Texas DSHS expands COVID sequencing efforts as first omicron case is discovered in U.S.
AUSTIN (Nexstar) — On Wednesday, the first omicron case was officially detected in the United States. While Texas awaits more information on the latest variant, its sequencing efforts are ramping up this month.
It’s a new COVID sequencing network that was announced at the beginning of November, with the first samples being analyzed this week.
Previously, the Department of State Health Services depended 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, funneled through the CDC, through May of 2023 and will increase the state’s sequencing by 25%.
“When the [viruses] replicate, they have the chance to mutate,” said Chief DSHS Epidemiologist, Dr. Jennifer Shuford. “Sequencing gives us the opportunity to see how, when and where those viruses are mutating.”
Dr. Shuford believes the new variant could already be in the state.
“It’s just a matter of detecting where it is,” Dr. Shuford said.
The sequencing process starts with samples from PCR tests.
“COVID samples get sent to the virology team for extraction, and then the RNA gets delivered to us, and we start the sequencing,” said Bonnie Oh, a DSHS molecular biologist.
Then, those samples make their way through a three-day analysis.
“What we do is look at each part of that genetic sequence. We can look for changes so we know the original one that came out in China and we know the changes that have happened since then,” Dr. Shuford said.
The new partnership also gives Texas more control over where the state will pull samples from.
“The CDC has done a fantastic job of really trying to sample all across the United States and getting a good number from Texas. When they use their contract labs, though, we don’t have the chance for input on really where that sampling across the state is happening,” Dr. Shuford said.
Pulling samples from a wide range of places is important given Texas’ size.
“We want to make sure that we will be able to recognize when a variant pops up in El Paso, even if it’s not over in Tyler,” Dr. Shuford said.
At just below 3%, Central Texas – Trauma Service Area O, for example, has a relatively low COVID hospitalization rate. But in the panhandle – TSA A – they’re reporting 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, then, we just aren’t able to accept all those patients that need to be transferred,” said Dr. Todd Bell, the health authority in the city of Amarillo with Texas Tech University Health Sciences Center.
He said, for now, the hospital systems there are strained, but not broken.
Dr. Shuford said the best way the state can fight the continued mutations and new variants of COVID is to get more of the population vaccinated, even if we’re not sure how effective it is against omicron yet.
“What we do know from previous variants, though, is that our vaccines have been effective, and that even if they aren’t 100%, effective at preventing infection, that they maintain protection against severe illness, hospitalization and death. And so we have reason to believe, based on previous experience, that vaccines will still be beneficial,” Dr. Shuford said.