India must step up genome sequencing efforts

If indeed India is reeling under highly-infective strains in circulation, this has serious implications for the country’s vaccination efforts.

If the Covid-19 surge in the national capital, and likely elsewhere, is indeed linked to higher infectivity of mutant SARS CoV-2 strains in circulation—AIIMS director Randeep Guleria seems to sugges this—it is unfortunate that the Union government isn’t updating the public with data on this. Guleria, as per a Times of India report, said that index cases, in the second wave, infecting 80-90% of the people they came in contact with as opposed to 30-40% in the first wave suggests that the strains in circulation have increased infectivity.

Data from the Indian SARS CoV-2 Consortium on Genomics (INSACOG)—10 laboratories tasked with analysing the genomes of variants in circulation in India—enumerating cases of the UK, South Africa and Brazil variants from a set of samples sequenced was last made public by the government in March 30; it seemed to indicate that the prevalence of the UK, South Africa and Brazil variants was low. The government subsequently had stated that it had no evidence at the time that any of the variants, including the ‘double-mutation’ variant, were responsible for the surge in new infections. However, daily new cases breaching last year’s peak much faster than it took to get there at that time would perhaps point to increased infectivity playing a significant role.

If indeed India is reeling under highly-infective strains in circulation, this has serious implications for the country’s vaccination efforts. The South African strain seems resistant to many leading vaccine—the Serum Institute of India recently had to return money to the South African government after its Covishield (the AstraZeneca vaccine that it had licensed) was shown to be ineffective against the variant. Also, as per a government release on March 24, B.1.617, or the double-mutation variant—the two mutations confer higher immune escape and increased infectivity—was found in 15-20% of the samples from Maharashtra that were analysed.

While launching the INSACOG in December 2020, the government had announced that 5% of all positive samples from each state will be analysed as well as 100% of samples from international travellers testing positive, with retrospective effect (from November 23 onwards). However, on March 30, the government said that just above 11,000 samples had been analysed—just about a tenth of the ‘5% from states’ target. Bear in mind the INSACOG laboratories, as per the government’s guidance document, can process upto 30,000 samples a month, but as per a report by Down to Earth, the laboratories were facing funding problems and difficulty in getting the samples well into March, three months after the INSACOG was announced. Against such a backdrop, it is very likely that the circulation of infective variants, and thereby, their role in the surge, is getting ignored.

With the likelihood that existing vaccines will prove ineffective and the fact that Covid-fatigue has set in nearly everywhere in the globe after a year of battling the pandemic, the government will have to rely on ‘Covid-19 appropriate behaviour’—mask-use, distancing, hand hygiene, etc—to beat down new infections. The messaging to drive awareness on this will need to underline the role of highly infective variants. But that can’t happen if the government is reluctant to make the relevant data public. It needs to learn from other jurisdictions such as the UK that leads the sequencing efforts globally. Without information put out in a digestible manner—and the underlying data collection effort—chances are India will end up worse than before as surging infections force the hand of the states and the Centre on economy-hobbling restrictions.