Using next-generation sequencing to determine strains of the COVID-19 virus

UT Health San Antonio discovered the first ommicron cases in Bexar County.

SAN ANTONIO — Since the coronavirus pandemic began nearly two years ago, there have been more than a dozen strains of virus. Here at UT Health San Antonio, they have a lab that differentiates between each of the strains in an effort to save lives.

UT Health San Antonio uses a technology called next-generation sequencing to distinguish the genetic makeup of thousands of genes at once from many different samples. Doing this will go a long way in the fight against COVID-19.

“It’s very exciting that we’re doing the testing here in San Antonio,” said Dr. Marjorie David, director of the Molecular Diagnostics Laboratory at UT Health San Antonio.

Her lab is sequencing COVID-19 virus samples in collaboration with UT Health San Antonio’s Greehey Children’s Cancer Research Institute, the Genome Sequencing Facility, and GCCRI’s bioinformatics team. They test and rank samples from the operations of UT Health San Antonio, as well as University Health and nonprofit Community Labs. The work is funded by the San Antonio Metropolitan Health District and the Texas Department of State Health Services.

“There’s a collaborative project that we’re part of that recently started with DSHS working with multiple different institutions in Texas that are determining SARS-COV2 sequencing,” Dr. David us.

Next-generation sequencing is needed to find out the strain of the virus, trace the virus transmission routes worldwide, detect mutations to prevent the spread of new strains, identify viral mutations that could affect the potency of the vaccine, and targeting the strain at potential COVID-19 therapies.

The sequencing process begins with two monstrous Panther instruments.

“Together, we can test up to 2,000 samples per day,” said Dr. David.

For the first few months of the pandemic, it had to be done by hand.

“We couldn’t do many at once. We hadn’t approved all of these automated instruments yet,” added Dr. David ready for it.

From there, the samples go to this lab where they extract nucleic acid and then check the viral load with a PCR machine.

“Which is similar to the original COVID tests that were first developed at the start of the pandemic,” Dr. David us.

From there, they sequence the sample in this machine, the MiSeq instrument, and a computer processes all the data.

“Just to show the bioinformatics process, which can take a day, one to two days,” said Dr. David.

That is the last step to determine the variant in question. Here are the first few cases of omicron discovered in Bexar County.

“We are very excited that this local sequencing is taking place throughout Texas because we have personally invested locally in our population and that it really helps us communicate better with our local health departments as well,” said Dr. David.

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