A masked duo hold hands as they walk gingerly across a parking lot on Feb. 9, 2021.

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In recent months, Gallatin Health Officer Matt Kelley has shared data with the public that indicate the number of new coronavirus cases is declining, but he has also warned that COVID-19 cases, hospitalizations and deaths could begin climbing again, particularly if new variants of the virus begin circulating in Montana.

Critical to understanding how to manage the pandemic is knowing whether COVID-19 variants are present and how common they are, but that data is limited.

Since tracking began in November, only 115 of the thousands of virus samples from Montana have had their genetic material sequenced as part of a national effort to understand and characterize COVID-19 variants, according to the state Department of Public Health and Human Services. None of the sequenced samples have been identified as a COVID-19 variant.

Given the limited genetic sequencing, it is possible COVID-19 variants are present but undetected.

“Idaho, Montana, North and South Dakota, Nebraska, all of the states in the Northern Plains region, there haven’t been any variants detected there yet, but really, there’s not a whole lot of data from those states to know what’s going on,” said Seth Walk, Montana State University associate professor of microbiology and immunology. “I won’t say that’s the fault of anyone. ... I don’t think we missed the boat per se, but I think we need to do this now.”

The reason for the limited analysis is capacity, said Debbie Gibson, with DPHHS’ laboratory services bureau.

The state has been sending most of its samples for genetic analysis to the U.S. Centers for Disease Control and Prevention, which is able to accept only a limited number, Gibson said. Samples DPHHS suspects might contain a variant — because, for example, they come from people who have been traveling — are sent to the state of Wyoming, which provides a faster turnaround time than the CDC.

The current system leaves the United States behind more than 30 countries in monitoring for COVID-19 variants.

There is no standard for what percent of samples that test positive for COVID-19 should be sequenced, but Science Magazine reported Tuesday that a White House document released last week called for sequencing 5%. The United States is now sequencing fewer than 1%.

To improve capacity, DPHHS is working with the Montana University System, as well as some private labs, to use new federal funding to develop in-state capability to identify COVID-19 variants.

Walk, the MSU professor, is among those partnering with the state.

His lab has assisted DPHHS with diagnostic testing — identifying whether samples are positive for COVID-19 — for months and will soon begin genetic sequencing of some samples as well. He plans to begin with analysis of about 100-200 of the positive samples his lab receives daily from across Montana.

“We’re going to try to figure out what is here, what’s our baseline, and we’ll continue to monitor it over the next few weeks and months to see whether things emerge or are spreading,” Walk said.

Sequencing the virus’ genome enables scientists to detect changes to the virus that could give it new abilities.

For instance, the B.1.1.7 variant, first identified in the United Kingdom, may be more transmissible than the original virus, which could lead to more infections, according to the CDC.

“There’s always going to be mutations in viruses when they spread around. We see this all the time. Viruses just evolve very quickly and they mutate,” Walk said. “But there are certainly mutations that are more concerning to us than others because they have the potential at least to change how the virus gets around, so how easily it is to be transmitted, or they can become more virulent, so cause more severe disease, or can escape our treatments, which, right now, is primarily the vaccine.”

Jim Murphy, chief of DPHHS’ communicable disease control and prevention bureau, said tracking and identifying COVID-19 variants is critical to the state’s response to COVID-19.

“You always want to monitor what might change when you monitor disease,” he said. “We want to be able to know what’s circulating and if it’s more transmissible because that impacts our message. For example, we might need to keep some measures in place longer. We also need to know if the vaccine is effective against these variants because that impacts how we approach vaccine distribution.”

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Perrin Stein can be reached at or at 582-2648.