Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine

Abstract

The newly emerged Omicron SARS-CoV-2 has several distinct sublineages including BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we have engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralize USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of >20; the neutralization geometric mean titers (GMTs) against the four viruses are 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s are 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.

Trial registration: ClinicalTrials.gov NCT04368728.

Fig. 1. Serum neutralization of Omicron BA.1-, BA.2-, and BA.3-spike mNG SARS-CoV-2s and USA-WA1/2020 after three doses of BNT162b2.

A panel of 22 human sera collected 1 month after dose 3 of the BNT162b2 vaccine were tested for the 50% fluorescent focus-reduction neutralization titers (FFRNT₅₀) against recombinant USA-WA1/2020 (black circles), Omicron BA.1- (blue circles), BA.2- (green circles), and BA.3-spike (red circles) mNG SARS-CoV-2s. The serum collection scheme is described in Fig. S3 as previously reported. The BA.1-, BA.2-, and BA.3-spike mNG SARS-CoV-2s were produced by engineering the complete Omicron spike genes into the mNG USA-WA1/2020. Each data point represents the geometric mean FFRNT₅₀ obtained with a serum specimen against the indicated virus, as detailed in Tables S1. The neutralization titers for BA.1-, BA.2-, and BA.3-spike mNG SARS-CoV-2s were determined in duplicate assays; the FFRNT₅₀s for USA-WA1/2020 mNG SARS-CoV-2 were determined in two independent experiments, each with duplicate assays. Data are presented as the geometric mean of titer (GMT) with 95% confidence intervals (CI). The bar heights and the numbers above indicate GMTs. The whiskers indicate 95% CI. The dotted line indicates the limit of detection of FFRNT₅₀. Statistical analysis was performed with the use of the Wilcoxon matched-pairs signed-rank test. The statistical significances of the differences between geometric mean titers against the USA-WA1/2020 and Omicron BA.1-, BA.2-, or BA.3-spike SARS-CoV-2 are all p (two-tailed) <0.0001. The statistical significances of the differences between geometric mean titers against the BA.3 and Omicron BA.1-, or BA.2-spike SARS-CoV-2 are p (two-tailed) <0.0001, and p (two-tailed) = 0.004, respectively.