Texas scientists search for potentially virulent new omicron COVID-19 variant as state health officials push vaccination

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Scientists across Texas are scouring COVID-19 tests for evidence of the omicron variant of COVID-19, a potentially virulent but still mysterious new strain that was identified in the U.S. on Wednesday after circulating in other countries for weeks.

But it’s anyone’s guess, and a matter of much speculation in the Texas medical community, what sort of impact omicron might have on Texas when it lands here, which experts say is likely to be soon.

That’s because so much is unknown about the new variant: the severity of the illness it causes, whether it can resist vaccines and natural antibodies and whether it’s more contagious than the delta variant that has burned through Texas and the U.S. for months.

“There’s more that we don’t know than what we do know at this point,” said Dr. Jason Bowling, epidemiologist for University Health in San Antonio, which works with UT Health San Antonio to look for new COVID-19 variants, including omicron.

Last Friday, the World Health Organization classified the omicron strain as a variant “of concern” after scientists in South Africa reported that it appeared to be spreading quickly there.

On Wednesday, the U.S. Centers for Disease Control and Prevention said in a statement that the California and San Francisco Departments of Public Health confirmed the first U.S. case of omicron in a person who had traveled from South Africa on Nov. 22.

The person had mild symptoms, is self-quarantined, was fully vaccinated and tested positive for COVID-19 on Monday.

Omicron’s arrival in the U.S. came as no surprise to federal health officials and will be met with similar anticipation in Texas, where experts believe it could show up in state and local sequencing efforts as soon as this week.

“It’s almost certainly here,” said Dr. Benjamin Neuman, a Texas A&M University professor and chief virologist at its Global Health Research Complex, which does sequencing for COVID-19 variants.

On Monday, federal health officials concerned about omicron urged eligible vaccinated adults to get their booster shots to increase their protection from COVID-19, in whatever form it might take over the winter, and to keep masking, hand-washing and social distancing when possible.

In Texas, state health officials say they are ready to assist hospitals should another surge happen over the holidays and they are ramping up their own efforts to identify more variants in more parts of the state.

But their largest push, at least publicly, is for vaccination and booster shots. About 55% of Texans were fully vaccinated as of Dec. 1. Some 18.7% of fully vaccinated Texans have had boosters, according to state health numbers.

“Prevention is important, and vaccination remains our best prevention tool,” said Chris Van Deusen, spokesperson for the Texas Department of State Health Services.

Delta still the big worry in Texas

The delta variant is still the most prevalent variant worldwide. Delta raged over the summer, spiking new cases, hospitalizations and daily death counts in Texas and other states to some of the highest levels of the pandemic.

Discovered in India in late 2020 but first identified in the U.S. in March, delta is still being blamed for yet again increasing chaos in some areas of the country, such as West Texas and the Panhandle, New Mexico, Colorado and states farther north.

Texas health officials are already eyeing those trends and are on the lookout for a potential holiday surge, whether it's caused by delta, by omicron or some other as-yet-undiscovered variant.

Texas hospitals are still in the throes of a staffing shortage after almost two years of deadly surges and a summer wave of deaths and hospitalizations that saw record numbers of ICUs filled to capacity.

With more than 13 million Texans still not fully vaccinated, the fear of the medical community here is that another wave will further strain a health care system that is already exhausted and depleted.

At the moment, without more data about omicron, delta is still the variant likely to cause the most problems this winter, Neuman said.

“Today, it’s the delta wave that worries me. Not omicron yet,” Neuman said. “We've got to wait and see what omicron does, if anything. But with cases rising across the country — that's entirely being driven by delta.”

Even so, the world is watching the movements of omicron, which has been identified in some 200 cases in nearly two dozen countries worldwide in the week since South Africa first reported the variant in a case from early November.

Scientists still don’t know where the variant originated.

The variant “of concern”

Now that it’s in the U.S., how long it will persist is far less certain. But omicron’s genetic makeup — unlike those of many other COVID-19 variants — opens the possibility for a stronger, more contagious, more severe COVID-19 to emerge.

That’s what landed omicron on the list of five COVID-19 variants currently labeled by the WHO as variants “of concern,” meaning that their genetic makeups give them the potential to create large surges or worsen the course of the pandemic.

The most powerful so far has been the highly contagious delta variant, which infected people at a faster rate than any other strain and kept other variants from spreading widely. Omicron could change that, experts say.

“I think it still remains to be seen if [omicron] is going to overtake the delta variant, but ... it’s possible that might happen,” Bowling said. “For a while, it’s been all delta, delta, delta. There might be a new kid on the block.”

That’s one reason omicron, though still a statistical blip on the global pandemic scale, has captured more headlines and public attention as it emerged than other variants.

Another reason: trauma from the delta variant, the strongest of all COVID-19 strains so far, which crept in relatively unnoticed by anyone outside the medical community before causing an alarming new surge.

