Where did ‘weird’ Omicron come from?

Abstract

but WHO skipped the letters Nu and Xi, it said, “because Nu is too easily confounded with ‘new’ and Xi was not used because it is a common surname.”) One reason for concern about Omicron is that sequenced samples indicate it has rapidly replaced other variants in South Africa. But that picture might be skewed. For one, sequencing might have been focused on possible cases of the new variant in recent days, which could make it appear more frequent than it is. PCR data provide broader coverage and a less biased view, but there, too, samples with the S gene failure indicate a rapid rise of Omicron. The rising frequency could still be due in part to chance. In San Diego, a series of superspreading events at a university resulted in an explosion of one particular strain of SARS-CoV-2 earlier this year, Andersen says: “It was thousands of cases and they were all the same virus.” But the virus wasn’t notably more infectious. South Africa has seen relatively few cases recently, so a series of superspreading events could have led to the rapid increase of Omicron. “I suspect that a lot of that signal is explained by that and I desperately hope so,” Andersen says. Based on a comparison of different Omicron genomes, Andersen estimates the virus emerged sometime around late September or early October, which suggests it might be spreading more slowly than it appears to have. The other reason to be concerned is Omicron’s confusing genome. Its spike protein, which latches on to receptors on h…