A transmission electron micrograph of SARS-CoV-2 virus particles. Image: NIAID/Flickr, CC BY 2.0
- The BA.1 sub-lineage was the ‘original’ form of the omicron variant. Mutations of this variant resulted in the BA.2 sub-lineage.
- An INSACOG scientist told The Wire Science that BA.2 is now the dominant sub-lineage of the omicron variant in India.
- The transmissibility, disease severity and ability to evade vaccine-induced immunity of the two sub-lineages are “roughly similar”.
Almost three months after the omicron variant surfaced, one of its sub-lineages has started making the news.
Is it a serious threat? Do we have to be alarmed?
The BA.1 sub-lineage was the ‘original’ form of the omicron variant. Mutations of this variant resulted in the BA.2 sub-lineage.
On February 22, the WHO said that the fraction of patient samples sequenced that had the BA.2 variant has been “increasing relative to BA.1 in recent weeks”. However, the new sub-lineage has yet not become the dominant strain worldwide.
According to data aggregated by Outbreak.info, a project of three labs at a nonprofit research facility in California, 83 nations have reported the presence of the BA.2 sub-lineage in their territories. In fact, this sub-lineage has covered a large part of all continents except Africa, where only six countries have reported its presence.
On average, the sub-lineage hasn’t been found in more than 15% of samples in any country that is sequencing genomes. This data is based on sequencing data that researchers have submitted to the GISAID database.
“These sequences are a sample of the total number of cases – often a biased sample – and may not represent the true prevalence of the mutations in the population,” according to Outbreak.info.
A country sequencing fewer samples than ideal is at risk of being wrong about the spread of a given sub-lineage within its borders.
No government agency in India has said officially if BA.2 has become the dominant sub-lineage in India. The Indian SARS-CoV-2 Consortium on Genomics (INSACOG) hasn’t published its weekly bulletin since January 10. The bulletin on that date only said: “BA.2 lineage is a substantial fraction in India.”
Nonetheless, an INSACOG scientist (unnamed because he wasn’t authorised to speak to the press) told The Wire Science that BA.2 is now the dominant sub-lineage of the omicron variant in India.
Characteristics of BA.2
There are many characteristics, but two are particularly important: transmissibility and disease severity.
“Studies are ongoing to understand the reasons for this growth advantage, but initial data suggests that BA.2 appears inherently more transmissible than BA.1,” the WHO’s February 22 statement said. But it added an important caveat: “This difference in transmissibility appears to be much smaller than, for example, the difference between BA.1 and Delta.”
That is, the transmissibility gain between the delta variant and BA.1 is greater than that between BA.1 and BA.2.
The other critical parameter is disease severity. Greater transmissibility doesn’t necessarily mean more severe disease. BA.1 has been known to cause less severe disease than the delta variant even though it is more transmissible.
According to the WHO’s February 22 statement, the BA.2 sub-lineage has been found to cause more severe disease than BA.1 in hamsters – but that real-world evidence from among humans is pending.
A study by Japanese scientists, released on February 19, indicated that both BA.2 and BA.1 could be similar vis-à-vis their infections. Their data indicated, they wrote, “that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar.”
Data from Denmark, South Africa and the UK have also reportedly reached similar conclusions.
“Many countries now have substantial presence of BA.2. No difference in disease severity [between the two sub-lineages] has been found,” the WHO’s COVID-19 technical lead Maria Van Kerkhove has said.
Nonetheless, the WHO has deferred to other studies still underway before making a definitive statement on disease severity.
Some of these studies are also evaluating the impact of the BA.2 sub-lineage on vaccines and existing diagnostics methods.
Real-world data from the South African, Danish and British studies demonstrated that “immunity from vaccination or natural infection is high,” the WHO has said.
There have also been cases of reinfection – that is, a person first getting infected with BA.1 and then with BA.2. But they have also been too rare (at the level of populations) to have meaningful implications. Nonetheless, studies are also underway to understand them.
Not a separate variant
Eric Feigl-Ding, an epidemiologist and a senior fellow at the Federation of American Scientists in Washington D.C., recently tweeted that the WHO must declare BA.2 to be a new ‘variant of concern’ (VOC).
20) It is now 100% clear that the @WHO needs to declare #Ba2 a high risk “variant of concern”. Dear @mvankerkhove @doctorsoumya @DrTedros @gabbystern @DrMikeRyan — please make it so. VOC declaration of BA2 now ASAP!
See 🧵 below. https://t.co/2FpJHqPhIV
— Eric Feigl-Ding (@DrEricDing) February 20, 2022
This may not be possible. According to Kerkhove, because the omicron variant has been declared a VOC, its sub-lineages – including BA.2 – are also VOCs. In fact, BA.2 hasn’t even been classified as a ‘variant’.
BA.1 and BA.2 have slightly different genomes but that doesn’t warrant a separate name, since clinically they don’t differ much.