Inactivated SARS-CoV-2 Variant Omicron, Lineage BA.5 (USA/COR-22-063113/2022)

The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus closely related to the human SARS-CoV virus (the cause of the 2002-2004 SARS epidemic). Like most RNA viruses, coronaviruses evolve rapidly, with their evolution typically observable and measurable on timescales of months or years. This evolutionary timescale is comparable to viral transmission events and ecological dynamics (e.g., changes in the number of infected individuals over time, immunity profiles, and population mobility). Therefore, evolutionary, ecological, and epidemiological processes influence each other, a hallmark of RNA viruses. Viral evolution depends on the rate at which mutations arise and spread through a population. Natural selection can target favorable mutations, such as the D614G mutation, which confers increased infectivity.

In late November 2021, the discovery of Omicron viruses, initially composed of three sister lineages (BA.1, BA.2, and BA.3), marked a new phase in the pandemic. Unlike previous outbreaks, which saw the emergence of highly divergent lineages, the new phase was dominated by successive sweeps of the Omicron sublineage. Shortly after BA.1 became globally dominant, it was replaced by BA.2. BA.2 further diverged into sublineages including BA.2.12.1 and BA.2.75, as well as BA.5. BA.5 reached high prevalence worldwide and is phylogenetically distinct from the BA.2 sublineage. Since BA.5 became globally dominant, multiple sublineages of Omicron viruses have emerged, but none has yet successfully surpassed BA.5. Instead, they exhibit remarkable convergent evolution, with multiple shared mutations in the spike gene.