Scientists race to study variants in India as cases explode

by Joseph K. Clark

“We need more sequencing, targeted sequencing to be done and shared in India and elsewhere to know how much of this virus is circulating.” Viruses mutate constantly, and the infection surge has increased opportunities for new versions. But India was slow to start the genetic monitoring needed to see if those changes were happening and making the coronavirus more infectious or deadly.


When there isn’t enough sequencing, there will be blind spots, and more problematic mutations could go undetected until they’re widespread, said Alina Chan, a postdoctoral researcher at Broad Institute of MIT and Harvard tracking global sequencing efforts. Ravindra Gupta, a professor of clinical microbiology at the University of Cambridge, said: “It has all the hallmarks of the virus that we should be worried about.” First detected in the coastal Maharashtra state last year, the new variant has been found in samples in 19 of the 27 states surveyed. Meanwhile, a variant first detected in Britain has declined in India in the past 45 days.

Dr. Gagandeep Kang, who studies microorganisms at Christian Medical College at Vellore in southern India, said researchers need to figure out if the variant can infect those who previously had COVID-19 and, if so, whether it could result in severe disease.

“I don’t get why people don’t see this as important,” she said.

Sequencing efforts in India have been haphazard. Chan said the country uploads 0.49 sequences per 1,000 cases to GISAID, a global data-sharing effort. The U.S., which had its troubles with genetic monitoring, uploads about 10 in 1,000, while the U.K. does so for about 82 per 1,000 cases.

Late last year, Indian government institutions were ordered to buy domestic raw materials wherever possible, keeping with Prime Minister Narendra Modi’s goal of turning India “self-reliant.” This proved impossible since all materials for sequencing were imported, resulting in more paperwork, said Anurag Agarwal, the director of the Institute of Genomics and Integrative Biology. He said the obstacles were most pronounced between September and December, but his lab could find workarounds and continued sequencing.

Other labs didn’t, and scientists said that should have been when India ramped up its sequencing because cases were declining then.

Even after a federal effort started on Jan. 18, bringing together ten labs that can sequence 7,500 samples weekly, the actual work didn’t begin until mid-February due to other logistical issues, said Dr. Shahid Jameel, a virologist. He chairs the scientific advisory group advising the consortium.

By then, India’s cases had begun spiking. Jameel said India had sequenced around 20,000 samples, but only 15,000 were publicly reported because some were missing vital data. Until late last month, he said a third of the samples sent by states were unusable.

And now, the raging virus has infected many of the lab staff doing the work. “Many of our labs are facing this problem,” he said.

Pathi reported from Bengaluru, and Associated Press writers Danica Kirka in London and Chonchui Ngashangva in New Delhi contributed to this report.

The Associated Press Health and Science Department receives support from the Howard Hughes Medical InstitutInstitute’sent of Science Education. The AP is solely responsible for all content.

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