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Houston Has a Problem: All the COVID Variants of Concern

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March 03, 2021 -- Houston has had cases of every concerning variant of the virus that causes COVID-19, according to a large new genome sequencing study.

Public health authorities have flagged the six variants identified in the study as problematic, because they have gene changes that may make the virus more contagious or help it escape immunity from vaccines or past infections.

The new finding comes as Texas Governor Greg Abbott announced that he would lift the mask mandate there, and “open Texas 100%.”

The preprint study, which has not yet been fully vetted by outside scientists, decoded genomes of SARS-CoV2 viruses isolated from more than 20,400 COVID patients, a number that represents about 4% of all the COVID cases seen in that city over the past year. 

Houston is the fourth largest city in the U.S. with an ethnically diverse population and an international port.  It’s also home to some of the nation’s top virus hunters.

The study used a large enough sample of viruses to give a “deep and realistic” picture of the situation there, said Keith Jerome, MD, PhD, head of the virology division at the University of Washington, in Seattle.

“This is a very impressive piece of work,” said Jerome, who was not involved in the research. “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 study’s authors say that Houston may be the first city to find all the variants, but it probably isn’t the only one to have them.

"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, medical director of diagnostic microbiology at Houston Methodist Hospital.

The genomes analyzed for 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 Network, which is always on the lookout for new viral variants.

The variants detected in the study first showed up in testing in December, Long says, and more cases were detected in January and February of this year.

Researchers found 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.

None of the patients with infections caused by variants lived in the same household, and none had traveled internationally, suggesting that the cases came from domestic travel and were being passed through community contact.

Long says that so far, the number of variants they've seen is so low that they haven't influenced the trajectory of Houston's daily case count. The investigators have no evidence that the variants cause more severe symptoms in patients who've had them.

But he says they're watching closely to see whether these new versions of the virus 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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