Genomic sequencing studies of SARS-CoV-2 samples from across the State done in national as well as State scientific institutions have indicated wide and intense transmission of various mutant variants, including variants of concern (VOC), confirming the worst fears of many public health experts.
“Sequencing of samples from across all districts as on April 1 done by the Institute of Genomics and Integrative Biology (IGIB), New Delhi, has revealed the presence of the variant B.1.1.7 (first detected in the U.K.) and B.1.617 (“double mutant” reported from India) in 40% of the samples. Given the high infectivity potential of these variants, we project that this proportion would have now increased to 70%. In about 2% samples, the presence of B.1.351, first reported in South Africa, was also found. A few samples analysed from Thiruvananthpuram district at the Rajiv Gandhi Centre for Biotechnology has indicated the presence of B.1.1.7 as well as a variant with a different double mutation,” a senior member of the expert committee on COVID, told The Hindu .
Lockdown suggested
“The situation is quite alarming. Disease transmission has reached a point wherein mass testing alone is not going to make a difference. Our recommendation would be that the State go in for a two-week cyclical lockdown to bring down disease transmission immediately,” he added.
The B.1.1.7 variant is 43% to 90% more contagious than the original wild-type virus, researchers from London School of Hygiene and Tropical Medicine had reported. The same team reported in Nature on March 15, 2021, that the hazard of death associated with B.1.1.7 is 61% (42–82%) higher than with pre-existing variants.
Virus samples from Kerala from the first half of March, analysed by the IGIB had not revealed the presence of any VOC. However it is the State-wide samples in the second half of March and some current samples (last week) from Veeranakavu, Kuttichal, Kattakada areas in the capital district which revealed the presence of circulating virus variants.
As the State’s case graph began rising exponentially,the government last week asked Rajiv Gandhi Centre for Biotechnology (RGCB) and the multidisciplinary lab at the Kozhikode MCH to take up virus sample studies, involving amplification of the virus’ spike protein receptor-binding domain, to assess if any mutations had taken place.
10 current samples
Accordingly, the State public health lab and the microbiology lab at the Thiruvananthapuram Medical College had handed over 10 current samples each to the RGCB. It is learnt that of the 10 samples provided by MCH, three had the N501Y mutation found in the B.1.1.7 variant. The remaining samples had a combination of two mutations, L452R and T478K.
It might be recalled that L452R is one of the mutations found in the “double mutant” B.1.617 variant found predominantly in Maharashtra. According to a pre-print in biorxiv.org, L452R can reinforce the virus’s affinity to the ACE2 receptor, increase viral replication and escape even T cell immunity.
The mutation T478K is predominantly found in the variant B.1.1.222, first detected in Mexico in April 2020. The L452R and T478K mutation together had been found earlier in SARS-CoV-2 samples from Chhattisgarh, Orissa and Bihar.
The B.1.351variant carries two spike protein mutations, N501Y, which makes it very contagious, while the E484K mutation renders the virus powerful enough to dodge the body’s immune system response and blunt the efficacy of vaccines against it.
The State has decided to continue the current genome sequencing studies and to analyse more samples from districts.
