COVID-19 strains in Houston reportedly more contagious
METHODIST HOSPITAL: Genetic analysis of samples finds origins, mutations of virus
Most of the novel coronavirus strains circulating in the Houston area are a type that a controversial report recently said had mutated to become more contagious, according to a Houston Methodist Hospital analysis of the genetic makeup of the first infections treated here.
The Methodist analysis, which has not yet been peer reviewed, found the virus that causes COVID-19 was introduced into the Houston area beginning in early March from a multitude of geographic regions, including Asia, Europe and South America.
“We now have a snapshot of what the virus looked like after arriving in Houston,” said Dr. James Musser, Methodist’s chairman of pathology and genomic medicine and a study author. “That snapshot is crucial as we keep an eye out for more and less severe strains of the virus.”
Musser added that knowing where the virus originated and is mutating will help public health officials track new infection spikes and guide strategies and initiatives, particularly if more dangerous strains
cluster in some areas more than others. It also provides clues about mutations that could impact antiviral resistance, vaccine development and other novel therapies.
The Methodist study found no evidence yet of mutations making any particular strain of the virus more lethal than others.
But 70 percent of the specimens examined, taken from COVID-19 patients treated at Methodist from early March to March 30, have a mutation to the “spikes” the virus uses to attach to and enter human respiratory cells. Researchers at Los Alamos National Laboratory reported last week the mutation doesn’t make people sicker, but appears to facilitate the spread of the infection.
That finding was met with skepticism by many scientists, including Musser. Francis Collins, director of the National Institutes of Health, told the Washington Post that the paper “draws rather sweeping conclusions” about the mutant strain. Dr. S. Wesley Long, a first author on the Methodist paper, said, “no one has done research to prove the strain spreads more easily from one person to another.” He called the paper “speculation.”
Still, the Los Alamos paper has caused concern. Musser said it has generated much attention in the scientific community as well as the popular media.
The Los Alamos paper also hasn’t been peer reviewed. Both it and the Methodist paper are examples of what’s known as “pre-prints,” preliminary reports made public ahead of peer-reviewed publication because of the discoveries’ time-sensitive nature.
The Methodist study of the eight-hospital system’s first 320 COVID-19 patients represents just the third such genomic analysis of the virus’s spread in a U.S. community — and the largest to date. The others were in New York City and Seattle.
One expert called Methodist’s sequencing of so many patients “a herculean effort” that will be “very relevant” to the area’s effort to control the virus’s spread as the economy reopens.
“This sort of genomic mapping provides greater specificity in trying to follow where disease clusters begin and may spread in the future,” said Gerald Parker, director of the pandemic and biosecurity policy program at Texas A&M’s Bush School of Government Service. “It will aid in diagnostics and contact tracing.”
The single-continent seedings of the virus in New York and Seattle contrasted with the multiplecontinent seedings in Houston. Seattle’s came mostly from Asia, and New York’s mostly from Europe. The strain that Las Alamos scientists argue is more contagious, now the dominant one, is from Europe.
Parker stressed that it’s important to know that Houston is seeing a diversity of strains, not just the one from Europe.
Musser attributed the international origins of the outbreak in Houston to the city being “an ethnically diverse, international city and transportation hub.”
He said the presence of a strain in Houston tied to South America wasn’t a surprise because of the city’s connection with Latin America. But he acknowledged it was “a little bit different” given that most of the cases seen early involved European and Asian strains. The existence of a South American strain surprised some scientists, but Long said it just means the variation was first observed there.
The earliest cases in the Houston area — the first was confirmed March 5 — involved people infected during a Nile River cruise, an outbreak likely caused by an Asian or European strain, said Musser. He said there is no strain associated with Africa.
During the study period, Methodist’s lab tested 3,080 specimens for COVID-19. The testing yielded 406 positive cases, which represented 40 percent of all confirmed cases in the area at the time, said Musser. He attributed that disproportionate amount to Methodist having its own molecular diagnostic test when testing around the city was in short supply.
The test allows Methodist researchers to sequence all the genetic material in a virus — its genome. Genomes from a number of virus samples allow researchers to compare mutations.
So far, it added, the mutations have not changed the function of the coronavirus in a way that would affect vaccine development, the study authors wrote. But because the virus’s “spikes” are the target of many vaccine candidates, mutations to them particularly bear watching, they added.
The study also said there was no resistance-related mutations to antiviral drugs such as remdesivir, recently approved by the Food and Drug Administration as an emergency COVID-19 treatment. The strains studied likely would respond well to remdesivir, the study added.
The team tested the hypothesis that distinct viral types were associated with disease severity but found little evidence to support the idea. But Musser said the matter warrants further study with a larger sample size and that such analysis is currently underway at Methodist.
Musser warned against reading too much into the study because 320 viral samples represents a small amount for a pandemic that has infected more than 4 million people globally. But he noted that Methodist continues to conduct genomic analyses of all its COVID-19 patients and now has more than 1,000 cases sequenced. He is currently working on an academic paper on those cases.
“There were clearly mutations in the virus, some of which need to be followed very carefully in future,” said Musser. “Some mutations may well represent beginnings of new virus families that could cause differences in severity or an ability to elude the immune system.”
The Methodist paper has been submitted for review to a prominent scientific journal. The preprint is not the final version of the article.