The Washington PostDemocracy Dies in Darkness

India is No. 102 in coronavirus genetic sequencing, leaving many unknowns on variants amid the surge

India’s terrifying coronavirus surge has repeatedly broken records for new infections and deaths — numbers that experts say are probably undercounts due to inconsistent reporting and limits on testing.

Coronavirus has crushed India’s health system. Patients are on their own.

One trigger for the wave seems clear. Scientists point to government policies — including Indian Prime Minister Narendra Modi permitting large election rallies and religious festivals — and public complacency, as many people thought the pandemic was easing in India.

But public health experts cannot yet determine how much the huge outbreak is being driven by highly transmissible variants of the virus — which, unlike government policies, know no borders. That’s because India is sequencing only a sliver, 0.06 percent, of its often more than 300,000 daily coronavirus cases to check for genetic changes.

Scientists have a powerful new tool for controlling the coronavirus: Its own genetic code.

“We just don’t know” the degree to which variants are driving the surge, said Bronwyn MacInnis, a genomic epidemiologist at the Broad Institute in Boston. “Everyone has their eyes on what’s happening there and waiting for data.”

India ranks 102nd in the world for genetic sequencing, according to a Washington Post analysis of data from the GISAID Initiative, which provides a global database of coronavirus genomes. The United States comes in at 36 — a slight increase from December, when it ranked 43rd.

“Though VOCs [variants of concern] and a new double mutant variant have been found in India, these have not been detected in numbers sufficient to either establish [a] direct relationship or explain the rapid increase in cases in some States,” India’s Ministry of Health and Family Welfare said in a statement last month, before the latest surge reached the world’s radar. “Genomic sequencing and epidemiological studies are continuing to further analyze the situation.”

India in particular is watching two variants: B.1.1.7, which first emerged last fall in Britain, and B.1.617, which was first detected in India in October.

“It may very well be a combination of the two, or others that we don’t know yet,” said MacInnis. “All options are open until we have more data.”

B.1.1.7 is highly transmissible and the most dominant variant scientists know of in global circulation. It has been detected across India, primarily in the north, said Ravi Gupta, professor of clinical microbiology at the Cambridge Institute for Therapeutic Immunology and Infectious Diseases.

B.1.617 is sometimes called the “double mutant” because of two genetic changes that could make it more transmissible. According to Gupta, it’s so far found to be dominating cases in India’s Maharashtra state, which includes Mumbai.

This past winter, India launched a sequencing body, the Indian SARS-CoV-2 Genomics Consortium, with the aim of sequencing around 5 percent of all cases. That never happened.

Sequencing takes a high level of infrastructure and funding. India, which spent very little per capita on health care before the pandemic, has not been able to quickly make the investments to scale up, said Gupta.

But even the United States, which has more resources to spend on genetic sequencing, has lagged behind in contrast with countries such as Britain, which ranks eighth.

The United States has “the technical ability for the right labs and expertise” but other factors, such as navigating “logistics and political mandates,” initially were relatively slow to fall into place, MacInnis said. Now with support from the U.S. Centers for Disease Control and Prevention, as well as the level of new U.S. infections dropping off, however, the rate of genetic sequencing has increased, she said.

Gupta said getting people vaccinated, while continuing to study what’s driving infections, remains the most important way to cut transmission.

“Countries need to realize it’s unfortunately just not going to go away,” said Gupta, referring to the coronavirus. “Countries need to know what’s circulating and what to do about it.”

Scientists have repeatedly warned that the longer the virus circulates, the more chances it has to genetically change — at times becoming more transmissible and, possibly, more deadly or vaccine resistant.

“I’m not ‘most concerned’ about one particular” variant, Kristian Andersen, a professor in the department of immunology and microbiology at Scripps Research, wrote in an email. “I’m concerned about all of them and I’m concerned that we are continuously underestimating how important it is that we massively drive down the number of COVID-19 cases in an effort to prevent current and future variants a chance to continue to spread and emerge.”

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