Houston Methodist discovered 28 cases of coronavirus variants in its latest batches of virus genomes sequenced from patients with positive COVID-19 tests, including what might be the state’s first confirmation of four cases of the Brazil variant known as P.1. Houston is the first city in the U.S. to have all the major variants documented by genome sequencing.


“There is evidence to indicate that the Brazil P.1 variant may spread faster and be resistant to certain vaccines and monoclonal antibody therapies – much like the South Africa variant known as B.1.351 – and may still be able to cause disease in some people who are inoculated with Pfizer or Moderna vaccines,” said James M. Musser, M.D., Ph.D., chair of the Department of Pathology and Genomic Medicine at Houston Methodist. “The numbers of the major variants we have identified in our large sequencing study are disquieting. The genome data indicate that these important variants are now geographically widely distributed in the Houston metropolitan region.”


To get ahead of the virus and detect mutations that may correlate with patient outcomes, such as causing more severe disease or detrimentally impacting antibody treatments and vaccines, Houston Methodist began sequencing strains of the COVID-19 virus from positive tests beginning in February 2020. Processing sometimes as many as 1,700 samples per week, Houston Methodist is leading the SARS-CoV-2 genome sequencing efforts in the U.S., thus far sequencing 20,453 of Houston’s coronavirus genomes since the start of the pandemic.


In the most recent batches of 3,000-plus genomes, the U.K., South Africa and Brazil variants were detected. These three types represent the major “variants of concern” designated by public health and medical authorities. The concern is that these three variants may be more transmissible and perhaps less susceptible to some vaccines and monoclonal antibody therapies. The California and New York variants also were detected. 


Given the immediate community impact of these findings, a report was posted on the preprint server medRxiv. The manuscript, titled “Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern,” has also been submitted for peer-review to a medical journal. Musser is the corresponding author on the study.


Identifying and tracking the emerging variants in this way is becoming critical, because we’re now in a potentially dangerous phase where the virus is mutating in ways that may help it to survive. These variants are coming about as the virus tries to find strategies to evade our immune systems, which are now in the process of being primed to fight the virus as humans gain immunity through vaccinations or natural infections. The study also serves as an important public health reminder that we must be vigilant in practicing prevention measures, such as wearing masks, social distancing and proper handwashing, even after we get vaccinated.


Genomic surveillance is key, because it provides an early warning system that can catch threatening mutations before they spread too far. It will allow scientists to either alter the vaccines we now have or add to the current vaccines with boosters to fight the mutants.


“The best defense is a good offense. The only way to successfully play whack-a-mutant is to know precisely where they are and how many of them are present in a community,” said Musser, who is one of the top infectious disease pathology experts in the country. “We cannot detect variants of concern, such as those from South Africa and Brazil, by using only PCR or antigen tests, so that makes them more difficult to identify and track. To identify these important variants, our lab sequences the genome of every positive COVID-19 sample identified in Houston Methodist’s hospital system.”


Texas has uploaded more coronavirus genomes than any other state to GISAID, the international genome database, with Dr. Musser and his colleagues at Houston Methodist being one of the largest SARS-CoV-2 genome sequencing operations in the country.


Other collaborators working with Musser on this study were S. Wesley Long, Randall J. Olsen, Paul A. Christensen, Sishir Subedi, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Kristina Reppond, Madison N. Shyer and Jessica Cambric with the Center for Molecular and Translational Human Infectious Diseases Research at the Houston Methodist Research Institute; Ilya J. Finkelstein from the University of Texas at Austin; Jimmy Gollihar with the U.S. Army Combat Capabilities Development Command Army Research Laboratory at UT Austin; and Robert Olson and James J. Davis with the University of Chicago and Argonne National Laboratory.


This study was supported by funding from the Houston Methodist Academic Institute Infectious Diseases Research Fund and with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract number 75N93019C00076.