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[scion]

Meet the people who warn the world about new covid variants

Scientist racing to track the evolution of covid tap into a little-known system developed by a few young researchers in Scotland.

by Cat Ferguson
July 26, 2021
covid strain tracking concept
MS TECH | CDC
https://www.technologyreview.com/2021/07/26/1030017/covid-variants-pangolin-pango-volunteers/?utm_medium=tr_social&utm_campaign=site_visitor.unpaid.engagement&utm_source=Twitter

In March, when covid cases began spiking around India, Bani Jolly went hunting for answers in the virus’s genetic code.

Researchers in the UK had just set the scientific world ablaze with news that a covid variant called B.1.1.7—soon to be referred to as alpha—was to blame for skyrocketing case counts there. Jolly, a third-year PhD student at the CSIR Institute of Genomics and Integrative Biology in New Delhi, expected to find that it was driving infections in her country too.

Because her institution is at the forefront of covid research in India, she had access to sequences from thousands of covid samples taken around the country. She began running them through software that grouped them according to branches of covid’s family tree.

Instead of dense clumps of B.1.1.7 cases, Jolly found a cluster of sequences that didn’t look quite like any known variant, some of them with two mutations of the spike protein that were already suspected to make the virus more dangerous.

Jolly talked to her advisor, who suggested that she reach out to other sequencing labs around India. Their data, too, showed signs that a local outbreak had given rise to a new family of the virus.

Before long, journalists got wind of the new development, and Jolly began to see articles about “double mutants” and the “Indian variant.”

She knew researchers could do more with a useful label than a "scariant" nickname. So she went to the place where a small group of scientists give new variants their names: a GitHub page staffed by a handful of volunteers around the world, led primarily by a PhD student in Scotland.

Those volunteers oversee a system called Pango, which has quietly become essential to global covid research. Its software tools and naming system have now helped scientists worldwide understand and classify nearly 2.5 million samples of the virus.

In April, Jolly posted on the GitHub page about what she'd found in the sequences. (She was the second user to flag the new variant; the first flag had been waved a few days before, by a researcher in the UK.) The Pango team looked up the genomes in public sequence database GISAID and agreed there had been a significant change to the virus. They quickly gave the strain a new name: B.1.617. That family has since grown to include the infamously transmissible variant known, in the media, as delta.

“Pango makes it really easy to see if other people are seeing what we’re seeing,” Jolly says. “If they’re not, it is really easy to report what’s being seen in India, so people can track it in other regions.”

Researchers, public health officers, and journalists around the world use Pango to understand covid’s evolution. But few realize that the entire endeavor—like much in the new field of covid genomics—is powered by a tiny team of young researchers who have often put their own work on hold to build it.
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https://www.technologyreview.com/2021/07/26/1030017/covid-variants-pangolin-pango-volunteers/?utm_medium=tr_social&utm_campaign=site_visitor.unpaid.engagement&utm_source=Twitter