Texas DSHS expands COVID sequencing efforts as first omicron case is discovered in US

AUSTIN (Nexstar) – On Wednesday, the first omicron case was officially discovered in the United States. While Texas awaits more information on the latest variant, its sequencing efforts are increasing this month.

It’s a new COVID sequencing network that was announced in early November, with the first samples analyzed this week.

Previously, the Department of State Health Services relied on the Center for Disease Control and Prevention for its virus sequencing. But thanks to a partnership with the University of Texas’ School of Public Health, the state is beginning to conduct its own sequencing to analyze which variants are already here.

The partnership will be funded by the federal government, channeled through the CDC, through May 2023 and will increase state sequencing by 25%.

“When [viruses] replicate, they have the chance to mutate, ”said Chief DSHS Epidemiologist, Dr. Jennifer Shuford. “Sequencing allows us to see how, when and where these viruses mutate.”

Dr. Shuford believes the new variant could already be in the state.

“It’s just a matter of discovering where it is,” said Dr. Shuford.

The sequencing process starts with samples from PCR tests.

“COVID samples are sent to the virology team for extraction, and then the RNA is delivered to us and we start sequencing,” said Bonnie Oh, a DSHS molecular biologist.

These samples then go through a three-day analysis.

“What we do is look at every part of the genetic sequence. We can look for changes so we know the original that came out in China, and we know the changes that have happened since then,” said Dr. Shuford.

The new partnership also gives Texas more control over where the state will draw samples from.

“The CDC has done a fantastic job of really trying to sample across the United States and getting a good number from Texas. However, when they use their contract labs, we do not have the opportunity to get input on where the sampling is taking place across the state,” Said Dr. Shuford.

It is important to draw samples from a large number of locations given Texas’ size.

“We want to make sure we’ll be able to recognize when a variant shows up in El Paso, even if it’s not over in Tyler,” said Dr. Shuford.

With just under 3%, Central Texas – Trauma Service Area O has e.g. a relatively low COVID hospitalization rate. But in panhandle – TSA A – they report an 18% COVID hospitalization rate.

“We have a lot of small towns in our community in the Texas Panhandle that refer patients to hospitals in Amarillo. And with that, we just are not able to accept all the patients that need to be transferred,” said Dr. Todd Bell. , the health authority of the city of Amarillo with the Texas Tech University Health Sciences Center.

He said, for now, the hospital systems there are strained but not destroyed.

Dr. Shuford said the best way the state can combat the continued mutations and new variants of COVID is to get more of the population vaccinated, though we are not sure how effective it is against omicron yet.

“What we do know from previous variants, however, is that our vaccines have been effective and that although they are not 100% effective in preventing infection, they maintain protection against serious illness, hospitalization and death. And so we have reason to believe, based on past experience, that vaccines will still be beneficial, ”said Dr. Shuford.

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