- NEWS EXPLAINER
Why call it BA.2.12.1? A guide to the tangled Omicron family
For the foreseeable future, the coronavirus SARS-CoV-2 will continue evolving into new variants that lead to waves of infections. In 2020 and 2021, the World Health Organization (WHO) announced the emergence of variants of concern by giving them names from the Greek alphabet. But this year, Omicron has remained in the spotlight, with members of its family — subvariants — fuelling surges as they evade antibodies that people have generated from previous infections and vaccines. For example, the Omicron subvariant BA.2.12.1 is gaining ground in North America, now accounting for about 26% of the SARS-CoV-2 genomes submitted to the GISAID data initiative, and BA.4 and BA.5 are spreading rapidly in South Africa, comprising more than 90% of genomes sequenced.
Given the subvariants’ increasing dominance, Nature spoke to researchers to make sense of the current wonky names, and to learn why the WHO hasn’t given them Greek monikers that could spur policymakers to take stronger action.
How do scientists first identify a variant?
SARS-CoV-2 acquires mutations as it replicates in cells. Technically, this means that millions of variants probably arise every day. But the majority of mutations don’t improve the virus’s ability to survive and reproduce, and so these variants are lost to time — outcompeted by fitter versions.
Are new Omicron subvariants a threat? Here’s how scientists are keeping watch
A small portion of variants do, however, gain traction. When this happens, researchers conducting genomic surveillance flag samples that all have the same set of distinct mutations. To find out whether these samples constitute a new branch on the SARS-CoV-2 family tree, they contact bioinformaticians who have established nomenclature systems for the virus. One popular group, called Pango, consists of about two dozen evolutionary biologists and bioinformaticians who compare the samples’ sequences with hundreds of others using phylogenetic software.
The group’s name derives from a software program called Pangolin, originally created by bioinformatician Áine O’Toole at the University of Edinburgh, UK. If the analysis suggests that the new samples derived from the same recent common ancestor, it means that they are a distinct lineage on the coronavirus tree. In determining whether to name the lineage, Pango considers whether the variants have appeared more frequently over time, and whether their mutations are in regions of the virus that might give it a competitive edge. At this point, a lineage label doesn’t indicate risk. Rather, it allows scientists to keep an eye on a variant and learn more.
“We want to name everything that jumps out at us at an early stage so that we can define it and track it, and see if it is growing quickly relative to other lineages,” says Andrew Rambaut, an evolutionary biologist at the University of Edinburgh and a member of Pango. “You probably won’t hear of most of the lineages we name,” he says, because they couldn’t compete with other versions of SARS-CoV-2 and have disappeared.
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
24,99 € / 30 days
cancel any time
Subscribe to this journal
Receive 51 print issues and online access
204,58 € per year
only 4,01 € per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Nature 606, 446-447 (2022)
doi: https://doi.org/10.1038/d41586-022-01466-9
Are new Omicron subvariants a threat? Here’s how scientists are keeping watch
Omicron blindspots: why it’s hard to track coronavirus variants
Why does the Omicron sub-variant spread faster than the original?
The next variant: three key questions about what’s after Omicron
COVID-19: How Omicron overtook Delta in three charts
Where did Omicron come from? Three key theories
