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NYC to Fund Coronavirus Surveillance Sequencing as Congress Proposes $2B for Nationwide Program

NEW YORK – The New York City Department of Health and Mental Hygiene (DOHMH) and the US Congress are launching separate efforts to boost next-generation sequencing-based surveillance of the SARS-CoV-2 virus.

On Wednesday, the NYC health department issued an emergency procurement request for contractors to perform whole-genome sequencing of samples that have tested positive for SARS-CoV-2.

According to the request, which expires Feb. 5, 2021, preference would be given to contractors who can "perform at least 96 sequences of positive COVID-19 tests per week upon contract notification, with the capability to ramp up to at least approximately 150 to 350 sequences per week after four weeks" and who can generate and analyze data in less than seven days.

During a Tuesday press conference, NYC health department Commissioner Dave Chokshi said that since Jan. 1, 2021, approximately 1,500 samples from New York residents have been sequenced between the city's public health lab, the state public health lab, and academic labs. He added that he expects sequencing capacity to ramp significantly over the next week.

On Thursday, Sen. Tammy Baldwin (D-Wisc.) and Reps. Ami Bera (D-Calif.) and Scott Peters (D-Calif.) proposed to fund a nationwide coronavirus surveillance program, to be administered by the Centers for Disease Control and Prevention, with more than $2 billion.

Baldwin plans to introduce the "Tracking COVID-19 Variants Act" in the Senate, to be followed by a House companion bill. In addition to funding next-generation sequencing to identify and track new and emerging SARS-CoV-2 variants, the bill provides $10 million for a demonstration program to facilitate public health research.

The bill also calls for national guidance from the CDC, "including guidance related to the sharing of specimens obtained from patients, the secure sharing of information about such specimens necessary for an effective public health response to COVID–19, and the appropriate use of viral sequence data derived from such specimens." It specifically mentions support for the agency's Advanced Molecular Detection Program.

"Variants represent a growing threat to the health and security of our nation, and right now the US is lagging behind other countries in tracking new and emerging variants of this deadly virus," Baldwin said in a statement. "The US should be a world leader in this effort, and that means we must invest more funding and resources to allow the CDC to ramp up national sequence-based surveillance and support our public health infrastructure so we can better identify, survey, and understand these variants, and better protect all Americans from this public health crisis."

The Tracking COVID-19 Variants Act notes that the US is sequencing only .3 percent of COVID-19 cases, "lagging far behind other nations." By comparison, the UK has sequenced approximately 6.8 percent of total coronavirus cases, according to a recent report from the COVID-19 Genomics UK Consortium.

"Increasing sequencing capacity will play a key role in not only identifying, tracking, and mitigating the impact of the genetic new strains, but also vaccine development and distribution, testing, and getting our economy back on track," Stefano Bertuzzi, CEO of the American Society for Microbiology, said in a statement.

Peters represents California's 52nd congressional district, which includes northern San Diego, where sequencing giant Illumina is headquartered.

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