Explained: Which Covid-19 strains present are in India

As worries mounted over a recent study showing 7,684 mutations in the SARS-CoV-2 genome in India, the country on March 24 reported a new variant of the virus.

Setting off alarm bells, the variant, being called the ‘double mutant’, has been found in over 200 samples in Maharashtra, the hardest-hit state by the second wave.

If safety protocols are not followed, new versions that can spread faster or dominate the previous version could emerge, they warned as worries mounted over a recent study showing 7,684 mutations in the SARS-CoV-2 genome in India.

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“That doesn’t mean 7,000 variants are going around in the country. This only shows that the virus is mutating as expected, and we have documented what these mutations are,” Rakesh Mishra, CSIR-CCMB director and study co-author told PTI.

What is the difference between a mutant and a strain?

A mutation means a change in a nucleic acid base or amino acid molecule, and a virus containing this change is termed a mutant, explained virologist Upasana Ray. Mutations eventually accumulate to generate variants that differ from the original virus more and more, and so, a variant can have limited or even cumulative mutations. However, mutation is not unique to SARS-CoV-2, she said. The longer a virus stays in the population and spreads, the more the mutations and hence more variants.

The Health Ministry said from 400 cases reported on March 18, the infections by mutant strains have increased to 795 in the country. The ministry has clarified that there are only three variants of concern, detected in the United Kingdom (UK), South Africa and Brazil.

Here is a list of the variants detected in India:

Double mutant

The Union Health Ministry of India said the new "double mutant" variant of SARS-CoV-2 was detected in Delhi, Maharashtra and some other places that have been found in at least 18 states and union territories. As per epidemiologists, "double mutant" refers to an entirely new variant that has the characteristics of two already identified variants.

Also read: Covid-19: What is the ‘double mutant’ variant that has set off alarm bells?

UK variant

The coronavirus variant first identified in the UK, known as B.1.1.7, is deadlier than other variants circulating there, a new study confirmed. Overall, the risk of death with B.1.1.7 was 67% higher than the risk with other variants in England. As with earlier variants, patients' risk of death increased with age, male gender, and pre-existing medical conditions.

National Centre for Disease Control (NCDC) Director S K Singh said 771 cases of variants of concern (VOCs) have been detected in a total of 10,787 positive samples which include 736 samples positive for viruses of the UK (B.1.1.7) lineage. The UK variant of SARS-CoV-2 was first reported in India on December 29.

South African variant

In India, 34 samples were found positive for viruses of the South African (B.1.351) lineage. Strains from South Africa and Brazil have been detected in travellers coming to India from these countries. In order to curtail the spread of these variants, the government issued revised guidelines for international arrivals on February 17.

Brazilian variant

One sample for the Brazilian (P.1) lineage has been found positive in India. The South African and Brazilian variants have the potential to reinfect persons who have been previously infected with SARS-CoV-2.

Low prevalence

The analysis by CSIR-CCMB found that novel variants worrying many countries globally have so far only low prevalence in India. These include the variants with the immune-escape E484K mutation and the one with the N501Y mutation found to have a higher transmission rate. While the E484K mutation is found in both the South African and Brazil variant lineages, the N501Y mutation is found in the UK variant.

Multiple variants can "escape" vaccines

As for vaccines, Covishield developed by AstraZeneca and Oxford University by the Serum Institute of India and the homegrown Covaxin from Bharat Biotech are effective against the variants of the virus first identified in UK and Brazil.

There has been a rise in the number of daily infections in five states: Maharashtra, Kerala, Chhattisgarh, Punjab, and Madhya Pradesh in the past few days. Of these, Maharashtra and Kerala are the most worrying, accounting for about 75 per cent of the total active Covid-19 cases in the country. On March 25, India added over one lakh coronavirus infections in just two days with 53,476 new cases in a span of 24 hours, the highest single-day rise so far this year, pushing the nationwide Covid-19 tally of cases to 1,17,87,534, according to the Union Health Ministry data updated.

(With agency inputs)