La Crosse scientist uses a unique tracking system for regional COVID-19 outbreaks

LA CROSSE, Wis. (WKBT)- Dr. Paraic Kenny is the director of the Kabara Cancer Research Insititute at Gundersen Health System. In a normal year, his lab would be researching cancer tumor cells.

“I’ve been studying cancer for 25 years, but this has really been a change of pace for us in response to an epidemic that was coming to our region,” said Kenny.

Dr. Kenny and Dr. Craig Richmond shifted gears to researching COVID-19 genomes. Since March, the two of them have sequenced over 500 coronavirus genomes.

To break it down, when viruses make copies of themselves, sometimes they make a spelling mistake in one of the letters of their genomes, which causes mutations.

“And by tracking the sequence of those spelling mistakes, and how they move through the population, we can figure out where the virus has been, and which individuals have likely been infected by people from a common source,” said Kenny.

Dr. Kenny gained national attention from the Washington Post for using this sequencing in March through May to track an outbreak in Postville, Iowa at a meat packing plant.

Then again in June and July, Dr. Kenny saw another new sequence of genomes, causing an outbreak that La Crosse residents might remember this past summer.

“It’s one person who walked into one bar at the wrong time carrying the virus and quickly spread it to many people,” said Kenny.

He calls this a super-spreading event, and now his findings are shedding light on the outbreak in cases we saw at a local college.

“It seems like at the start of the student return the prevalence disease within the population was very, very low,” said Kenny.

Despite students returning to school from all parts of the country, Kenny and Richmond have been able to pinpoint only two strains of coronavirus that have infected the college population.

“We know from our data that almost all of the students who came back were coronavirus free without testing,” said Kenny.

Dr. Kenny said the timeline and sequencing shows it was what students did after returning to school that caused the spread.

“The behavior and the culture of students in terms of getting together and enjoying themselves and partying a lot provides very fertile room for spreading a virus like this. So that probably.. almost certainly underlies the explosive spread that we’ve seen in the city over the past four to five weeks,” said Kenny.

According to Kenny, these two strains of the ‘college’ covid sequences, are being found in places they could be deadly.

“La Crosse over the past number of weeks had some outbreaks in nursing facilities. And we have sadly, determined that in many cases, that same virus that we’re detecting in individuals in this vulnerable.. very very vulnerable population is exactly the same virus that’s spreading in these student parties,” said Kenny.

Dr. Kenny and Dr. Richmond are working hard to process 64 sequences per week,  just the two of them.

Dr. Kenny said this technology, if taken full advantage of, could help contact tracers and slow the spread of Covid-19 in our region.