Tennessee lags in tracking COVID-19 variants

Tennessee is behind all but five states when it comes to tracking the variants of the virus that causes COVID-19, according to a key metric collected by the Center for Disease Control.

As of May 12, Tennessee had analyzed the genetic sequence of only .38 % of  positive COVID-19 samples, compared to more than 10% in Wyoming. Only Oklahoma, Arkansas, Mississippi and Iowa reported sequencing smaller percentages.

That means that, for now, Tennessee has less information about which variants are circulating in the state — information that could be critical in keeping future spikes in infections at bay. 

“As we learn about characteristics of different strains, that will influence the way providers do treatment, influence the way the next generation of vaccines are made and what what the components of that vaccine will be so that they can protect against new and emerging strains of the disease,” said John Dunn, Tennessee’s State Epidemiologist with the Department of Health’s Communicable and Environmental Diseases and Emergency Preparedness program. 

Dunn attributed Tennessee’s initial lag to lack of experience sequencing viruses associated with respiratory illnesses. He also said other state labs also had closer ties to academic centers, which allowed them to act more quickly. 

In February, the White House stated a goal of sequencing 5% of COVID samples taken nationwide. Right now, only Hawaii and Wyoming exceed that benchmark on the state level.

Scientists and public health officials have long used genomic surveillance to figure out which strain of the flu to include in the annual flu shot, or to track outbreaks of foodborne illnesses. But the pandemic requires an unprecedented effort to track how the virus is mutating, and few states had the infrastructure ready to meet the challenge. 

“That doesn’t mean to say [states] don’t have the potential expertise, but there’s also been no continuing medical education,” says Vaughn Cooper, a professor at the University of Pittsburgh and the School of Medicine and the director of the Center for Evolutionary Biology Medicine, as well as the co-founder of the Microbial Genome Sequencing Center, a company that sequences virus samples.  “There’s been no investment in these kinds of facilities. There’s been no connections with companies that could answer the call quickly. So we have a lot of infrastructure to build.”

In order to ramp up sequencing in Tennessee, Dunn says the state will need more sequencing equipment, as well as more staff to do the sequencing and analyze the data. A provision of the American Rescue Act allocated Tennessee  more than $4.6 million to support sequencing efforts. 

Another consideration is where to keep samples — many commercial labs destroy them as soon as they process whether a test is positive or negative — and the capacity to collect, organize, and analyze the data associated with the samples. 

“We want to know, is it more severe or is there more hospitalizations or more death? Is there a different set of symptoms that are being manifested in patients who have that new strain? … Is it a younger population, older population, more rural population versus urban, those types of things, to see if that particular strain type is acting differently in the population,” Dunn said. 

William Schaffner is a professor at Vanderbilt University School of Medicine specializing in infectious diseases. “It takes resources, it takes time, it takes energy and freezer space,”  he says of effective surveillance programs. 

Schaffner also collaborates with the Tennessee Department of Health on COVID-19 related projects. For now, he said,  the state is being strategic with the samples that it is sequencing.

“If the virus suddenly creates an outbreak someplace in an enclosed population like a nursing home or a prison or a meatpacking plant or something like that, those are circumstances of particular epidemiologic public health interest, where they will go in and try to get specimens and have them sequence, where perhaps finding a variant is more likely,” he said. Samples from people who have traveled abroad might also be particularly valuable, he said. 

And the sequencing done in conjunction with the CDC has already yielded useful information. A variant first identified in Britain, the B.1.1.7 variant, is now the dominant strain in Tennessee, and more prevalent than in any other state, representing more than 80 percent of samples analyzed. 

There is still time to boost surveillance capacity, in part because global surveillance thus far has shown that the virus mutates relatively slowly. The variants circulating right now, including the British variant dominant in Tennessee, still have more in common with the ancestral strain of the virus than not — and the vaccines work against them. 

But as long as the virus is able to jump from body to body, it will continue to change, and other variants will emerge. And community spread of the virus in Tennessee is still high. Schaffner said that tracking if and how the virus changes, as well as continuing following public health recommendations, remain key.

“Wearing your mask and social distancing —those things really help prevent infection, even with this highly contagious British variant,” Shaffner said. “The other thing and we can be very grateful for is that the vaccines we currently are using here in the United States work very well against this British variant. So, if you needed another reason to get vaccinated, here it is.”