Karnataka rechecks 1.3K genomic sequences for UK Delta Covid sub-variant

Members of the state Covid-19 Genomic Surveillance Committee have reanalysed more than 1,300 Covid samples for the presence of AY.4.2, a sub-lineage of Delta and a variant under investigation, which is already rising in the UK.

Though no AY.4.2 has been detected in the reanalysed samples so far in Karnataka, researchers have noted the presence of both mutations A222V and Y145H individually in a number of samples. These are the two key mutations in the spike protein of the newly designated AY.4.2.

According to data aggregating site Outbreak.info, in India 13 AY.4.2-positive samples have been found in 63,136 samples sequenced so far. In comparison, in the UK, it has been found in 13,895 samples out of 10,45,504 sequenced.

In Russia, researchers have reportedly said this Delta subvariant maybe 10% more infectious than the original Delta and could ultimately replace it.

Explaining the situation in Karnataka, Dr Vishal Rao, member of the state Covid-19 Genomic Surveillance Committee said, “In the last four runs, more than 1,300 samples were sequenced at Strand Life Sciences, which were reanalysed for the presence of AY.4.2. No AY.4.2 has been detected so far.

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“We have, however, noted the presence of both mutations A222V (in 140 samples in total, eight in the AY.4 lineage) and Y145H (four in total, of which three are in the AY.4 lineage) individually in the 2,671 samples sequenced mostly between June and October this year.”

Citing the UK Health Security Agency’s Technical Briefing on October 22, Dr Vinod Scaria, a scientist at CSIR Institute of Genomics and Integrative Biology, Delhi, tweeted saying the growth rate of AY.4.2 was 17% and that the secondary attack rate among household contacts was 12.4% when for Delta it was 11.1%.

Secondary attack rates are based on positive tests among contacts in household settings. According to the briefing document, there are 15,120 confirmed AY.4.2 cases in the UK as of October 21.

Scaria told DH the rule of thumb now is to sequence more proportions of Covid samples when the cases are less, since the maximum diversity is observed when cases are low.

“Sequencing more only at the peak of a wave is going to capture more of the same kind, the variant which was successful. We need to sequence more now, especially sequence travellers who are positive. AY.4.2 is what the UK found. There are probably many more which nobody is looking for and not finding. We are probably missing it. The UK consistently finds new variants because of a nationwide and comprehensive sequencing programme,” Scaria said.

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