Why don’t we know more about the Indian variant?

India’s low supply of hospital beds, medical equipment, and vaccines is handicapping the country’s ability to contain a second devastating wave of COVID-19. So too is another shortage: India’s paucity of facilities to sequence the virus’s genome, a process that would help scientists understand how the virus is jumping from person to person and how to tailor treatments and vaccines to stop further spread.

The genetic code of the virus works like an instruction manual, which keeps updating to improve the virus’s chances of survival. When a virus mutates thousands of times, a few strains emerge that are better at infecting humans or causing serious symptoms. Sequencing the virus’s genome helps scientists determine what makes new strains more efficient enemies.

There’s already concern that the virus spreading in India evolved from British or South African lineages of the virus and is more infectious than other versions of COVID. India’s current wave is so massive that COVID infections in the country now account for every second case reported around the world. In an interview with AFP, the World Health Organization’s top scientist Soumya Swaminathan on Saturday warned that “the epidemiological features that we see in India today do indicate that it’s an extremely rapidly spreading variant.”

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But the country’s lack of genome sequence data means the Indian variant isn’t fully understood, says Amit Dutt, principal investigator at Tata Memorial Center’s ACTREC diagnostic division. The scientific community doesn’t know for certain whether it spreads faster or is better at evading the body’s immunity, posing a risk to India and to countries around the world that are now spotting the variant in their own communities.

Last December, the Indian government identified a network of 10 laboratories under the name Indian SARS-CoV-2 Genomics Consortium (Insacog) to bolster genome sequencing across the country, but the work has been slow. India has sequenced 11,047 of the 1.4 million samples sequenced worldwide, according to Gisaid, a global science initiative that provides access to coronavirus data. Scientists recommend that 5% of all samples undergo genome mapping (genome mapping is like sequencing, but less detailed). But presently not even 0.05% of positive cases in India undergo genome mapping, says Sudhir Kalhan, chairman of the Institute of Minimal Access, Metabolic, and Bariatric Surgery at New Delhi’s Sir Ganga Ram Hospital. 

Sanjiv Navangul, managing director and CEO at Bharat Serums & Vaccines, blames India’s inadequate sequencing on the network of labs being starved for money. In a letter to Indian Finance Minister Nirmala Sitharaman that was published by The Wire, E.A. Sarma, a former senior bureaucrat in the government, wrote that India had earmarked INR 1.15 billion ($15 million) for the labs, but the first tranche of that funding, worth INR 800 million ($10.81 million), was only released at the end of March.

“Being ahead of the curve is important in a pandemic, and that can only happen when we understand how the virus is behaving,” said Navangul. By now India should have sequenced 2.5 million to 5 million samples to have a better understanding of the virus, he said.

Other countries have lagged behind on genome sequencing too, but India is one of the worst offenders, say doctors and scientists. The U.S. and the U.K. were caught off guard by the first wave of the pandemic, but they subsequently built up their defenses with analysis and genome mapping, says Kalhan.

Navangul says red tape is another reason India’s genome sequencing has fallen behind. It’s hard for scientists to obtain data on COVID samples from the Indian Council of Medical Research (ICMR), the top body in India for the formulation, coordination, and promotion of biomedical research.

Navangul says the data should be open source and widely shared to design better prevention measures and treatment. “The pandemic is considered bigger than a world war. It’s killing more people every day and…requires an approach that has to be all hands on deck,” he said. “Let us find ways to solve it.”

A dearth of genome sequencing is also a missed business opportunity for India, given its status as the world’s largest vaccine manufacturer. If it had a good grasp of the virus’s mutations, vaccine giants like Bharat Biotech and the Serum Institute of India could update COVID vaccines to keep up with the changing virus, Navangul said. “We will miss the bus if we don’t do this,” he added.

At the moment, the two vaccines being used in India, the Serum Institute’s Covishield version of the AstraZeneca jab and Bharat’s Covaxin, have proved effective, but over time they may lose their efficaciousness unless they keep pace with new virus features.

“If vaccine A is proven to be not so efficacious against the most predominant variant in a region, only genome surveillance can help change the vaccine and make the vaccination program more relevant to the region,” Dutt said. “The updated vaccine would not be a new or significantly different vaccine but may target a few additional mutant surface proteins of the virus.”

More data and a better understanding of the evolving virus would give Indian pharmaceutical companies more certainty about demand for their products and, as a result, more confidence to invest in future development, says Sanjay Parikh, executive vice president and cofounder of Indegene, a global health tech company. Without that insight, “we tend to underestimate the incidence of disease and are therefore so poor at planning resources, supply, distribution, and culture.

“The one thing that this pandemic has thrown up is the paucity of reliable data and the lack of a data-driven [and] evidence-based health care ecosystem and culture,” he said. “Nowhere is that more evident than in India itself.”

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