The omicron variant of COVID-19 has not been found in McLennan County as of Monday, but limited genetic sequencing and a low vaccination rate here could allow it to find a foothold and spread rapidly, local experts said.
The World Health Organization last month categorized omicron as a “variant of concern” after early evidence suggests it spreads more quickly than the now-dominant delta variant, which itself was more contagious than previous versions.
Dr. Farley Verner, the public health authority for Waco-McLennan County Public Health District, said there is “every reason” to assume the new variant will increase the local case count. He said numbers might be relatively low compared to previous surges, but there is still substantial spread in the county.
“If every positive test could be tested to see whether it’s delta or omicron over the next week, would we turn one up?” he said. “I’m quite sure we would. The thing is, once it shows up it increases rapidly.”
South Africa first reported the new variant on Nov. 24, which was discovered in a sample collected on Nov. 9 according to the World Health Organization. The WHO recommended countries ramp up surveillance testing and genetic sequencing, then submit that data to public databases like GISAID, which was founded in 2008 as the Global Initiative on Sharing Avian Influenza Data.
The database reports 175 Omicron cases in the United States, 35 of which are in Texas.
Verner said in places where the variant has taken hold, the number of infections doubles roughly twice a week.
The Waco-McLennan County Public Health District reported 21 new cases on Monday, raising the number of active cases to 196. One more COVID-19 death was reported, bringing total fatalities to 727. There were 27 COVID-19 patients in county hospitals, 18 of whom are county residents and 4 who are relying on ventilators.
The U.S. Centers for Disease Control stated the variant is likely to cause breakthrough infections in vaccinated people, and though they will some protection from serious illness they can pass the virus to unvaccinated people.
On Monday, Reuters reported the first death caused by the omicron variant after a patient in the United Kingdom died. The patient’s vaccination status was not reported.
As of Monday, 123,511 McLennan County residents, or about 52% of the eligible population, have been fully vaccinated, while 28,816 people have received booster shots.
In the past week, the number of fully vaccinated county residents has increased by 1,231.
Verner said after the majority of people who wanted vaccines got one, progress has fallen short of the hopes he and other health officials had.
“It’s been slow and steady at a disappointing level,” Verner said.
According to covidcg.org, a database that tracks variations and mutations of COVID-19, the U.S. is 20th on the list of countries ranked according to their rates of genetic sequencing of COVID-19.
Iceland is sequencing 472 samples per 1,000 tests, Denmark 398 and New Zealand 298. Japan sequences 102 samples per 1,000, Canada sequences 90 and Germany sequences 38 per 1,000. The United States sequences only 30 samples per 1,000.
The European Centre for Disease Prevention and Control reported the variant has been detected in 18 EU countries, including Iceland, Liechtenstein, Norway and 41 other countries.
Dr. Ari Rao, the pathologist who oversees Baylor Scott & White Temple’s sequencing lab, said the equipment the lab uses can sequence 96 samples at once and runs nearly 24 hours a day. The process used to take three to four days to complete, but technology improvements over the last three months has shortened that time to two days or less.
“From the beginning, we’ve been sequencing as many as we can,” she said.
She said only certain kinds of COVID-19 tests pull large enough samples for sequencing, and at-home and rapid tests are not among them.
“I think it’s not a bad thing that they’re getting tested on way or another, but it just puts a limitation on the number of samples available,” Rao said.
The Texas Department of State Health Services reported the first case of the omicron variant had been spotted in Harris County on Dec. 6.
A DSHS press release from Nov. 4, five days before the first omicron sample was taken in South Africa, stated the department would partner with labs and universities throughout the state to increase sequencing.
Before the partnership, the CDC handled all COVID-19 sequencing for DSHS.
According to Douglas Loveday, a press officer for DSHS, the CDC sequenced more than 5,000 samples from Texas from mid-October to mid-November, or about 7% of Texas’ caseload. He said the CDC has increased sequencing throughout the country, but did not know by how much.
“CDC plans to continue their sequencing program in the near future, but they can’t guarantee how long their funding will allow them to keep sequencing at this level,” Loveday said.
DSHS contracted with the University of Texas Health Science Center at Houston’s school of public health, which will coordinate with academic centers and commercial laboratories to sequence more genetic samples throughout the state. The school of public health will also work with the Meyers Lab at University of Texas at Austin to develop ways to improve the sample selection.