Even as the State strengthens testing and surveillance of travellers from UK, in an effort to be on guard against the UK variant of SARS-CoV-2 named B.1.1.7, epidemiologists have flagged the possibility that the virus could already be in circulation in the State.
The UK variant is believed to have first emerged in UK in September, and by November, it became prevalent in the southeast of England, accounting for 60% of recent cases in London. Global Initiative on Sharing All Influenza Data (GISAID) update on Saturday says that B.1.1.7 now amounts to 31% of all UK virus genomes collected since December 1.
“This new variant has been in circulation in UK since mid-September and it has been found in other nations like Denmark, Australia, Brazil, etc. Kerala handles a significant volume of international air traffic through its airports and has one of the highest proportions of expatiate population. Right now, the State’s case graph of new COVID-19 cases is on the rise too. When all these facts are added up, one should naturally maintain a high level of suspicion that if the B.1.1.7 variant is getting around, it would have reached Kerala by now,” a senior epidemiologist said.
In fact, the UK variant or even a hitherto unknown variant could have independently emerged anywhere in the country and be already in circulation because virus evolution is not dependent upon international borders or flight restrictions.
Genome sequencing
The Rajiv Gandhi Centre for Biotechnology (RGCB), the only scientific institution in the State which has full-fledged facilities for doing genome sequencing, has been randomly sequencing the SARS-CoV-2 samples it has been receiving for RT-PCR testing.
“We have sequenced samples till last week and have been looking at all four genes of the virus expressing major proteins. We have not found the UK variant B.1.1.7 so far, but then, the RGCB is handling only samples from Thiruvananthapuram and Kollam districts. Our repository of SARS-CoV-2 now contains the Wuhan, U.S., and Taiwan variants, all of which have minor or inconsequential mutations, said R. Radhakrishnan, Head of Laboratory Medicine and Molecular Diagnostics, RGCB.
“The RGCB can easily do genomic surveillance in the State to check for the UK variant as there is no need to go for whole genome sequencing. To check for the mutation, we just have to look at the virus spike protein’s receptor binding region, which is just a small portion of the 4,000 nucleotide length of the spike protein,” Dr. Radhakrishnan said.
Unless the State is regularly doing genomic surveillance, one would hardly know about virus mutations that could already be taking place.
“In fact, Kerala is the only State that has recognised the importance of genomic surveillance and has already initiated the same,” said Vinod Scaria, senior scientist at CSIR-Institute of Genomics and Integrative Biology (IGIB).
The State government has already tied up with IGIB for initiating genomic surveillance of SARS-CoV-2 strains in Kerala, after a pilot study done by IGIB found that the predominant virus clade A2a circulating in Kerala was marked by the mutant variant D614G.
The government has been sending samples from all districts since November to IGIB for genomic analysis. The final protocols were being drawn up and the study would commence soon, Dr. Scaria said.
Genomic sequencing of some 4,300 samples from across the country during June to September has not detected this new UK variant. If it is already circulating in Kerala, all systems are in place to detect it, he added.
