Can India find a way out of its Covid nightmare?

Virologist SHAHID JAMEEL, who is the director of Trivedi School of Biosciences, Ashoka University, speaks to Bobby Ghosh about the causes of India’s devastating second wave and what the world should learn from it. Edited excerpts:

India is suffering the world’s worst Covid-19 crisis. Last fall and winter, it looked like India was doing very well in managing its Covid outbreak. Looking back now, what did we miss?

We were still on a rising curve in August, and it seemed like India would cross the 100,000-per-day mark. The peak came in mid-september, when we were pulling roughly 97,000 cases. But then, suddenly the graph started dropping and for the next five months, the graph kept dropping, dropping.

There were some seroprevalence surveys being done and it appeared that maybe 20 per cent to 30 per cent of the overall population had been exposed. In large cities, like in Mumbai and Delhi, in the areas that were surveyed, it appeared as though 50 per cent to 60 per cent had been exposed. That blindsided us.

There were also theories suggesting India’s mortality rate was low; it wasn’t. It was comparable to Pakistan and Bangladesh. But India was comparing itself to the US and Europe. So there were multiple factors that led us into falsely believing that we were out of it. As a result, we let our guard down at a time when we should not have.

What led to the recent surge of cases and death?

In mid-february, our daily caseload was at its lowest, fewer than 11,000 per day. But mutant viruses were already circulating at low levels before then. Sequencing data now tells us that what we’re calling the Double Mutant variant — the technical name is B.1.617 — was already seen in December, but it was very minor and nobody really paid attention to it. That, and the introduction of the UK variant (B.1.1.7) into India in January, finally caught up with us and led to the surge that started from about the third week of February.

The variants are far more infectious and move faster. In the first wave, we would see one person in a family getting infected, and if they isolated themselves, the rest of the family was fine. Not so this time. Now, by the time you realise one person has it, the whole family is down. I’m part of a sequencing consortium — there are 10 labs in all, and we meet every alternate day to exchange notes. There’s a dashboard that tells us what’s happening. So when we look at different parts of the country, we see several variants that are going around.

In Punjab almost 80 per cent the virus circulating is the UK variant. And it’s the same is in Haryana. But in Delhi, we have the UK variant and the Double Mutant, both. In Maharashtra, there’s more of the Double Mutant, up from 15 per cent to 20 per cent in February to roughly 35 per cent to 60 per cent now, depending upon where you look.

Could you explain why it is being called the Double Mutant?

It’s actually a misnomer. This is a mutant virus that has 15 different changes from the original. Six mutations are in the spike protein, and two of those are in a very critical region called the receptor binding motif. This is the region of the spike protein that allows the virus to enter the cell. It is also the region that is targeted by antibodies that neutralise the virus. So, any small changes in this region have the potential to increase the entry of the virus into cells and evade neutralising antibodies.

Of the two key mutations in the Double Mutant variant, one was first seen in Denmark, in the mink population. That mutation was then found in humans in California. It was responsible for the expansion of the outbreak in Southern California. The second mutation is very similar, but not identical, to one found in the South African variant, which is responsible for partially evading antibodies.

These two mutations came together for the first time, as far as we know, in this Indian variant.

You said the Double Mutant was present last December, but only caught fire in February. Might there be other variants out there, now only in isolated pockets but with the potential to take off in the same way?

There could be, and that’s why genomic surveillance is so important — to catch minor variants before they explode in the population.

According to World Health Organization recommendations, you should be sequencing about 0.3 per cent of the confirmed cases. India was much below that rate. By December, India was only at 0.05 per cent. But with the establishment of this sequencing consortium of 10 labs, we’ve been sequencing at about 1 per cent since February.

By now, about a million sequences have already been obtained from infected people around the world, and these sequences are publicly available.

Hopefully, if we do things well now, we will be able to prevent a big third wave. We may not be able to prevent a third wave, because that’s how viruses naturally cycle down before they become endemic, but at least we can reduce the magnitude and also extend the period between the waves, by doing some active genomic surveillance.