New York City has the tools to test for variants, but screens only 1 percent of new cases.
NYC Health and Hospitals set up a coronavirus testing site at Penn Station near the Amtrak gates in November.
NYC Health and Hospitals set up a coronavirus testing site at Penn Station near the Amtrak gates in November.Credit…James Estrin/The New York Times
In New York City, despite its many major hospitals and research institutions, only about 55 coronavirus cases a day on average last month were sequenced and screened for more contagious variants.
That amounted to just 1 percent of the city’s new cases, a rate far below the 10 percent that some experts say is needed to understand the dynamics of the pandemic in New York at a time when variants that may blunt the effectiveness of existing vaccines have led to surging cases in Britain, Brazil and South Africa.
By the end of February, New York City health officials hope to have a more robust surveillance program in place that would involve sequencing the genomes — that is, examining the genetic material for mutations — of about 10 percent of new virus cases, according to Dr. Jay Varma, a senior public health adviser to City Hall.
With an average of more than 5,000 new cases a day in recent weeks, that would provide a good picture of which variants are present in New York and how widely they are proliferating, Dr. Varma said.
But the effort to reach that benchmark is underscoring how, a year into the pandemic, local, state and federal officials have often been slow to mobilize resources for public health needs.
“Trying to get laboratories that are primarily focused on things like human genome sequencing specifically for cancer or other conditions to shift their interest to work on pathogens sometimes takes effort,” he said.
The capacity to sequence the genomes of as many virus samples as necessary already exists, scattered across the city, though it has been largely untapped.
“Every institution is doing their own thing,” Professor Adriana Heguy of New York University’s Grossman School of Medicine, whose team has been sequencing some 96 samples a week and whose research last year helped establish that New York’s pandemic arrived via Europe, not China.
With its major academic medical centers and research institutions, there are far more sequencing machines in New York than would be needed to check the coronavirus genomes from every positive case, were anybody inclined to do so.
“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.
— Joseph Goldstein The New York Times