“Our machines could handle thousands or hundreds of thousands,” said Dr. Neville Sanjana, a scientist with a lab at the New York Genome Center in Lower Manhattan. “So the capacity is just not the issue.”

The issue for research laboratories — strangely enough, amid a pandemic that has probably infected more than a quarter of New Yorkers — is access to samples. In New York, there is no high-volume pipeline of positive virus samples from hospitals or testing sites to research laboratories to conduct genetic surveillance.

“It’s really just organizing that sample collection — that, I think, is what’s missing,” said Dr. Sanjana, whose research has involved searching for which medicines might block infection by inhibiting the human genes that the coronavirus hijacks.

What is needed, scientists said in interviews, is for the city or another entity to essentially bifurcate the current coronavirus testing process. Each day, tens of thousands of New Yorkers provide swabbed samples, which are generally sent to a few large laboratories for testing. If those labs could set aside a portion of the samples, those portions could later be used for genome sequencing if they turned out to be positive.

“It’s solvable, but it needs resources and it needs people to coordinate,” Professor Heguy said, as she listed the necessary steps: A portion of the original sample would need to be set aside; RNA would need to be isolated from it; and someone would need to transport the RNA samples to a laboratory that does genome sequencing.

The city’s goal of expanding sequencing at least tenfold will require enlisting a range of outside laboratories and research projects, big and small. The city anticipates that the largest share of the genomic sequencing will happen at a laboratory in Long Island City, Queens, that is run by a small robotics company.

The company, Opentrons, also runs a facility in Manhattan called the Pandemic Response Laboratory. That laboratory was built last year to help the city solve the testing crisis that emerged during the summer, when big commercial laboratories were struggling to handle the soaring caseload. People were having to wait several days, and sometimes a week or two, for coronavirus test results. The laboratory now tests 20,000 samples a day.



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