Genome sequencing unveils COVID-19 variants prevalent in Bexar County

Right now, 99% of cases in Bexar County are the Delta variant

SAN ANTONIO – The emergence of new strains of COVID-19 has put an emphasis on the science behind them.

Scientists in San Antonio have been busy during the pandemic, tracking variants in our community. Right now, they’re keeping a close eye on Omicron.

SARS-CoV-2 is the virus behind COVID-19. As it survives in our community, it changes.

“The primary tenant of virology is so long as the virus circulates, it will multiply,” Dr. Anita Kurian, the assistant director at Metro Health, said. “So long as it multiplies, it will mutate.”

The only way to identify which strain it is, is to test the virus.

The team at the Molecular Diagnostic Laboratory of the Department of Pathology and Laboratory Medicine at The University of Texas Health Science Center at San Antonio is running those tests to identify which strains of COVID we have in our community.

“We’re looking at the entire genetic makeup of those samples,” Dr. Marjorie David, the director of the lab said. “We’re able to compare them to known databases.”

That’s how they’re able to identify strains like Alpha, Delta, and Omicron.

The genomic strains have obvious signs that make them different. Those combinations throughout the genome are the signature of the variants.

Looking at the genomic sequence of Delta vs that of Omicron, the Omicron variant has a “huge number of unique alterations in the Spike gene compared to Delta,” according to Dr. David.

“We’ve, you know, brought up a sequencing for SARS-CoV-2 as we’ve adapted to the pandemic and and sought to find ways to help Bexar County to to follow how SARS-CoV-2 is behaving within our own community,” Dr. David said.

Through genomic sequencing, they’ve been able to identify sublineages of each variant. Sublineages are slight variations that are occurring within variants like Delta and Alpha.

Right now, in our community, 99% of cases are the Delta variant. It’s wiped out the Alpha variant because of its transmissibility.

“That’sapparently what we’re going to be seeing or what we predict to see with the Omicron variant as well,” Dr. David said.

There are still no detected cases in our area, but with a positive case in Harris County, Dr. David says it’s only a matter of time.

“Those alterations or mutations that it acquires would give it an advantage above other of other of the same type of SARS-CoV-2 virus that’s circulating.” Dr. David said.

Her team of 10 is getting positive tests from UT Health San Antonio, as well as University Health Systems and Metro Health.

When the tests arrive, that’s when the work begins to extract the viral nucleic acid in a secure room.

They’ll check the viral load to make sure enough of the virus is present and then the genetic sequencing happens on the MiSeq machines 30 to 192 samples at a time, all of which takes 10 to 14 days.

When the UT Health San Antonio lab is done identifying the variants, they don’t report back to patients or clinicians.

Identified results go to Metro Health as well as Texas Health and Human Services and the Texas Department of State Health Services. De-identified results get sent to University Health System as well as UT Health San Antonio.

“Never did. I think I would be involved in virus sequencing in my career, but I’m very happy to be able to help out in the pandemic and serve the community,” Dr. David said.

In an effort to share more information with the public about their work in genome sequencing, Dr. David’s team is creating an online dashboard that will share variants of interest and concern that we are seeing here in Bexar County.

That website should be up and running in the next month to a month and a half.

About the Authors:

Leigh Waldman is a news reporter at KSAT 12. She joined the station in 2021. Leigh comes to San Antonio from the Midwest after spending time at a station in Omaha, NE. After two winters there, she knew it was time to come home to Texas. When Leigh is not at work, she enjoys eating, playing with her dogs and spending time with family.

Joe Arredondo is a photojournalist at KSAT 12.