The country’s current surge in Covid-19 cases is because of the BA.2 sub-variant of Omicron — which drove the third wave in January, along with BA.1 — and another sub-variant that has branched off from it, called BA.2.38.
Earlier this week, Delhi reported its first couple of cases of the BA.5 sub-variant of Omicron — this was one of the sub-variants that led to an increase in cases in South Africa a couple of months ago. The first BA.5 case in India was reported in late May in Telangana.
Cases of such sub-variants that are driving surges at many places globally are on the rise in India as well, but they currently account for only a small percentage of cases. Importantly, experts believe that there is no clinical significance of this change.
Which Covid-19 variants are currently the most in circulation?
Genome sequences uploaded to the global database GISAID show that BA.2.38 — which branched off from BA.2 — is dominant in the country, accounting for 30% of all sequences over the last 30 days.
This was followed by the BA.2 sub-variant itself, accounting for 28% of samples, shows an analysis of the GISAID data by outbreak.info.
(Outbreak.info is a project from Scripps Research that aggregates Covid data across scientific sources in order to track pandemic trends and integrate research and datasets into a single searchable library.)
Although BA.4 and BA.5 were detected in the country at almost the same time (in the beginning of May), BA.5 has been spreading faster, accounting for 7% of the sequences uploaded to the global database in the last 30 days.
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So far, India has reported at least 120 sequences of the BA.5 sub-variant, most of them in Tamil Nadu and Karnataka (43 each). As for the other sub-variant that led the Covid-19 surge in South Africa — BA.4 — 33 cases have been identified, which account for less than 1% of sequences uploaded to the global database over the last 30 days.
Another sub-variant of Omicron, called BA.2.12.1, is also in circulation — and has accounted for 5% of sequences over the last 30 days. At least 190 sequences of this sub-variant have been uploaded to the global database — most of them coming from Telangana (69), Karnataka (46), and Tamil Nadu (45).
What do we know about these sub-variants so far?
* BA.4 and BA.5 were detected by South Africa in January and February respectively. The variants triggered a surge of infections, and became dominant by May this year. They are now spreading to Europe, with BA.5 becoming the dominant variant in Portugal.
BA.4 and BA.5 have around 13% to 15% transmission advantage over BA.2, and can also circumvent some of the immunity. These variants have two mutations that were thought to be of concern by researchers: F486V that lab studies have associated with the ability of the virus to evade some of the existing immunity, and L452R that was found in the Delta variant associated with the ability to infect the lungs.
However, experience from other countries shows that the variants do not lead to an increase in severe disease, hospitalisation, and deaths. This time around, doctors have hardly seen Covid-19 pneumonia in patients, which had led to the increase in oxygen requirement and deaths during the Delta-variant driven second wave of the summer of 2021.
* The BA.2.12.1 variant, which was first detected in New York, is thought to be 23% to 27% more transmissible than the BA.2 sub-variant. It is also thought to evade some of the immunity gained through previous infection and vaccination.
* As for BA.2.38, which was recently re-classified, it has now been established that it leads to milder disease, just like its parent sub-variant BA.2.
So what has changed between the January wave and the current wave?
The biggest difference, researchers from INSACOG say, is that there is no cluster formation with any of the emerging sub-variants.
When Omicron was on the rise in December-end and January, there was clear cluster formation, which helped researchers quickly connect the dots that the increase was driven by the new variant.
Scientists from INSACOG say that the emerging variant is not responsible for the current surge in Covid-19 cases across the country.
“In a country of a billion people, detecting a few cases of a variant is of no meaning. We haven’t seen these cases occurring in clusters. Neither have we seen any changes in the symptoms or rate of hospitalisation so far,” a senior scientist from INSACOG said on condition of anonymity.
The scientists will hold further discussions with the National Centre for Disease Control (NCDC) to try and correlate the findings of genome sequencing with the epidemiological data on the ground.
The researcher said, “Although BA.2.38 was recently re-classified and is now present in many samples, we have not found any epidemiological evidence to suggest any change in the disease patterns.”
Another scientist from one of the regional INSACOG labs, said, “We are seeing more cases of BA.2.38 now, but there is no cluster formation. For example, when Omicron first started spreading in the country, we were able to see the clusters, and very quickly chart who passed the infection to whom. That hasn’t happened with the current new variants.”
Genome sequences uploaded to the global database GISAID show that BA.2.38 — which branched off from BA.2 — is dominant in the country, accounting for 30% of all sequences over the last 30 days. 
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