Virginia Division of Consolidated Laboratory Services Tracking COVID-19 Mutation
Sunday, May 24, 2020
As reported online for The Roanoke Times, when the virus that causes COVID-19 entered Virginia in March, scientists at the state lab wanted to determine whether it was traveling into the commonwealth from different places around the globe.
They turned to next-generation sequencing technology that they had been using to trace outbreaks of foodborne illnesses to genetically decode SARS-CoV-2. They have used samples taken from Virginians infected with the virus to help public health officials understand how the virus mutates and how it is being transmitted.
So far the sequencing team at the Virginia Division of Consolidated Laboratory Services have identified five divergent clusters of the virus.
“Viruses aren’t perfect. So when they are replicating themselves, they will accidentally make a mistake when copying the genome,” bioinformatics lead scientist Logan Fink said. “Sometimes the mistakes are injurious, and may cause it to not survive very long. Sometimes the mistake gives it an advantage, and it will become the dominant one in a population.”
They don’t know yet whether the different clusters of SARS-CoV-2 in Virginia have mutated to the virus’s advantage, meaning it can survive longer and spread more easily. Or if the mistakes will cause it to die out. And sometimes mistakes don’t matter.
“The only way we measure whether its advantageous or not advantageous is whether we continue to see it in the population,” Fink said.
Fink and his colleague bioinformatics lead scientists Kevin Libuit analyze the data. Lauren Turner, foodborne and advanced pathogen characterization lead scientist, works with the samples.
The three talked about the work and what they hope to contribute.
“It helps us to confirm how the disease is spreading throughout the commonwealth, and the world. It allows us to see any type of mutation that leads to discrepancies or variances in the functional expression of the virus,” Libuit said. “That might have implications in vaccine efficacy or symptom severity of illness.”
COVID-19 is not only a new illness, but one that causes no symptoms in one person but kills the next. It has caused severe respiratory distress, strokes, organ failure, rashes and prompted overreaction by immune systems in some people. At first it was thought that children were not affected. Now it is coming to light that they, too, can suffer severe and fatal symptoms.
It’s not known whether any of the mutations to the virus prompt the different symptoms.
“That’s a great question,” Libuit said. “But at this point, the genomic information we have we can make hypotheses, but to definitely say that, there needs to be a lot more information, not just in Virginia but across the globe, and even further academic partners to confirm those kind of assertions.”
Virginia was an early participant in the Centers for Disease Control SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance. SPHERES is a growing consortium of public, university and commercial labs.
The goal is to monitor changes in the virus as it circulates. The information is expected to help not just public health researchers looking to better understand how it is transmitted, but researchers who are developing treatments and vaccines.
“It’s a big effort and to standardize the way we are doing this so we can answer the questions,” Libuit said. “Also to make sure laboratories that are developing this sequencing don’t have to start from ground zero.”
Turner said Virginia was quick into the mix because it was early to invest in an initiative started six years ago to have capacity in all the state to track foodborne illnesses such as salmonella and E. coli. It’s important when people are falling ill from food to trace it to the source and to know if cases are related.
That same ability to know if cases are related is also important during outbreaks of COVID-19.
She said if they are able to provide this information to the Virginia Department of Health, it would know whether there was one or more clusters of the virus circulating in a nursing home.
“What we would like to do is to the serve the purpose we always have for public health and provide them the data that helps them to make the decisions they need to make,” Turner said.