The coronavirus SARS-CoV-2 genome has evolved as it transmits through its human hosts, but luckily the novel variants worrying many countries globally have had a low prevalence here. But, the low prevalence of — immune-escape ‘E484K’ mutation and the ‘N501Y’ mutation with higher transmission rate — could also be simply because not enough sequencing has been done.
“More coronavirus genomes need to be sequenced across the country to accurately identify the emergence of these two and any other new variants,” asserted CSIR-CCMB Director Rakesh Mishra on Friday.
CCMB scientists led by Dr. Mishra, having genome sequenced over 5,000 coronavirus variants so far, have also found that a few novel variants are spreading more in some States. “We now have emerging evidence that ‘N440K’ is spreading a lot more in southern states. Closer surveillance is needed to understand its spread properly. Accurate and timely detection of new variants that may show greater infectivity or worse clinical symptoms, including immune escape, will be extremely important to preempt disastrous consequences,” he said.
The Director and his team consisting of Surabhi Srivastava, Sofia Banu, Priya Singh, Divya Tej Sowpati have just published a paper — “SARS-CoV-2 genomics – an Indian perspective on sequencing viral variants” — presenting an exhaustive analysis of the coronavirus variants and how they have evolved over the course of the pandemic in the country. (https://data.ccmb.res.in/gear19/).
Variants discovered
In this paper, the scientists explain how different coronavirus variants gained prevalence and one of the variants ‘A3i’ had mutations that were predicted to make its spread slower. It was overtaken by the globally prevalent ‘A2a’ variant, carrying the ‘D614G’ mutation, by June 2020. The ‘A2a’ variant has remained in global dominance for the major part of last year.
This paper documents the spike mutation landscape of SARS-CoV-2, showcasing the ones that have emerged with high prevalence, which have implications in COVID-19 surveillance and management, vaccines, therapeutics, and the emergence of reinfections.
“We need to have a focused approach towards monitoring the virus mutations. India has not been sequencing SARS-CoV-2 isolates to full capacity, having deposited only about 6,400 genomes so far. The Indian government’s initiative of INSACOG, which aims to sequence 5% of all positive cases, should soon address this,” observed co-corresponding author Divya Tej Sowpati.
‘Curb spread’
The take home of this comprehensive work is that due to the natural process of mutation, variants will keep emerging, hence the best way to control the potential damage is to exercise extensive genome surveillance and take measures to prevent the spread of new variants as and when detected.
“While vaccines may be very helpful, the social vaccine of face masks, hand-hygiene and physical distance is the most effective weapon we have against this pandemic,” adds Dr. Mishra. “Lesser spread of the virus also decreases the scope for emergence and accumulation of harmful mutants,” pointed out lead author Surabhi Srivastava.
