MADISON – Thousands of daily cases. Hundreds of thousands of deaths. Hundreds of millions of vaccine doses. As the tallies of COVID-19’s effects in the United States have mounted to a dizzying scale, a team of University of Wisconsin-Madison scientists has kept its focus on the tiniest shifts in the virus’s genetic material.
Beginning with the first known case of the virus in Wisconsin in February 2020, researchers at UW-Madison’s AIDS Vaccine Research Laboratory have been sequencing the genomes of as many virus samples as they can process, reading each letter of the viruses’ genetic codes. The researchers have been adding to a family tree of infections globally to help fight the disease on intercontinental, interpersonal and intercellular scales.
A bill introduced last week by Wisconsin Sen. Tammy Baldwin would fund an expansion of virus genome sequencing across the U.S. Sequencing tries to keep tabs on the virus that causes COVID-19 as it shifts and evolves, sometimes into more contagious variants. As the virus’ genetic material is replicated in people it has infected, random mistakes are carried forward. The more people the virus infects, the more likely mistakes are to happen.
“The current estimate is that it makes one of those mistakes – a mutation – for about every two new people infected,” says Thomas Friedrich, professor in the UW School of Veterinary Medicine. “Over time, as different viruses take different paths to infect more people, they accumulate different combinations of mutations. We can use those like fingerprints to track how different lineages of the virus spread through space and time.”
Drawing samples from patients in the UW-Madison-partnered UW Health system and from positive tests in nearby Milwaukee County, labs run by Friedrich and UW School of Medicine and Public Health Professor David O’Connor have sequenced virus from more than 3,200 infections. Their most pressing concern is surveillance, keeping watch for the arrival of virus variants believed to be more adept at infecting people or possibly carrying mutations that make vaccines and common treatments less effective. Together at the AIDS Vaccine Research Laboratory, they have posted surveillance results online as soon as sequences are complete.
“In Madison and Dane County, where we’ve sequenced about 5 percent of the positive test cases throughout the epidemic, we can have a fair degree of confidence that if there was a significant number of the variants that first caused concern in the United Kingdom or in South Africa, we would have seen it by now,” O’Connor says. “And the fact that we haven’t means that if these viruses are here, they’re here in low enough levels that we don’t have to worry too much – yet.”