COVID genome sequencing can help New York battle variants

Regional News

A lab assistant uses a pipette to prepare Coronavirus RNA for sequencing at the Wellcome Sanger Institute that is operated by Genome Research in Cambridge, Thursday, March 4, 2021. Cambridge University microbiologist Sharon Peacock understood that genomic sequencing would be crucial in tracking the coronavirus, controlling outbreaks and developing vaccines, so she began working with colleagues around the country to put together a plan when there were just 84 confirmed cases in the country. The initiative helped make Britain a world leader in rapidly analyzing the genetic material from large numbers of COVID-19 infections, generating more than 40% of the genomic sequences identified to date.(AP Photo/Frank Augstein)

ALBANY, N.Y. (WUTR/WFXV/WPNY-TV) — The Centers For Disease Control and Prevention (CDC) released $20 million so the New York State Department of Health (DOH) could work with other labs in the state to conduct genome sequencing on COVID-19 tests. It will help the state keep a close eye on any COVID variants that could seriously impact public health.

Five labs were selected to help the state in its efforts: SUNY Upstate Medical University, Cornell University, the University at Buffalo, the University of Rochester Medical Center, and New York Medical College (NYMC).

Contracting with NYMC happened over a short period of time. NYMC received an application for the project in July and has already begun sequencing tests. Testing at the five labs will include areas outside of New York City, said Vice President of Research and Principal Investigator of the project at NYMC, Dr. Salomon Amar.

Cornell University has been doing genome sequencing in Thompkins County since 2019 and reporting its findings to the county and state health departments, said associate professor Dr. Diego Diel. Cornell’s contract with the DOH means its lab will receive tests from other counties in the Finger Lakes Region.

Dr. Amar says that the state took the right action in contracting with labs operated by academic institutions. Outside of determining which variant is predominant, the sophisticated protocols surrounding research at academic institutions will ensure the accuracy of COVID-19 genome sequencing. “I’m convinced an academic institution will do it properly,” he said.

Sequencing of more tests throughout the state will help track dominant variants but by combining the sequencing with patient health information, Dr. Amar said researchers will be able to also identify which comorbidities put people at a greater risk. It will also help them determine if a certain population is at a greater risk of serious illness from a particular variant.

On August 3, 121,015 people in New York were tested for COVID, 3,115 tested positive. The state’s testing facility, Wadsworth Center, said it is able to sequence 90 samples a day. Cornell said they can test 96 samples a week.

Dr. Amar said he couldn’t give specific numbers but that NYMC was “gearing up” its sequencing capabilities in earnest and that it has “significant capability.”

Below is the DOH’s response to NEWS10’s inquiry:

Since the start of the pandemic, the Wadsworth Center has sequenced approximately 13,570 virus samples statewide to date—with most specimens selected at random from throughout the state with an effort to have geographic representation—and the Delta variant has been found approximately 527 times thus far in New York, based on sequences reported to GISAID. We look at the whole sequence of the virus, which means we have the ability to compare and contrast sequences with all of those currently available. The effectiveness of the COVID-19 vaccines remains strong even against newer strains, including against variants of concern such as the Delta variant, which is why the New York State Department of Health urges all eligible New Yorkers to get vaccinated as soon as they are able.

DOH

SUNY Upstate Medical Center said it has already tested and sequenced two million samples from across the state. Officials said the contract with the DOH will allow them to expand on variant tracking efforts.

“In addition to surveillance, the data generated will help build our understanding of disease manifestations, therapy or vaccine evasion and efficacy, and will support other discoveries to inform public health intervention. Sequencing results from the partner laboratories will be reported to the New York State Department of Health and the Global Initiative on Sharing Avian Influenza Data,” the center said on its website.

Regardless of the actual number of tests that can be sequenced, it’s substantially more than the Wadsworth Center could test on its own. It will most definitely help paint a better overall picture of COVID variants in New York, Dr. Amar said.

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