2021 began with India declaring victory against the novel coronavirus – even as experts warned against it.

The bubble burst pretty quickly.

India is currently in the middle of a ferocious second wave, recording 1,61,736 new Covid-19 cases on Tuesday, overtaking Brazil to become the second-most affected country in the world.

One of the factors propelling the second wave is the emergence of a new, fast-spreading Indian variant of the virus. It is being called a “double mutant” variant because it has two mutations. It has been found in 61% of samples put through genome sequencing in Maharashtra, the worst hit state in India, as the Indian Express reported on April 14, strengthening suspicions that the current surge is powered by a more transmissible strain.

Labelled B.1.617, the double mutant variant was first detected in India, but has been now found in eight countries, with 70% of samples containing the mutations originating from India.

Early warnings from Vidarbha

In February, Maharashtra’s eastern region of Vidarbha saw the virus raging with a ferocity not seen earlier. Genome sequencing of the infected blood samples by researchers found the E484K mutation in a sample from Amravati and the N440K mutation another from Amravati, the Indian Express reported on February 18.

The E484K mutation, previously seen in the fast-spreading Brazilian and South African variants, makes the virus highly transmissible. The N440K mutation, found earlier in samples from Andhra Pradesh, helps the virus evade the body’s immune response. In other words, antibodies induced as a result of vaccination or an old infection become ineffective to counter the virus as should be the case under normal circumstances. Each time a virus mutates, it gives rise to a new variant. Not all variants are a matter of concern. But the variant in Maharashtra appeared to be.

“At that time, we flagged [to the Centre] that it was a rapidly spreading variant affecting a less exposed population,” said Shashank Joshi, a doctor who is part of the Maharashtra Covid-19 task force.

Confusing messaging

But what followed after that was a slew of conflicting information.

Officially, the Maharashtra government denied the presence of any foreign variants or anything out of the ordinary, for that matter. But Randeep Guleria, the director of Delhi’s All India Institute of Medical Science, said in a television interview that the new strain found in Amravati is “highly transmissible and dangerous”.

Finally, days later, the Centre formally acknowledged the presence of the E484K and N440K mutations – but the Indian Council of Medical Research’s director general Balram Bhargava in the same press conference played down the role of the mutations in the surge in Maharashtra.

Amid these denials, things started going from bad to worse in no time at all. On March 22, India recorded nearly 47,000 cases – the highest daily rise since November. The situation in Maharashtra, which accounted for over 60% of the cases, was of “grave concern”, the Centre said.

A ‘double mutant’ variant, but ‘don’t panic’

Two days later, the Union health ministry finally confirmed the existence of an Indian “double mutant” strain of the virus containing the E484Q and L452R mutations. The strain was subsequently named B.1.617. First detected in India, it has now been found in eight countries, with 70% of samples containing the mutations originating from India.

While E484Q is similar to the E484K mutation, the L452R, like the N440K mutation, is associated with antibody evasion. Both the mutations were found in 15-20% of the analysed infected samples from Maharashtra, the health ministry said in its March 24 statement. “Such mutations confer immune escape and increased infectivity,” it added.

But these mutations, the Centre cautioned, were not found in sizable numbers to “either establish or direct relationship or explain the rapid increase in cases in some states”.

The ICMR’s Bhargava was even more emphatic while answering queries of journalists. “There is no cause for panic. Mutations are sporadic, not significant,” he insisted.

Sticking to the basics

Bhargava’s position on the mutations – “not significant”, “don’t panic” – mirrors, to a large extent, the government’s overall stance on the subject. The rationale seems to be to not spread alarm and focus on the basics of mask-wearing and hand hygiene.

In fact, several independent scientists have also taken a similar line. The logic is: new mutations or not, the fundamentals of disease-prevention remain the same.

Even Joshi, one of the first to sound an early warning, said he understood the Centre’s rationale. “You could say that we warned, but the Centre did not heed, and if they had, they could have nipped it in the bud,” he said. “But to be fair, they could not have. Because people in India don’t want to cooperate, they can only be coerced into following protocols.”

A counter-productive approach?

But other scientists say that this approach of not creating “panic” may have backfired.

“Had it been more widely known that a faster spreading variant was at play and that it was capable of immune escape, perhaps more care could have been taken,” said Gautam Menon who teaches physics and biology at Sonepat’s Ashoka University.

