As the coronavirus (COVID-19) pandemic continues, scientists at the Wisconsin National Primate Research Center (WiNPRC) have kept their focus on the tiniest shifts in the virus’ genetic material.

Beginning with the first known case of the virus in Wisconsin in February 2020, researchers in the WiNPRC’s Global Infectious Disease Division have been sequencing the genomes of as many virus samples as they can process, reading each letter of genetic code.

It’s critical to expand virus genome sequencing across the U.S. as COVID-19 shifts and evolves, sometimes into more contagious variants. The more people the virus infects, the more likely genetic mutations will happen.

“The current estimate is that it makes one of those mistakes — a mutation — for about every two new people infected,” says Thomas Friedrich, WiNPRC scientist and University of Wisconsin–Madison School of Veterinary Medicine professor. As different viruses take various paths to infect more people over time, he adds, they accumulate different combinations of mutations. Researchers can use those combinations like fingerprints to track how different lineages of the virus spread through space and time.

Drawing samples from patients in Dane County and nearby Milwaukee County, Friedrich and WiNPRC colleague David O’Connor, UW–Madison School of Medicine and Public Health professor, have sequenced viruses from more than 3,200 infections. Their most pressing concern is keeping watch for virus variants believed to be more adept at infecting people or possibly carrying mutations that make vaccines and common treatments less effective. They post surveillance results online as soon as sequences are complete.

Nationally, fewer than 0.5 percent of all viruses have been sequenced. In Dane County, the researchers have sequenced 5 percent of all cases, a figure that represents their decades of experience and their work at WiNPRC to stay ahead of global HIV, influenza and Zika virus pandemics.

A coordinated sequencing system in the U.S. could help end this pandemic and the next. “You will see a benefit for HIV, for influenza, for whatever comes along,” O’Connor says. “You want to be able to track which viruses are circulating because it will save lives.”

Note: The UW–Madison researchers received funding from the Centers for Disease Control and Prevention’s SPHERES program (Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance), Fast Grants (a group of nonprofits and private donors) and the Wisconsin Partnership Program.