Virginia’s state lab is one of the first in the country to sequence samples of virus that causes COVID-19

By: - April 8, 2020 12:01 am

Dr. Denise Toney, the director of Virginia’s state laboratories, answers questions at a briefing on the spread of COVID-19 in Virginia. (Ned Oliver/Virginia Mercury)

Buried in the genetic code of the new coronavirus, SARS-CoV-2, which causes COVID-19, are mutations that can help scientists learn more about where the disease started and how it’s continuing to spread.

Virginia’s state laboratory is one of three public health labs in the country to begin unraveling that code, Gov. Ralph Northam announced at a news briefing on Monday. 

In coordination with the Centers for Disease Control and Prevention and international health partners, the state’s Division of Consolidated Laboratory Services will begin sequencing virus samples from patients across the commonwealth. By compiling a repository of genetic information, health officials hope to learn more about how the disease began circulating in different communities and whether certain mutations are associated with outbreaks.

“We’re sequencing the entire genome of the virus,” DCLS Director Denise Toney said Monday. “We want to determine what are the similarities and what are the differences between what Virginia has and what they’re seeing in European countries, for example, versus southeast Asia versus Washington state.”

The technology, often called “next-generation sequencing,” has actually been around for more than a decade, said Dr. Paul Skolnik, an infectious disease expert and chair of medicine at the Virginia Tech Carilion School of Medicine. It’s been used extensively to sequence the genetic code of other infectious diseases, especially HIV.

But unlike HIV — which mutates rapidly and can even circulate in individual patients as swarms of closely related viruses — SARS-CoV-2 appears to be changing much more slowly. Both Skolnik and Toney said it’s too early to classify different strains of the disease, and still unclear whether it will ever have that level of variability.

A transmission electron microscopic image from the first U.S. case of COVID-19. The spherical viral particles, colorized blue, contain cross-sections through the viral genome, seen as black dots. (CDC Public Health Image Library)

“Usually, there has to be a certain percentage of difference between the sequences to allow us to call something more than one strain,” Skolnik said. 

He cautioned that more research has to be done before scientists can determine how much variability exists within the virus. But based on the behavior of other coronaviruses, he said it’s unlikely that SARS-CoV-2 will change fast enough, or extensively enough, to be broken into multiple strains.

What scientists have seen are “divergent clusters” of the disease, Toney said. So far, there have been roughly seven similar mutations recorded around the world in countries with widespread transmission.

By sequencing samples from COVID-19 patients from Virginia and comparing them with other variants, state health officials have already learned that the disease entered the commonwealth through multiple sources (rather than being spread through exposures to a single patient). Toney said local samples matched with versions from southeast Asia and Europe, as well as other areas of the United States. 

Comparing viral sequences can help experts determine which mutations are responsible for outbreaks and which seem to respond to containment measures, she added. It could also help epidemiologists track the disease within communities, determining whether it was introduced by different sources or whether a single version was widely transmitted.

“It can give us clues to whether two nursing homes are linked, for example,” Toney said. “If the strain types are very, very similar and clustered together, it suggests they may have a similar mode of transmission.”

From a global perspective, sequencing a wide variety of COVID-19 samples is a valuable tool in developing new treatments and vaccines, Skolnik said. Identifying mutations in the virus allows scientists to determine commonalities between different variants. Knowing which targets are shared in samples around the world will allow researchers to develop drugs that are most effective in interfering with its replication.

“Then, it will give us great insight into what made this particular coronavirus so lethal,” he added. “In that we can understand, from the genetic sequence, what proteins are made and how those proteins differ from coronaviruses that have circulated for eons in the human population. There’s something particular that this particular coronavirus had that made it able to destroy and attack tissue in the lungs.”

So far, the state lab has only sequenced a few samples of the virus, Toney said. DCLS is currently working with the Virginia Department of Health to identify which samples would yield the most information through sequencing.

“If they have no idea how you got exposed, that could make you a good person to sequence,” she added. “Maybe it turns out your virus is linked to, say, the Nile River cruises. Then that could link to a nursing home outbreak, or maybe some clusters we’re seeing in the Northern Virginia area. It can help point to where your exposure may have been.”

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Kate Masters
Kate Masters

Kate grew up in Northern Virginia before moving to the Midwest, earning her degree in journalism from the University of Missouri. She spent a year covering gun violence and public health for The Trace in Boston before joining The Frederick News-Post in Frederick County, Md. Before joining the Mercury in 2020, she covered state and county politics for the Bethesda Beat in Montgomery County, Md. She was named Virginia's outstanding young journalist for 2021 by the Virginia Press Association.