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A team of researchers in Houston, Texas, has sequenced the genomes of SARS-CoV-2 isolated from 20,400 COVID-19 patients treated at a single health system there, and they’ve found cases of all the major variants that public health experts say could increase the transmission of the virus or the severity of infection.

The finding came as Texas Gov. Greg Abbott announced he would lift the state’s mask mandate and “open Texas 100%.”

Houston is the fourth largest city in the United States, with more than 7 million people. It’s one of the most ethnically diverse, with a large international port. It’s also a medical hub, home to some of the best hospitals and research laboratories in the country.

“This is a very impressive piece of work,” said Keith Jerome, MD, PhD, head of the Virology Division at the University of Washington, in Seattle. “It is one of the most comprehensive looks that we’ve had of the viruses in a given area anywhere in the United States.”

The genomes sequenced in the study represent about 4% of all the infections in the Houston area over the past year, enough to give a “deep and realistic” picture of the situation there, said Jerome, who was not involved in the research.

“We can identify variants even when they’re at a very low frequency in our population. So, although we’re the first city in the country to have reported all of these variants, it’s likely that there are other cities in the country that have all these variants and simply aren’t aware,” said study author Wesley Long, MD, PhD, medical director of diagnostic microbiology at Houston Methodist Hospital.

The genomes analyzed from the study date back to March 2020. The Houston Methodist health system is part of a global network of genome sequencing labs called the Artic ARTIC Network, which is always on the lookout for new viral variants.

The preprint study, which posted on Tuesday, reports 23 cases of the B.1.1.7 variant, which was first identified in the United Kingdom; two cases of the B.1.351 variant, which was first reported in South Africa; and four of the P.1 variant, which arose in Brazil.

The B.1.1.7 variant is more contagious than the earlier versions of the virus and may cause more severe disease. The variants from South Africa and Brazil have changed in ways that enable them to evade immunity from the vaccines or past infection. These three have been recognized by public health authorities around the world as “variants of concern.”

In addition, researchers found 162 patients infected with the B.1.429 or B.1.427 variants from California. These have been labeled “variants of interest” because they may have changed in ways that help them spread more easily or evade immune protections. The researchers found 39 people who were infected with the P.2 variant from Brazil, which is also being closely watched for problems.

“I’d say they started really showing up in December,” Long says. The majority of Houston’s variant cases came in January and February.

Long says that so far, the number of variants they’ve seen is so low that those variants haven’t affected the number of cases they’ve seen. The investigators have no evidence that the variants cause more severe symptoms.

But he says they’re watching closely to see whether the variants will compound the fallout from the region’s recent catastrophic snow and ice storm.

“Although people weren’t able to go to work and weren’t able to go to school, a lot of people were cohabitating with different groups of people,” Long said. Strangers who had heat or power took in residents who didn’t have utility service. “So, we’re waiting to see if we see any bump in infection from that,” he said.

Viruses mutate all the time. Most of the time, these mutations have little to no effect, but sometimes they change in ways that give them an advantage, helping them spread more easily or become more efficient at infecting human cells. They can also change in ways that help them escape the proteins the body makes to block them and keep them from infecting cells.

“People need to know that the variants, although concerning, are not magical,” Long says. The same public health measures that have been working should still work to help keep the virus under control: staying at home, washing hands frequently, limiting gatherings, and wearing masks.

“We still need to wear masks,” he said. “We still need to socially distance.”

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