Dhruv Khullar writes:

Last March, during the first wave of the pandemic, Adriana Heguy set out to sequence coronavirus genomes. At the time, New York City’s hospitals were filling up, and American testing capacity was abysmal; the focus was on increasing testing, to figure out who had the virus and who didn’t. But Heguy, the director of the Genome Technology Center at N.Y.U. Langone Health, recognized that diagnostic tests weren’t enough. Tracking mutations in the virus’s genetic code would be crucial for understanding it. “No one was paying attention to the need for sequencing,” Heguy told me recently. “I thought, I can’t just sit here and not do anything.” Within weeks, her team had sequenced hundreds of samples of the virus collected in New York City and published a paper with three key findings: the virus had been circulating in the city for weeks before the lockdown; most cases had come from Europe, not China; and the variant infecting New Yorkers carried a mutation, D614G, that scientists soon confirmed made it far more contagious than the original virus isolated in Wuhan.

Heguy’s efforts were prescient. The world is now confronting a growing number of coronavirus variants that threaten to slow or undo our vaccine progress. In recent months, it’s become clear that the virus is mutating in ways that make it more transmissible and resistant to vaccines, and possibly more deadly. It’s also clear that, at least in the United States, there is no organized system for tracking the spread or emergence of variants. As Heguy sees it, the U.S. has more than enough genome-sequencing expertise and capacity; the problem is focus. “Efforts in the U.S. have been totally scattered,” she said. “There’s no mandate to do it in a timely fashion. The government is kind of like, Let us know if you find something.” Funding has also been a major constraint. “It boils down to money,” Heguy said. “With money, I could hire a technician, another scientist, get the reagents and supplies I need.” Because of their better-organized efforts, other countries have been more successful in identifying new versions of the virus: “The reason the U.K. variant was identified in the U.K. is that the U.K. has a good system for identifying variants.” The U.K. has, for months, sequenced at least ten per cent of its positive tests. “If you’re doing ten per cent, you’re not going to miss things that matter,” Heguy said. “If a variant becomes prevalent, you’ll catch it.”

Heguy’s lab sequences ninety-six samples a week—as many as will fit onto a single sample plate, which has eight rows and twelve columns. The process—receiving, preparing, sequencing, and analyzing samples, then reporting the results—takes time and resources, and diverts attention from other research. “Mostly we do this out of a sense of moral obligation,” Heguy told me. “This feeling that the country shouldn’t be left in the dark.” As we enter what seems to be the endgame of the pandemic, tracking and analyzing variants—which could fill hospitals and reduce the effectiveness of therapies and vaccines—is more important than ever. [Continue reading…]