Coronavirus variants

A laboratory technician in ARUP Laboratories’ Molecular Infectious Diseases Lab prepares a specimen for COVID-19 molecular diagnostic testing. ARUP is sequencing a portion of specimens that test positive for SARS-CoV-2 to detect possible variant strains of the virus, including the UK variant.

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Despite a dearth of genetic sequencing in the United States, labs have identified five cases of variant strains of the coronavirus in Jackson Hole.

Teton County’s tests go to a variety of places, including the Wyoming Public Health Laboratory and private companies like Lab Corp. ARUP Laboratories, a nonprofit reference lab at the University of Utah, was the first to find evidence of the B.1.1.7 variant in Jackson and is looking for ways to spot other variants also spreading globally.

Three labs have now identified the B.1.1.7 variant, first identified in the United Kingdom, in three unrelated Teton County cases. The other two cases were related to one of those three positives.

“I think we can say that there are almost certainly more instances of the variant than we’ve detected,” Teton District Health Officer Dr. Travis Riddell said.

So far research suggests that the B.1.1.7 variant is between 50% and 70% more transmissible than the original strain of SARS-CoV-2.

Genetic sequencing, which specifically identifies how a virus has mutated, is expensive, and ARUP doesn’t sequence every sample, said Dr. Adam Barker, director of ARUP’s Institute for Clinical and Experimental Pathology. Instead, the lab uses a particular molecular assay when looking for positive COVID-19 samples.

The assay looks at three genes in the original SARS-CoV-2 strain, the presence of which denotes a positive test. However, the B.1.1.7 variant has a mutation in the “S gene,” part of the spike protein, so with the test ARUP uses, only two of those genes show up.

“If the S gene is not detected, but the other two genes are detected, then we send it on for sequencing,” Barker said.

Wyoming Department of Health spokeswoman Kim Deti said similar screenings for mutations are also happening at the state lab.

Not all variants show up using such screenings because their mutations might not register using the assays the labs use. ARUP’s screening now works only for the B.1.1.7 variant, Barker said, but the lab is developing ways to look for other major strains that have started to move around the world from countries like South Africa and Brazil.

Finding the other variants is far more random. Labs, including the Wyoming Public Health Laboratory, genetically sequence a certain portion of positive tests.

“We are sequencing here in Utah 10% of our positives, just because we’re looking for all the variants,” Barker said.

Mutation is normal for a virus like SARS-CoV-2, which is a RNA virus. RNA viruses have a smaller genome than DNA viruses and encode few proteins; they also have a tendency to mutate often.

Some mutations could be evolutionarily detrimental. Based on how viruses infect a person and then spread to others, the variations that take off generally have a tendency to be more contagious and better at finding new hosts.

“It just has a tremendous selective advantage,” Riddell said. “It can pretty quickly become a dominant strain.”

Even as some strains become more prevalent the virus continues to adapt. The New York Times reported recently that seven variants had originated in the United States, all with similar mutations in the spike protein, though it is not yet clear if they are more contagious.

Using genetic sequencing, Barker said, his lab has tracked the variants as they spread across the country, creating a sort of epidemiological road map. For instance, one variant in Utah, the B.1.1.8, was similar to the one found in the United Kingdom, but it didn’t take off outside Utah and a few bordering towns because of lockdown measures.

One of the biggest outstanding questions is how the variants affect the performance of the COVID-19 vaccines that are being rolled out.

“The emergence of these variants and these evasive properties that they’re developing could really be indicating the beginning of just a major global arms race pitting our science against the virus’ ability to mutate,” Riddell said at a Feb. 5 community update.

South Africa, for instance, has paused its use of the AstraZeneca vaccine because it appears to be far less effective at stopping mild or moderate cases of the variant there. Companies like Johnson and Johnson, Pfizer, and Moderna have all seen decreased efficacy against the variants.

However, the decreases have been small, and, on the whole, vaccines remain effective against the virus.

“Any vaccine will provide you with really powerful protection against severe illness,” Riddell said Feb. 5.

While increased vaccination rates will inevitably slow the virus and its variants as they find fewer new people to infect, Riddell said the best thing to combat mutations is to follow public health recommendations and orders. Viral mutation happens as it replicates, so the fewer people who contract the disease, the fewer chances the virus has to change.

Proliferation of variants is in large part due to the widespread nature of the pandemic, said Barker at the Utah lab. Had cases been corralled better throughout the pandemic, fewer variants might have emerged.

Following that logic, if cases can be kept low until vaccination is more common the virus will have fewer chances to mutate, and the variants that have been identified might not travel as far. As much as people may not want to hear it, the best defense against the variants appears to be doubling down on the steps they’ve already been taking.

That even applies to people who’ve been vaccinated, because studies are still determining how well people can spread COVID-19 after they’ve been inoculated.

“Concern about these variants is not a reason to not get vaccinated. No matter which vaccine you get, it will still have that very, very important benefit,” Riddell said. “However, those of us who have been vaccinated really do need to keep wearing our masks and following all the other guidelines.”

Contact Tom Hallberg at 732-7079 or thallberg@jhnewsandguide.com.

Tom Hallberg covers a little bit of everything, from skiing to long-form feature stories. A Teton Valley, Idaho, transplant by way of Portland and Bend, Oregon, he spends his time outside work writing fiction, splitboarding and climbing.

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