Viral genome sequencing adds new tool for understanding and mitigating COVID-19

In March, Gundersen Medical Foundation's Microbiology Research Laboratory developed a test that detects coronavirus disease (COVID-19). The test allows Gundersen to produce results in-house for patient testing for COVID-19, reducing the wait time for test results from days to hours.

In addition to this work, Gundersen Medical Foundation's cancer research team, led by Paraic Kenny, PhD, quickly re-tasked its cancer genome sequencing equipment to focus on COVID-19. Their efforts help to better understand the COVID-19 infections in the La Crosse region and how they relate to the global pandemic.

Dr. Kenny and his team received Institutional Review Board approval to use specimens left over after standard COVID-19 testing is completed and successfully sequenced the complete viral genomes of six of the earliest cases of COVID-19 in La Crosse County.

"At the most basic level, the virus makes occasional 'spelling mistakes' when it copies its genome during infection and these mutations are faithfully carried in all subsequent infections by that particular virus," Dr. Kenny said. "By sequencing the whole viral genome, we have been able to map the different COVID-19 strains currently in La Crosse County. This allows us to go far beyond positive and negative test results to better understand how the virus spreads within our community and healthcare system."

Gundersen is now contributing to an international effort to understand how the virus evolves as it spreads. Early data have allowed documentation of multiple independent arrivals of different strains of the virus in La Crosse. Several viruses sequenced share molecular fingerprints with viruses that arrived directly in Washington state from China, while others have their origins in strains circulating in France in late-February. The team has also confirmed community spread of one sub strain.

Dr. Kenny's ability to rapidly profile new cases of the virus may help La Crosse County's Department of Public Health and Gundersen's Infectious Disease teams to map how this virus is spreading among individuals in our community.

"The project will help us understand patterns of cluster seeding and spread in the community," Dr. Kenny said. "By tracking and mapping the sources of individual sub-strain infections, we can quickly understand weak points leading to healthcare worker infection to try to mitigate them and prevent transmission to other staff and patients."

View a video of a work being done on COVID-19 samples.