Avera Medical Minute: Tracking Omicron and other COVID variants

Published: Jan. 10, 2022 at 10:35 PM CST
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SIOUX FALLS, S.D. (Dakota News Now) - At the start of the pandemic, Avera was one of the first health systems in the state to develop its own PCR test to detect the COVID-19 virus in patients.

The health system has now expanded on that testing and is working to detect new COVID-19 strains and variants.

That work is being done at the Avera Institute for Human Genetics.

The Avera Institute for Human Genetics was inaugurated in 2006 to bring precision medicine to the Avera Health system.

Over the last 15 years, staff has been on the cutting edge of next-generation genome sequencing.

The COVID-19 pandemic provided an opportunity to showcase how their work can make a big impact.

“Avera is on the forefront for genetics in this region and this is an excellent way to provide support and to showcase our innovation at Avera and to also benefit the citizens and the community of Avera at the same time,” said Dr. Erik Ehli, the Scientific Director at Avera Institute for Human Genetics.

At the start of the pandemic, it was in this lab that Avera developed its own PCR test to detect the COVID-19 virus in sick patients. Now they’re sequencing some of those COVID-positive tests to track the trajectory of the COVID-19 virus and detect new variants.

“This type of technology is very valuable in its ability to put in order the nucleotides of the genome and from that information deduce what variant or what strain of the virus individuals are infected with,” said Dr. Ehli. The lab strategically pulls a number of positive COVID-19 tests from throughout the region.

“So these come from as far as Marshall and Granite Falls, Aberdeen, Yankton, Pierre,” said Leslie Cooper, Avera Laboratory Operations Manager. “So throughout Iowa, Nebraska, South Dakota, and Minnesota.”

These positive cases are then processed through a number of laboratory steps to prepare them to be loaded onto the sequencing analyzer.

“Once that sequence has been identified we can compare that to the virus sequence and identify the changes that are present,” said Ph.D. Candidate Brandon Johnson

Changes in sequences are then compared to other identified strains to identify what variant strain is present.

Sequencing is a complex, time-intensive process, but it’s a vital one to be able to track and trace the trajectory of the virus.

Essentially, this work provides a snapshot picture of what variant strains are present in a sample giving Avera a compilation of data that shows how COVID variants are changing over the course of the pandemic

“This provides invaluable information to our physician leaders as well as our public health officials to make informed decisions about the course of the pandemic in our community,” said Johnson.

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