Cross-neutralization of Omicron BA.1 against BA.2 and BA.3 SARS-CoV-2

Abstract

The Omicron SARS-CoV-2 has several distinct sublineages, among which sublineage BA.1 is responsible for the initial Omicron surge and is now being replaced by BA.2 worldwide, whereas BA.3 is currently at a low frequency. The ongoing BA.1-to-BA.2 replacement underscores the importance to understand the cross-neutralization among the three Omicron sublineages. Here we test the neutralization of BA.1-infected human sera against BA.2, BA.3, and USA/WA1-2020 (a strain isolated in late January 2020). The BA.1-infected sera neutralize BA.1, BA.2, BA.3, and USA/WA1-2020 SARS-CoV-2s with geometric mean titers (GMTs) of 445, 107, 102, and 16, respectively. Thus, the neutralizing GMTs against heterologous BA.2, BA.3, and USA/WA1-2020 are 4.2-, 4.4-, and 28.4-fold lower than the GMT against homologous BA.1, respectively. These findings have implications in COVID-19 vaccine strategy.

Fig. 1. Cross-neutralization of human sera from unvaccinated individuals who were infected with Omicron BA.1 SARS-CoV-2.

A Omicron BA.1-, BA.2-, and BA.3-spike mNG SARS-CoV-2s. The full-length spike gene from Omicron BA.1, BA.2, or BA.3 was engineered into an mNG USA-WA1/2020 SARS-CoV-2. The mNG gene was engineered at the open-reading-frame-7 of the viral genome. Amino acid mutations, deletions, and insertions (Ins) are indicated for BA.1, BA.2, and BA.3 spikes in reference to the USA-WA1/2020 spike. L leader sequence, ORF open reading frame, NTD N-terminal domain of S1, RBD receptor binding domain of S1, S spike glycoprotein, S1 N-terminal furin cleavage fragment of S, S2 C-terminal furin cleavage fragment of S, E envelope protein, M membrane protein, N nucleoprotein, UTR untranslated region. B Scatterplot of neutralization titers. A panel of 20 human sera collected from Omicron BA.1-infected individuals were tested for the 50% fluorescent focus-reduction neutralization titers (FFRNT₅₀) against recombinant USA-WA1/2020 (gray circles), Omicron BA.1- (blue circles), BA.2- (green circles), and BA.3-spike (red circels) mNG SARS-CoV-2s. The neutralization titer for each virus was determined in duplicates. The serum information and FFRNT₅₀ values are summarized in Table 1. Each data point represents the geometric mean FFRNT₅₀ obtained with a serum specimen against the indicated virus. The bar heights and the numbers above indicate geometric mean titers (GMTs). Error bars indicate the 95% confidence interval (CI) of the GMTs. Data are presented as GMT with 95% CI. Statistical analysis was performed using the Wilcoxon matched-pairs signed-rank test. Two-tailed P values of the GMT against BA.1-spike and USA-WA1/2020, BA.2-spike, or BA.3 spikes are all <0.0001. C FFRNT₅₀ values with connected lines for individual sera. Two sera exhibiting slightly higher FFRNT₅₀s against BA.2 virus than that against BA.1-spike SARS-CoV-2 are indicated by symbol asterisk (serum ID 1 and 2 in Table 1).