La Crosse scientists using unique system to track Covid-19 outbreaks, tracks new variants in the region

Five variants of COVID-19 are now traced to our region, and a local expert says we aren't quite out of the woods yet when it comes to the pandemic.

LA CROSSE, Wis. (WKBT) — Five variants of COVID-19 are now traced to our region, and a local expert says we aren’t quite out of the woods yet when it comes to the pandemic.

“We’ve been sequencing Covid-19 strains here at Gundersen since March of last year,” Dr. Paraic Kenny, the Director of Kabara Cancer Research Institute, Gundersen Health System.

So far, Dr. Paraic Kenny and Dr. Craig Richmond have sequenced 1,603 genomes.

“For much of that time we were tracking the variants that emerge within the virus genome as it replicates, and we were able to build up family trees of the virus, like this, that allowed us to track how the virus was moving,” said Kenny.

To break it down, when viruses make copies of themselves, sometimes it makes a spelling mistake in one of the letters of its genome, which causes a mutation.

By tracking these mutations, Dr. Kenny and Dr. Richmond were able to record families of the viruses spreading through groups like college students, meat packing factory workers, nursing homes, and various other populations.

Doctor Kenny knew at some point global variants would make their way to La Crosse, it was just a matter of time.

“We’ve been tracking a total of 5 of them here in our region,” said Kenny.

The five are,  a Southern California variant (B 1.427 / B1.429), the United Kingdom variant (B 1.1.7), a New York variant (B 1. 526), the Brazil variant (P.2), and the South African variant (B 1.351.)

“Three cases over the past few months of a strain called P2 that originated in Brazil. That’s something that’s came to our region, seems to have spread a little bit, but we haven’t detected much onward. Which is quite encouraging,” said Kenny.

Within the last week, the South African variant was detected by the team.

“It’s one of those that are giving rise to most concern because some of the vaccine trials that were done in South Africa with the vaccines that we’re using now didn’t work as well there as they worked elsewhere,” said Kenny.

There have also been traces of the UK Variant. Dr. Kenny says the biggest concern with that strain is the transmission rate.

“The B 1.1.7 in particular, is somewhere between 50-70% than the older Covid-19 strain that we’ve been dealing with for quite some time now,” said Kenny.

Kenny says another strain has been dominant in one county in the region as well.

“There’s one called B 1.526 which is a strain that emerged in the New York area, that again towards the end of last year came to dominate there. That’s a strain we’ve recently detected in Trempealeau County. And there it does seem to be associated with an outbreak centered on a high school,” said Kenny.

Dr. Kenny says he is most surprised the South African variant made it to La Crosse in such a short amount of time.

“We detected the fifth sub-strain of that virus in Wisconsin. And I think anytime that you find something that’s so rare in a relatively small community like ours, it makes you concerned that what we’re looking at is a tip of an iceberg situation,” said Kenny.

Dr. Kenny says he and Dr. Richmond will continue to process 64 of these samples per week to uncover any ‘iceberg’ situations.

Doctor Kenny says in most cases the vaccine and prior exposure will protect people against the variants, but to still be cautious.
He says it’s important to practice all the precautions doctors have advised over the last year.