The heightened alertness, Bowling said, is a good sign.

“We don't want people to panic, but it's important for people to have situational awareness,” he said. “So I think it’s better for us to have earlier notice to be aware that there’s a new variant so that people can kind of reexamine what they're doing for their efforts against COVID-19.”

The Brazos Valley variant

Finding new strains of COVID-19, such as delta and omicron, is not as easy as looking at a PCR or rapid antigen test, which tells the subject only whether they are positive for the virus.

It takes a lot of lab techs a lot of time to perform the genomic sequencing. Depending on the type of facility doing the sequencing, it may also require patient consent and other forms of red tape due to privacy laws, Neuman said.

Most of the sequencing in the state is done by universities partnering with major hospital systems, as well as genomic surveillance done by the CDC, which sequenced about 6% of new cases in Texas last month, state health officials said.

The lab at University Health in San Antonio, where Bowling is epidemiologist, processes about 3,000 COVID-19 tests per week and sends positive tests — some 6,100 since March — to UT Health San Antonio, which has a molecular diagnostic laboratory that sequences the positive tests and determines which variant it is. The results are shared with local public health officials and University Health.

The tests are not linked to any individuals, so people don’t get to find out which variant they had. But the tests are useful for keeping track of which variants are in circulation, officials said.

Samples come throughout the University Health system’s network of clinics, screening centers, hospital facilities and detention centers, among other locations.

The state’s own health agency itself does very little sequencing, maybe a few hundred samples a week, Van Deusen said. It’s done on samples the state collects from positive COVID-19 tests from the state health department’s on-campus lab in Austin, as well as at the request of hospitals and clinics that choose to send samples to the state because they don’t have access to their own technology or resources.

But that number is expected to rise substantially this week, as the state joins with commercial and academic labs across Texas to ramp up genomic sequencing for COVID-19 variants in a new program aimed at more quickly identifying new strains.

The new Texas Variant Partnership was announced in early November, long before the omicron variant came onto the radar, but it kicks off just as scientists around the world are racing to find cases and contain the spread.

“It was a long time in the making, but the timing is very good,” said Dr. Jennifer Shuford, chief epidemiologist at DSHS who oversees the state sequencing work. “When we have 99.9% of our specimens being delta, it’s a little unexciting to do sequencing. But you know, now that we do anticipate the introduction of omicron, we really want to be able to see where and when it’s emerging. The timing of this sequencing partnership is very fortuitous.”

It was the Texas A&M genomic sequencing operation, known as the Global Health Research Complex, that detected two uniquely Texas COVID-19 variants in April. They were named the Brazos Valley variants (BV-1 and BV-2) after the seven-county region where the university’s Bryan-College Station flagship school is located.

The school put out a press release when it happened, highlighting the fact that the BV-1 in particular showed potential resistance to antibodies as well as structures similar to other variants of concern, with mutations that pointed to fast transmission and serious illness caused by infection.

The Brazos Valley variants had some of the same interesting mutations now being seen in omicron, Neuman said.

“We actually found three cases of it in the end, and then it seems to have gone away — driven out,” he said.

Unclear on its impact

While the omicron variant appears to be highly contagious, researchers don’t know whether it will infect people at a faster rate or cause more hospitalizations than the delta variant, which represents nearly all the active cases in Texas.

It could also take another month, experts say, to figure out how effective vaccines or natural immunity will be against the omicron variant.

Omicron has been identified in about a couple dozen countries, but no deaths have been linked to it. A South African doctor who was instrumental in identifying early cases said the symptoms in omicron patients so far have been mild. And there are early indicators that vaccination helps protect against the variant.

At the same time, hospitalizations have spiked in recent weeks in the South African province where omicron was first identified — and where the new strain has overtaken the delta variant in prevalence among new cases. A South African infectious disease expert told Reuters on Tuesday that omicron is showing signs of being highly contagious.

And the structure of the omicron variant has an unusually high number of mutations, which caught the attention of the WHO last week both because it’s unique and because that structure could give the virus more opportunities to spread.

Researchers have many questions. If it does become the predominant strain, how sick will it make those infected? Will it be milder than the delta variant, kill fewer people, send fewer to the hospital? Or more?

If omicron overtakes delta and causes another surge in infections but with a milder illness, it may not have much effect on hospital capacity or on the impact of the pandemic in Texas.

“Right now, at least for us, it has been 100% delta for weeks,” said Dr. Randall Olsen, medical director of the Molecular Diagnostics Laboratory at Houston Methodist Hospital, where nearly every positive COVID-19 sample is tested to identify variants.

“Delta has outcompeted every other variant that we had prior to it. So [omicron] has got to initially be brought here, and then it will have to find a foothold,” he said. “And if it’s going to be successful, it’s going to have to displace delta as the major cause [of new cases.] It'll have to be a substantial pathogen to do that.”