Genomic studies yet to find virus variants of concern in State

Thiruvananthapuram The genomic and epidemiological surveillance study on COVID-19 being conducted across Kerala has so far not found any evidence of new SARS CoV2 lineages of concern. While a formal study report is yet to be released, much of the highlights are available in the public domain

“Over 700 genomes of SARS-CoV-2 have been sequenced from Kerala so far. We have identified several new lineages of the virus in the State and those found in other parts of the country. Some lineages need to be watched with caution, but genomic studies have so far not revealed anything alarming for Kerala,” Vinod Scaria, senior scientist, CSIR-Institute of Genomics and Integrative Biology (IGIB), who is leading the study, told The Hindu.

In September, the IGIB, which conducted a pilot study of some 200 virus samples from Kozhikode district, had reported that the virus strains circulating in the State at the time were marked by the D614G mutation, which made the virus very infective . It also reported that these strains were introduced into the State by inter-State travellers.

This was the first and the most comprehensive report on the evolution of SARS CoV2 isolates from Kerala, which gave the initial insights into the transmission dynamics of COVID-19 in the State. It was following this that the State tied up with the IGIB to do a State-wide study, collecting samples from all districts over a period, to understand the genetic epidemiology of COVID-19 in the State.

The study was to essentially understand the emerging lineages/clades of SARS- CoV-2 in Kerala so that policy decisions and its implementation can be evidence-based.

Viruses mutate continuously and new lineages emerge. Samples sequenced between December and January has not given any evidence of new mutations which might signal any alarm or might be linked to the ongoing transmission in Kerala. The disease transmission pattern in the State also does not seem to indicate an unrestrained spread at any point in time which might suggest the emergence of a new strain.

The 501Y.V2 variant or the B.1.351 lineage which has rapidly spread in South Africa and has the immune escape E484K mutation (mutation which can evade human immune system response) has not yet been detected in any samples from Kerala so far, Dr. Scaria said. It also does not mean that the variant may not emerge in the State.

“We have previously identified some 19 genetic variants in India with immune escape potential, of which the N440K mutation which was found in over 30% of the samples collected from Kurnool, Andhra Pradesh, in August-Septemberhas started appearing in several States, including Kerala. This is a variant we need to watch out for,” he added.

“We have only looked at samples collected over a single time point from Kerala. We will need to continue the genomic surveillance to identify trends, whether any variant is taking over the transmission. We hope that the January-February lot of samples will give us a better idea about this,” Dr. Scaria said.

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