‘Double mutant’ variant of virus found as cases hit 53,000
India has detected a novel variant of the Sars-Cov-2 in seven states, and especially in high numbers in Maharashtra, the health ministry said on Wednesday, a discovery that experts said could, in part, explain a surge in cases although officials said it may be too soon to draw conclusions.
India recorded 53,410 new Covid-19 cases on Wednesday, the highest since October 23.
The variant carries mutations that include those denoted by the letters E484Q and L452R, which have separately been linked to characteristics that make the virus spread more readily and defeat, to some extent, immunity from a vaccine or past infection.
Two of these, E484Q and L452R, have been seen as a combination in a variant the government described as “double mutant”. It was found in a large number of samples, 206, in Maharashtra, which is in the grip of its worst wave of infections yet. “These mutations have been found in about 15-20% of samples and do not match any previously catalogued VOCs,” the ministry said in a statement. VOCs refers to variants of concern.
The director of the National Centre for Disease Control, Dr Sujeet Kumar said at the government’s weekly briefing on Covid-19 later in the day, that while 206 samples from Maharashtra had the new variant, “ data does not allow for us to make a direct correlation yet for the rise in cases.”
But other experts said the likelihood of a correlation is very high. “If 20% of samples in states like Maharashtra have shown mutant variants, it is very likely that the surge in Covid-19 cases is being driven by these mutations,” said Dr Gagandeep Kang, one of India’s top vaccinologists.
The officials at the briefing also said that samples from six more states recorded this variant, with Delhi having the next highest numbers at 9.
The government also confirmed the discovery of large number of people with the UK variant (B.1.1.7) in Punjab (336 cases) and in the case of this variant too, Delhi recorded the second-highest number of samples with this variant at 75. The UK variant is one of three VOCs. The other two were first seen in South Africa (B.1.351) and Brazil (P.1). In all, 771 samples from 18 states have turned up positive for these VOCs. “Since INSACOG initiated its work, 771 variants of concerns (VOCs) have been detected in a total of 10787 positive samples shared by States/UTs. These include 736 samples positive for viruses of the UK (B.1.1.7) lineage. 34 samples were found positive for viruses of the South African (B.1.351) lineage. 1 sample was found positive for viruses of the Brazilian (P.1) lineage. The samples with these VOCs have been identified in 18 States of the country,” the health ministry said. INSACOG stands for Indian SARS-CoV-2 Genomic Consortia.
Officials who asked not to be named said most of these were of people who came back from other countries and their contacts. In Punjab, CM Amarinder Singh said on Tuesday that most of the B.1.1.7 variants (326 out of 336) were found in samples taken from the community.
“Mutations in viruses occur naturally. It is a law of nature and we should per se not panic. We should remember if the virus does not replicate, it will not mutate — hence, the way to combat mutations is to suppress the chain of transmission,” said VK Paul, member (health), Niti Aayog, during the briefing.
Experts said the situation must now be closely watched, particularly in states where a large number of samples have the novel variant or the variants of concern. On Wednesday, Maharashtra accounted for 60% of the 53,410 daily new cases in the country and Punjab, 5%, although cases here have risen sharply from a low base.
Kang warned variants can have an impact on vaccine efficacy. “Vaccines may not be quite as effective against variants that are capable of immune escape, but it is very unlikely that vaccines will not protect at all against severe disease. We will have some protection from either prior infection and vaccination.”
An expert associated with the Maharashtra government’s Covid-19 response said the state is monitoring the variant’s impact closely. “It will become a cause for grave concern if mortality begins to increase. Presently mortality figures are considerably stable,” said this person, asking not to be named.
Dr Anurag Agarwal, director, CSIR-Institute of Genomics and Integrative Biology, said, “Presence of a variant of concern or suspected variant of concern does not automatically mean that they are causing the outbreak, but rather suggest caution and implementation of public health measures for containment. It is of course concerning, so these measures are being taken in parallel with investigations into the transmissibility, inhibition by antibodies of recovered people and inhibition by antibodies of vaccinated people, of such variants.”
Experts have long called for increasing genomic sequencing. The Indian consortium of labs under INSACOG carrying out genomic sequencing targeted 5% of all positive cases to be analysed beginning January, but, at a little under 11,000 , this number is short of the at least 48,000 it should have been, based on the number of 966,376 cases recorded between January 1 and March 23.
“The volume (of genomic sequencing) has been increased, I would say exponentially, in the past three months. Before INSACOG was established, we had sequenced 3,000 positive samples, which has gone up to about 11,000 now. It will obviously increase as we go on from here,” said Union health secretary Rajesh Bhushan at the briefing.
The Sars-Cov-2 virus was seen to be picking up about two mutations a month. But in mid-December, authorities in UK announced they had found a new variant with an unusually high number (17) of mutations and appeared to be spreading at a faster rate because it was more infective.
Later analyses showed this variant, which is regarded to get its most serious characteristic from the mutation N501Y, had a transmission advantage that was 0.4-0.7 times more than the predominant variant. This increase may seem minuscule but could lead to a significantly wider outbreak – as it eventually did in the UK, which struggled to bring down cases despite a lockdown over most of the winter.
On Wednesday, the government did not disclose how many other mutations are in the variant that has the E484Q and L452R. The two mutations occur on the spike protein, the portion of the virus that latches onto human cells and enters it.
The South African and the Brazilian variants both contain the E484K mutation. L452R is a mutation linked to a fast-spreading variant in California, US.
(with inputs from Eeshanpriya MS in Mumbai)