Communications of the ACM
Unlocking the Covid Code
DNA sequencing has been the key tool in identifying and tracking Covid variants.
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Edward Holmes was in Australia on a Saturday morning in early January 2020, talking on the phone with a Chinese scientist named Yong-Zhen Zhang who had just sequenced the genome of a novel pathogen that was infecting people in Wuhan. The two men — old friends — debated the results. "I knew we were looking at a respiratory virus," recalls Holmes, a virologist and professor at the University of Sydney. He also knew it looked dangerous.
Could he share the genetic code publicly? Holmes asked. Zhang was in China, on an airplane waiting for takeoff. He wanted to think it over for a minute. So Holmes waited. He heard a flight attendant urging Zhang to turn off his phone.
"OK," Zhang said at last. Almost immediately, Holmes posted the sequence on a website called Virological.org; then he linked to it on Twitter. Holmes knew that researchers around the world would instantly start unwinding the pathogen's code to try to find ways to defeat it.
From the moment the virus genome was first posted by Holmes, if you looked, you could find a genetic component in almost every aspect of our public-health responses to SARS-CoV-2. It's typically the case, for instance, that a pharmaceutical company needs samples of a virus to create a vaccine. But once the sequence was in the public realm, Moderna, an obscure biotech company in Cambridge, Mass., immediately began working with the National Institutes of Health on a plan. "They never had the virus on site at all; they really just used the sequence, and they viewed it as a software problem," Francis deSouza, the chief executive of Illumina, which makes the sequencer that Zhang used, told me with some amazement last summer, six months before the Moderna vaccine received an emergency-use authorization by the Food and Drug Administration. The virus's code also set the testing industry into motion. Only by analyzing characteristic aspects of the virus's genetic sequence could scientists create kits for the devices known as P.C.R. machines, which for decades have used genetic information to formulate fast diagnostic tests.
From The New York Times
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