The Omicron variant identified in Southern Africa in late November 2021 is the product of extensive evolution within an infection context that has so far left no obvious traces of intermediate forms since it diverged from the B.1.1 lineage (presumably at some time in mid to late 2020).
“Our analysis identifies three clustered sets of mutations in the Spike protein, involving 13 amino acids that have previously been highly conserved across SARS-CoV-2 and other Sarbecoviruses. This dramatic about-face in evolutionary dynamics at these 13 sites suggests that Omicron’s Spike protein structure has accommodated significant sequence change, likely in response to selective pressures favoring increased transmission,immune evasion, or viral replication—either at the population level or in a single or group of chronically infected individuals—and has potentially acquired new functionality.”
