Texas DSHS wants to work with UT to identify more COVID-19 variant cases

Austin

AUSTIN (KXAN) — The Texas Department of State Health Services says it is working to partner with the University of Texas at Austin to pinpoint different mutations of the coronavirus, like the United Kingdom and South African variants.

UT prepares and sequences positive COVID-19 tests at its Genomic Sequencing and Analysis Facility.

“What you typically do when you test for virus is you just say, ‘hey, is this virus genetic material present?’ Or sometimes it goes like, ‘hey, are the proteins the virus makes, are they present in the cell?’ And it’s sort of a yes or no answer,” explained Andreas Matouschek, support director at the UT Center for Biomedical Research.

Sequencing takes that testing a step further.

“Reading all 30,000 letters and reassembling it and saying like, ‘okay so is this exactly how the virus was a month ago or two months ago, or did something change? Did something new happen?'” Matouschek said.

So far, the team at the genomic lab has helped identify 25 cases of the UK variant on campus. Now the state wants to partner up to expand its own sequencing capacity.

“We serve as a backup lab for the Houston Health Department and are working to collaborate with UT to serve as each other’s backup lab. The proposed goal is to sequence at least 1% of positive samples,” DSHS spokesperson Douglas Loveday wrote in an email to KXAN.

“We have a whole army of sequencers here,” said Jessica Podnar, referring to the team’s sequencing equipment.

Podnar is the director of the UT Genomic Sequencing and Analysis Facility. Matouschek says UT is currently testing about 100 samples per week using a certain type of machine.

“Right now we’re gearing up to be able to use the NovaSeq, which is a much more high throughput instrument,” Podnar said.

She says while the smaller output machines put out about 96 positive COVID-19 samples in three days, the NovaSeq can sequence about 768 samples in two days.

At the beginning of the month, Loveday told KXAN that DSHS was still trying to get its capacity to about 500 per week.

Matouschek says health leaders and vaccine makers can use this information to slow the spread of the virus.

“Recommending stricter masking regulations or changing the masking bar or… if you notice that it starts to evade immune response, you know, you can start developing new vaccines and respond to these changes,” Matouschek said.

Matouschek says they have not yet found other COVID-19 variants, like the ones from South Africa or California, but are keeping their eyes peeled.

“We’re trying to see whether we can help find new variants of the virus that people are not even aware of yet,” he said.

DSHS told KXAN there are a few different ways they identify which COVID-19 test samples should be sent for genetic sequencing. Most, Loveday says, are flagged during initial PCR testing as “S gene target failure (SGTF).”

He says the state also has surveillance sites that routinely submit samples. Finally, Loveday says public health leaders can reach out to providers for COVID-19 testing samples that:

  • Are PCR positive close contacts of known variant cases,
  • Are PCR positive patients with a history of international travel to a location where there is known or suspected community spread of one or more SARS-CoV-2 variants of concern (B.1.1.7, B.1.315, P.1),
  • Patients with unusual or extremely severe COVID-19 illness presentation,
  • Patients who are fully vaccinated and become ill at least 2 weeks and no more than 3 months after the most recent vaccine dose,
  • Patients who develop COVID-19 in congregate living settings with attack rates over 75% within a 14 day period,
  • Specimens from COVID-19 associated pediatric deaths,
  • Specimens from potential reinfections where at least 2 PCR positive results are on record (even if we don’t have the first sample),
  • Other specimens where there is reason to suspect an infection with a SARS-CoV-2 variant of concern (such as SGTF or other target failure).

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