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Virginia health officials race to shift their sequencing strategy as omicron cases emerge

Right now, the state lab isn’t sequencing enough COVID-19 samples to confidently pick up on new variants
A woman is tested for COVID-19 in a parking lot in Richmond where the health department set up...
A woman is tested for COVID-19 in a parking lot in Richmond where the health department set up a temporary walk-up testing center.(Ned Oliver/Virginia Mercury)
Published: Dec. 3, 2021 at 7:23 AM EST
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For months, whenever a lab in Virginia sequences a sample of the virus that causes COVID-19, it’s almost unfailingly been linked to the delta variant.

“It’s been really hard to see anything but delta,” said Dr. Amy Mathers, director of the clinical laboratory at UVA Health. Nationally, it accounts for 99 percent of new coronavirus cases. Over the month of September, Mathers’ lab analyzed more than 1,000 samples from Virginia and didn’t find a single other variant. But after months of concern over the highly infectious form of the virus, public health experts have a new variant to worry about.

There’s much that’s still unknown about omicron, a new version of the SARS-CoV-2 virus first detected in South Africa and now identified in two U.S. states. Virginia has yet to report a case. But the emergence of the lineage — classified as a “variant of concern” by the World Health Organization and U.S. Centers for Disease Control and Prevention —  is forcing Virginia to revamp its detection strategy. That responsibility largely falls to the state’s public health laboratory, which has been analyzing samples of the virus since early in the pandemic.

More accurately known as whole genome sequencing, it’s a way of unraveling the entire genetic code of the virus. And as SARS-CoV-2 has evolved into new and sometimes more dangerous variants, it’s been a crucial tool in identifying cases linked to those lineages. COVID-19 tests can verify if a person’s contracted the disease, but only sequencing can confirm whether it’s a version of the virus caused by a variant of concern.

But Virginia, like many states, is still limited in its sequencing capacity. While there have been improvements over the course of the pandemic, the state has only sequenced around 2.7 percent of its total coronavirus cases, according to data from the CDC. It’s higher than some neighboring states (Kentucky and Tennessee, for instance, have sequenced less than 2 percent of their total cases), but lower than neighbors like West Virginia and far lower than national leaders including Vermont and Wyoming, which have each sequenced more than 20 percent of their cumulative cases.

Virginia, of course, has a much higher population than either state and has recorded more than eight to 10 times the number of COVID-19 cases. But Dr. Denise Toney, director of the state’s public health lab, has acknowledged she’d like to boost Virginia’s sequencing numbers.

Currently, the state has the capacity to sequence between 800 and 900 samples a week through its public health laboratory and two contracted partners — Mathers’ lab at UVA and Virginia Tech’s Fralin Center. However, Toney said Virginia would need to sequence between 1,100 and 1,400 samples a week to be 95 percent confident that it could pick up omicron if it was circulating in the community.

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.(Virginia Mercury)

The Virginia Mercury is a new, nonpartisan, nonprofit news organization covering Virginia government and policy.

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