NEW DELHI—As it battles a huge surge in coronavirus cases, India trails many other countries in the genomic sequencing necessary to track emerging variants, creating a blind spot for local and global health officials.
The country has become ground zero for the pandemic, topping 200,000 daily infection cases this week, higher than an earlier peak in September. With its population of more than 1.3 billion people and skyrocketing infections, India has a higher chance of developing variants, which may take root and spread beyond its borders, public health experts said.
“Where you have that many people affected, there’s a higher chance” of new strains because there are more opportunities for the virus to mutate, said
a postdoctoral researcher focused on gene therapy and cell engineering at the Broad Institute of MIT and Harvard. “The size of the infected population is what drives the emergence of new variants.”
Even with robust sequencing, countries can struggle to rein in highly infectious variants with public health interventions, experts said. Nations that don’t do much genomic sequencing are blind spots where a strain can develop and spread to multiple countries before discovery. Scientists still haven’t been able to determine definitively where the U.K., South African and Brazilian variants originated.
Last month, India’s health ministry said its labs had detected all three variants in collected samples, along with a new “double-mutant variant,” which public health experts say may have originated in India. The strain has two mutations, seen separately before in other variants, but never together in one variant.
Scientists say not much is known so far about the new strain. In other variants, one mutation has made the virus more infectious, while the second has helped the virus evade antibodies. The variant has already been detected in California, according to Dr.
director of the Clinical Virology Laboratory at Stanford University.
But India ranks 85th out of 134 countries in the percentage of Covid-19 cases sequenced, according to Covid-19 CG, a tracking tool from the Broad Institute. The tool uses data from the GISAID Initiative, a global database for coronavirus genomes. Only about 0.05% of India’s total cases have been sequenced, according to the data.
“We are grappling in the dark,” said Dr.
Amir Ullah Khan,
research director at the Centre for Development Policy and Practice. “There is no data and no discussion on how we are going to test the variants.”
In India, the job of sequencing positive Covid-19 samples is carried out by 10 state-run laboratories.
director of the CSIR Institute of Genomics and Integrative Biology, which operates one of the labs, said they can sequence 25,000 to 30,000 samples a month. It has been averaging only around 4,000 a month, though, because that was sufficient to determine the dominant strains when infection rates were lower. He said India’s ranking in the GISAID database is unfair because it didn’t take into account sequencing that hasn’t been deposited into GISAID’S database.
Even adding the uncounted sequencing would put India’s rate of sequencing at about 0.18%, according to a Wall Street Journal tally. By comparison, Australia has sequenced 47.4%, the U.K. has done 7.7% and the U.S. has completed 0.75%, according to Covid-19 CG.
Dr. Agrawal said India is doing enough sequencing to identify the dominant strains in regions hardest hit by the virus. In the northern state of Punjab, for example, the U.K. variant is most prevalent. In the state of Maharashtra, which is home to India’s financial capital, Mumbai, the double-mutant is the dominant variant, he said. The government labs plan to increase sequencing as needed to inform public health decisions in the coming months, he said.
“The sequencing will need to increase more at this point in time as the situation gets worse,” he added.
The double mutant strain identified in India has quickly shot around the world. At Stanford, Dr. Pinsky said he first heard of the variant on March 24 when the Indian government revealed its discovery. The next day, his lab detected the same variant in a sample taken from a California patient, he said. In the past three weeks, there have been six confirmed cases and 10 presumptive cases of the variant. At least one patient had recently traveled to India, he said.
“It was just amazing how rapidly this had spread,” Dr. Pinsky said.
Some health experts warned that India’s pace of sequencing is only enough to identify variants after they have firmly embedded themselves into the population.
“You’re just trying to learn what’s happened and then react,” said
founder of Theiagen Genomics, which helps public health officials keep tabs on outbreaks. “I don’t believe sequencing at that level is going to give you that early warning.”
When a country sequences more aggressively—say, at least 10% of positive cases—then it begins collecting enough data to detect a new variant when it first starts spreading, he said. That gives governments a fighting chance to try to slow it down.
The U.K.’s robust sequencing infrastructure armed authorities with the data to say a new strain was in circulation in December. The B.1.1.7 variant became more commonly known as the U.K. variant. The British government responded by imposing a strict lockdown on parts of the country. Dozens of countries banned flights and trains from the U.K.
The warning didn’t stop the variant from stampeding through much of the world, although scientists have said it may have originated elsewhere and could have been circulating before it was detected by U.K. scientists. Last week, the director of the Centers for Disease Control and Prevention said the U.K. variant is now the dominant strain in the U.S.
But in India, the effort to boost sequencing is encountering some of the same problems that plagued India’s initial Covid-19 testing rollout last year, including tight government control and a reluctance to let the private sector get involved.
Many testing facilities, which would provide positive Covid-19 samples to the labs, were dismantled after Delhi prematurely declared victory over the pandemic, said Dr. Khan of the Centre for Development Policy and Practice. The government’s focus has shifted to vaccines, he said, instead of determining which strains are fueling the current wave of infections.
“We are making the same mistake we were making last year,” he said. “We wasted lots of time because we weren’t testing.”
Indian states are supposed to send 5% of all positive Covid-19 samples to the labs, but they have fallen far behind, said Dr.
an infectious disease epidemiologist and former head of the Division of Epidemiology and Communicable Diseases at the Indian Council of Medical Research. He said the labs are grappling with operational issues in getting samples in time that show no signs of being resolved.
Dr. Agrawal said the main obstacle is developing the network to get samples quickly from the right areas. Any significant delays mean less timely information is informing public health decisions, he said.
Public health experts said that without more aggressive sequencing programs, countries like India don’t have enough data to effectively implement targeted restrictions in specific cities or regions. Less information on variants could also make it more difficult to assess the effectiveness of using existing vaccines, which can vary depending on the strain.
“It’s a question of ‘when is the next variant or next viral strain going to come around?’” Mr. Sevinsky said. “And did we learn enough to mobilize the sequencing and the testing and to implement measures that dramatically slow it down?”
Write to Shan Li at [email protected]
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