BA.2 likely drove 3rd wave in some states
The first real-world analysis of infection trends split by BA.2 and the other Omicron lineages offers several insights. These findings are based on the latest variant technical briefing by the UK Health Security Agency released over the weekend.
Did the even faster-spreading Omicron variant offshoot BA.2 drive India’s third Covid-19 wave? Data from the global genome sequence repository GISAID seems to suggest so, at least for several states from where genotyping data has been more consistently shared.
BA.2 is one of the offshoots of the Omicron variant and has recently been seen displacing its predecessor, the BA.1. The Omicron variant’s earliest lineages B.1.1.529 and BA.1 itself have been significantly more transmissible, having displaced the Delta variant from most parts of the world.
For a sub-lineage to spread even faster, the BA.2 is now a variant under investigation.
The new evidence on BA.2
The first real-world analysis of infection trends split by BA.2 and the other Omicron lineages offers several insights. These findings are based on the latest variant technical briefing by the UK Health Security Agency released over the weekend.
First, they corroborate that the BA.2 indeed spreads faster than BA.1 based on two metrics: sequencing data from across England and estimates of secondary infection rates within households. “Whilst growth rates can be overestimates early in the emergence of a variant, the apparent growth advantage is currently substantial,” the report said.
The secondary attack rate for BA.2 was 13.4%, compared to 10.3% in the case of BA.1. This gives BA.2 a crude 30% transmission advantage over BA.1, which itself is estimated to be 50% more transmissible than the Delta variant.
Second, they find that there is no difference in how resistant BA.2 may or may not be as compared to BA.1, which means vaccines are likely to be equally protective with the newer offshoot. It also cited an unpublished University of Oxford report that found antibodies from vaccinated people neutralised BA.2 and BA.1 to similar degrees.
All in all, it appears the BA.2 offshoot does not seem to be more resistant. In case of infection severity, the UKHSA report adds that there is insufficient data to make an assessment just yet.
BA.2 in India
According to genome sequencing data submitted by Indian labs to the GISAID database, more than half of the cases in the last month may be of BA.2, according to an analysis on outbreak.info.
This is relevant because nationwide, cases began to spike distinctly from early January.
In fact, a more detailed analysis of India data on GISAID by Texas-based molecular biologist Bijaya Dhakal suggests infections in several states has been dominated by BA.2.
Among the key states where the trend is clear are Delhi, Uttar Pradesh, Karnataka and Gujarat.
In Uttar Pradesh, a state which goes to elections and where large scale political rallies were held till January 8, the BA.2 became the most dominant variant to be sampled in the first week of the month itself. The state, like many others, has submitted a low number of samples, the data shared by Dhakal in a Twitter thread on Sunday showed, but the trend appeared to be distinct from January 2.
Similar findings for Karnataka, where BA.2 has likely replaced Delta, BA.1/BA.1.1, the molecular biologist added
In Delhi, the BA.1 and BA.1.1 switch to BA.2 appears to have happened at end of December itself, the latest date for which sample details were available. Union and Delhi government officials have separately corroborated this, saying that they had found BA.2 to have increased in proportion.
One of the most updated sequencing data is from Gujarat, where too BA.2 became dominant from at least the second week of January, the GISAID data showed.
But in Maharashtra, there “is almost a hodgepodge of all three important variants: Delta, Omicron BA.1/BA.1.1 and Omicron BA.2”, Dhakal wrote.
Genome sequencing data is subject to some bias because there are not always representative of community spread. But if a variant starts to be detected in an increasing frequency consistently, it is safe to assume it is becoming predominant.
In this context, India will likely answer the most significant question regarding BA.2: the offshoot is likely no more virulent (that is, causing more severe disease) than other Omicron lineages. Even though there has been a spike in many parts of the country, death and hospitalisation rates have remained low, consistent with the experience of South Africa and UK.
But the GISAID data also highlights significant genome surveillance blindspots, which could hamper India’s outbreak monitoring. For instance, Bihar the third most populated state, has submitted only one sequence to the database since September last year.