Menon’s argument seems particularly pertinent given the circumstances in which the second wave exploded. Despite the early warnings from Maharashtra, there was little public awareness in other parts of the country of potentially more virulent strains doing the rounds even as people resumed normal lives. As Menon wrote in a piece in The Wire recently:

Some variants are specific to regions of India, including one called B.1.36, found to be present in a good fraction of cases tested in Bengaluru. The specific mutation carried by the B.1.36 variant, called N440K, is widespread in cases from the southern states. Although data is skimpy, there is some evidence that the B.1.36 variant may be responsible for some reinfections. 

The B.1.1.7 variant [the UK variant] currently dominates new cases in Punjab. 

Another variant, recently named B.1.617, figures prominently in the sudden increase of cases in Maharashtra. This variant contains two specific mutations, called E484Q and L452R.

Despite the new variants spreading, several states saw large public congregations in the form of election rallies where few people would wear masks because it was largely believed that the virus was gone for good.

Some amount of panic, thus, may have actually helped reinforce Covid-appropriate behaviour that had gone for a toss since the onset of the winters when infections started declining sharply.

As Menon put it: “To be transparent in communicating risks is important in matters of public health, especially for epidemics, since social factors are important to how they spread and the public must be aware of dangers if it is to accept potentially harsh preventive measures.”

More than two million people took a dip in the Ganga at Haridwar on April 12, while India is in the grip of a second wave of the coronavirus pandemic. Photo: AFP

Even if one were to buy the government’s rationale of not spreading panic, it seems little happened at the policy level either to deal with the threat of these potentially game-changing mutations.

“We still don’t have a good idea of how broadly the new mutants, in particular the B.1.617 double mutant, may have spread across the country, “ said Menon. “That is one area where the lack of transparency and data availability will haunt us, I feel.”

Late movers, patchy data (still)

On March 24, while confirming the presence of the new double mutant variant, the health ministry said: “Genomic sequencing and epidemiological studies are continuing to further analyse the situation.”

This is telling. The B.1.617 strain was first detected in India way back in October.

Indian researchers have been carrying out sequencing exercises since the beginning of the pandemic – but as an academic pursuit. A centralised and focussed genome sequencing mechanism was put in place in the country only towards the end of last year when the government launched the Indian SARS-CoV-2 Genomic Consortia on December 30.

Not only did the process begin late, it has failed to take off. The consortia has been able to sequence only a fraction of its target, partly because of problems like the paucity of samples (Covid-19 testing labs had not preserved them) but overwhelmingly because of bureaucratic red-tape.

Scientists who are part of the government establishment agree that there should have been more alacrity in genome sequencing, given that the second wave seemed to be different from the first in many ways.

“One person is infected in the family, a large number are getting infected, so the secondary attack seems to be higher,” said DCS Reddy, who heads the research group on epidemiology and surveillance constituted by the Indian government’s National Task Force against Covid-19. “So whatever this strain is that is circulating seems to be more virulent.”

Lack of resources

To confirm that thesis, however, intensive genome sequencing is necessary, said Reddy. “But then, the length of your pants is always going to be dependent on how much cloth you have,” he said, pointing to a lack of resources.

The consortia includes just ten labs across India. As a result, samples from states like Kerala have to be processed as far away as Delhi, leading to logistical challenges – samples have to be transported at minus 20 degrees celsius.

Tarun Bhatnagar, a member of the National Task Force against Covid-19, said India’s pandemic response has had to factor in lack of resources at every level. “Let alone genome sequencing, even getting the so-called basics of testing and tracking to an optimum level took us a considerable amount of time as a country,” said Bhatnagar. “But it is getting into place, so better late than never. And so far as I know, we are soon going to get some more data.”

Race against time

However, virologist Shahid Jameel, who is the director of the Trivedi School of Biosciences at Ashoka University, said the quality of the data mattered too. Just sequencing was not enough to establish an “epidemiological linkage” between the new variants and the surge, he emphasised.

“It needs health workers at the local level who understand what samples to send for sequencing and at what frequency,” he said. “Otherwise it is not possible to assign causality.”

And we may be fast running out of time. As Jameel pointed out: “The daily growth rate of infections in India is over 1% and active cases are growing at over 7%. We continue to see huge crowds at election rallies and religious gatherings. Putting these together, my apprehension is that fast moving viral variants would have already spread beyond states like Maharashtra and Punjab. We are looking at a fairly serious situation.”