Why call it BA.2.12.1?A guide to the tangled Omicron family

In the near future, the coronavirus SARS-CoV-2 will continue to evolve into new variants that will lead to a wave of infection. In 2020 and 2021, the World Health Organization (WHO) will Name them from Greek letters.. But this year, Omicron continues to be in the limelight, and subvariants that are members of its family are helping people to surge in avoiding antibodies produced by previous infections and vaccines. For example, the Omicron subvariant BA.2.12.1 is well established in North America and accounts for approximately 26% of the SARS-CoV-2 genome submitted to the GISAID Data Initiative, as well as BA.4 and BA.5. Spreading rapidly in South AfricaConsists of over 90% of the sequenced genome.

Given the increasing dominance of subvariants Nature We talked to researchers to understand the current strange name and why WHO did not give policymakers the Greek Monica, which could encourage strong action.

How do scientists first identify variants?

SARS-CoV-2 acquires mutations when it replicates intracellularly. Technically, this probably means that millions of variants occur every day. However, most of the mutations do not improve the ability of the virus to survive and reproduce, so these variants are lost over time and overcome the more appropriate version.

However, only a small percentage of the variants gain traction. When this happens, researchers who perform samples of genome surveillance flags all have the same set of different mutations. Contact bioinformatics, which has established a virus naming system, to find out if these samples form a new branch of the SARS-CoV-2 family tree. One of the popular groups called Pango consists of about 20 evolutionary biologists and bioinformatics who use phylogenetic software to compare sample sequences with hundreds of other sequences.

The name of this group comes from a software program called Pangolin created by Áine O’Toole, a bioinformatics engineer at the University of Edinburgh in the United Kingdom. If the analysis suggests new samples from the same recent common ancestor, it means they are separate strains on the coronavirus tree. In deciding whether to name the lineage, Pango asked if variants appeared more frequently over time, and if those mutations were in the area of ​​the virus and could be competitive. Please consider. At this point, the lineage label shows no risk. Rather, it allows scientists to monitor varieties and learn more.

Andrew Lambo, an evolutionary biologist at the University of Edinburgh, said: And members of Pango. “Most of the strains we name are probably not heard,” he says. Because they couldn’t compete with other versions of SARS-CoV-2 and disappeared.

What is the name of the variant?

When naming variants, the Pango Commission uses a hierarchical system that shows the evolutionary history of variants and when they were discovered compared to other variants. The first letter of the name reflects when Pango labeled the lineage, A to Z, AA to AZ, BA to BZ, and so on. The next digit, separated by a full stop, indicates the order of branching from that lineage. For example, BA.1, BA.2, BA.3, BA.4, and BA.5 are the first five branches derived from the original Omicron ancestors. And BA.2.12.1 is the twelfth lineage that branches off from BA.2, and then the first named branch in that twelfth bush. All subvariants are variants, but researchers use the former term when they want to suggest that the lineage belongs to a larger group, such as Omicron.

If a mutant strain evades the immune system much more effectively than other mutant strains in circulation, causes more serious disease, or is much more contagious, WHO will call it a “variant of concern”. We may change the name to Greek letters. For example, multiple related mutations in a variant labeled B.1.1.529 last year, coupled with its rapid rise, Prompted WHO to change its name to Omicron While Pango’s technical name aims to help researchers track the evolution of SARS-CoV-2, WHO’s system prioritizes ease of communication with the general public. ..

Given all these variants, is SARS-CoV-2 evolving faster than other viruses?

That’s not always the case, says Ramboat. Researchers have found incredible diversity in SARS-CoV-2, but they are sequencing the virus at an unprecedented rate. Since January 2020, a record 11 million SARS-CoV-2 genomes have been uploaded to the popular GISAID data platform. In contrast, researchers have uploaded approximately 1.6 million influenza virus sequences to GISAID’s EpiFlu database since May 2008.

Still, Rambo says there are still many questions about how SARS-CoV-2 is evolving. This is due to the fact that sequencing is rarely performed in some parts of the world, and genomic surveillance is reduced in some raging countries.

Can Omicron subvariants such as BA.4 eventually receive Greek names?

Yes, it hasn’t happened yet. Some researchers have said that the currently proliferating Omicron variants, such as BA.4 and BA.2.12.1, communicate with government and the general public when considering COVID-19 control measures such as face masks. Claims to deserve a simpler name to help. , Is declining. They also pointed out that, unlike the less-discussed Delta subvariants in the media, BA.4 and BA.2.12.1 can overcome the immunity provided by previous infections with other Omicron subvariants. I am. This was unexpected, said Houriiyah Tegally, a bioinformatics engineer at the Epidemic Response and Innovation Center in Stellenbosch, South Africa. “Everyone thought that only new varieties would cause new waves, but now that Omicron can do that, it may be necessary to adapt the naming system,” she suggests. It is.

However, WHO has so far resisted this idea. WHO virologist Lorenzo Subissi states that the ability of antigenic escape does not differ significantly between submutants of Omicron. He adds that if future studies show that Omicron subvariants cause more serious illness than other Omicron varieties, the authorities’ assessments could change. Maria Van Kerkhove, WHO’s COVID-19 tech leader, also does not recommend replacing the tech label with the Greek name in the hope of driving leaders to take the ongoing pandemic more seriously. I add. “This is already a scary virus, but it still kills an unnecessarily large number of people,” she said, suggesting that world leaders should already pay attention.