“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 capacity is not the issue.”
The problem for research labs – oddly enough, in the midst of a pandemic that has likely infected more than a quarter of New Yorkers – is access to samples. In New York City, there is no high-volume pipeline of positive virus samples from hospitals or testing sites to research labs to perform genetic surveillance.
“It’s actually just about organizing this sample collection – that’s, I think, what’s missing,” said Dr Sanjana, whose research consisted of investigating what drugs could block the infection by. inhibiting human genes hijacked by the coronavirus.
What it takes, scientists say in interviews, is for the city or some other entity to essentially branch off from the current coronavirus testing process. Every day, tens of thousands of New Yorkers provide swab samples, which are usually sent to a few large labs for testing. If those labs could set aside part of the samples, those parts could then be used for genome sequencing if they tested positive.
“It’s solvable, but it takes resources and people to coordinate,” said Professor Heguy, listing the steps needed: part of the initial sample should be set aside; RNA should be isolated; and someone would need to transport the RNA samples to a lab that does genome sequencing.
The city’s goal of expanding sequencing to at least tenfold will require calling on a range of outside laboratories and research projects, large and small. The city predicts that most of the genomic sequencing will take place at a laboratory in Long Island City, Queens, run by a small robotics company.
The company, Opentrons, also operates a facility in Manhattan called the Pandemic Response Laboratory. This lab was built last year to help the city solve the testing crisis that emerged during the summer, when large commercial labs struggled to cope with the growing workload. People had to wait several days, and sometimes a week or two, for coronavirus test results. The laboratory now tests 20,000 samples per day.
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