Study of the key mutations in SARS-CoV-2 Omicron variant and their functional impact on innate immune response

Abstract

SARS-CoV-2 continues to evolve and cultivates new variants with increased transmissibility and immune evasiveness. Major efforts have been made to identify mutations in spike protein that contribute to the high affinity to human ACE2 receptor and significant loss of neutralization antibodies, resulting in high transmissibility and immune evasiveness. Nevertheless, viral accessory proteins also play a determining role in virus fitness and are often understudied for their involvement in immune evasion. Here, amino acid substitutions in SARS-CoV-2 accessory proteins of recently emerged variants were monitored and analyzed. Distinct mutational signatures were found in known interferon antagonists orf6 and orf9b in delta (B.1.617.2) and omicron (B.1.1.529) variants. Moreover, recombinant viruses carrying these dominant mutations were generated by lambda red recombination. Through live SARS-CoV-2 infection experiments, it was determined that the omicron variant displays increased interferon resistance when compared to the ancestral virus during both early and late infections. 3-fold increase in inhibition dose 50 (IC50) of interferon-β was measured. A slightly higher sensitivity to interferon-β, however, was displayed by the delta variant at late infections. Profiling of interferon-stimulated genes critical to inhibit SARS-CoV-2 infections was conducted in a cell model to identify potential escape of interferon mechanisms. The data here provides critical evidence of innate immune evasion in SARS-CoV-2 variants, which may contribute to the increased transmissibility. Moreover, establishment of lambda red recombination techniques has streamlined the generation of mutant viruses that facilitate downstream characterizations.