omicron may be maintained using vaccination approaches.

Fig. 1. ACE2 dependence and neutralization of the Omicron variant by Pfizer BNT162b2-elicited immunity.

a, Representative images showing infection foci in wells of a multi-well plate with titration of live SARS-CoV-2 Omicron virus on H1299-ACE2 and H1299 parental cells. Numbers above well images denote viral stock dilution. Scale bars, 2 mm. b, Number of foci as a function of Omicron virus stock dilution. Data are mean ± s.d. of six replicates from two independent experiments. c, Neutralization of Omicron virus compared with D614G ancestral virus by plasma from participants vaccinated with two doses of BNT162b2 and previously SARS-CoV-2 infected (blue) or uninfected (orange). Numbers in black above each virus strain are geometric mean titres (GMT) of the reciprocal plasma dilution (FRNT₅₀) resulting in 50% reduction in infection foci. The red horizontal line denotes the most concentrated plasma used. Twenty-one samples were tested from n = 19 participants in 2 independent experiments (n = 13 vaccinated and previously infected; n = 6 vaccinated only). Grey points denote measurements where 50% neutralization was not achieved with the most concentrated plasma used. P = 4.8 × 10⁻⁵, Wilcoxon rank-sum test. d, Geometric mean and 95% confidence interval of the fold change in neutralization between ancestral D614G and Omicron neutralization in plasma. Purple denotes all participants, blue denotes vaccinated individuals with previous SARS-CoV-2 infection, orange denotes vaccinated-only individuals, and yellow denotes all participants excluding those in whom 50% neutralization was not achieved. e, Mean predicted vaccine efficacy and 95% confidence intervals against symptomatic infection with Omicron using data from previous randomized controlled trials and the 22-fold difference between D614G and Omicron observed in this study^,. Predictions are for vaccinated and boosted (B, red) or vaccinated-only (V, blue) individuals.

Extended Data Fig. 1. Generation of H1299-ACE2 clonal cell line.

(A) The H1299 human non-small cell lung carcinoma cell line with YFP labelled histone H2AZ was spinfected with the pHAGE2-EF1a-Int-ACE2 lentivector. Cells were single cell cloned by limiting dilution in a 384-well plate. Clones were expanded into duplicate 96-well plates, where one plate was used to select infectable clones based on mCherry signal from infection with SARS-CoV-2 mCherry expressing spike pseudotyped lentivirus. Clones were chosen based on infectability and expanded from the non-infected replicate 96-well plate. (B) Flow cytometry of SARS-CoV-2 mCherry expressing spike pseudotyped lentivirus infection in H1299-ACE2 cells versus H1299 parental cells.

Extended Data Fig. 2. Comparison of SARS-CoV-2 infection in H1299-ACE2 and Vero E6 cells.

Both H1299-ACE2 and Vero E6 cells were infected with the same viral stock in the same experiment with D614G virus (A) or Beta virus (B) and a focus forming assay was performed. (C) Focus forming assay with stock of Omicron virus isolate on H1299-ACE2 and Vero E6 cells. (D) Comparison of passage 2 (P2) and passage 3 (P3) stock, where P3 stock was generated by infection of 1 mL of cell-free P2 stock in 20 mL of Vero E6 cells seeded at 2x10⁵ cells per mL and incubated over 4 days. Numbers above well images denote viral stock dilution. Scale bar is 2 mm.

Extended Data Fig. 3. Neutralization of the Beta variant by Pfizer BNT162b2 elicited immunity.

Neutralization of the Beta variant virus compared to D614G ancestral virus in H1299-ACE2 (A) or Vero E6 cells (B) in participants vaccinated with BNT162b2 and infected by SARS-CoV-2 (green) or vaccinated only (orange). Numbers in black above each virus strain are geometric mean titers (GMT) of the reciprocal plasma dilution (FRNT₅₀) resulting in 50% reduction in the number of infection foci. Numbers in red denote fold-change in GMT between virus strain on the left and the virus strain on the right of each panel. Red horizontal line denotes most concentrated plasma used. Samples were tested from the n = 19 participants described in Table S2 and S3, where n = 6 were vaccinated only and n = 13 were vaccinated and previously infected. p = 0.006 for both (A) and (B) as determined by the Wilcoxon rank sum test.