Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages

The SARS-CoV-2 Omicron is currently the predominant circulating variant in the COVID-19 pandemic. The dominating Omicron sublineages respond to host immune pressure and develop advantageous mutations or genetic recombination, which result in variants that are more contagious or better at escaping immune responses in response to previous infection or vaccination. Meanwhile, multiple genetic recombination events have been reported in coinfection cases, the majority of which have resulted from the recombination between co-circulating Omicron BA.1 (or BA.1.1) and Delta variant or BA.2. Here, we review the knowledge and characterization of recombination for SARS-CoV-2 at the population level, provide an update on the occurrence of newly circulating Omicron sublineages, and discuss the effectiveness of novel vaccines/therapeutic drugs against the Omicron variant.

Automated summary

The SARS-CoV-2 Omicron variant is currently the predominant circulating virus in the COVID-19 pandemic. It responds to host immune pressure by developing advantageous mutations or genetic recombination, resulting in variants that are more contagious or better at evading immune responses. Recombination events between Omicron BA.1 (or BA.1.1) and Delta variant or BA.2 have been reported in coinfection cases. This review provides an update on Omicron sublineages, discusses the effectiveness of novel vaccines/therapeutic drugs against the Omicron variant, and explores the population-level recombination of SARS-CoV-2.