GALVESTON, Texas – Researchers at the University of Texas Medical Branch have developed a method to detect regionally emerging COVID-19 variants that could guide treatment and vaccine design.
“We have a new computational method to detect novel emerging variants of SARS-CoV-2 at an early stage,” said Dr. Werner Braun, a professor in the Department of Biochemistry and Molecular Biology at UTMB. “We analyzed millions of sequences in the spike protein of the COVID-19 virus from all over the world and identified specific mutations that occurred together in SARS-CoV-2, including all major mutations in the spike protein of currently known variants of concern.”
Braun and his colleagues describe their work in a paper published Jan. 21 in Scientific Reports from Nature. An automated version of their method to find high-frequency mutations in a set of SARS-COV-2 spike sequences is available online at http://curie.utmb.edu/SAR.html.
COVID-19 steadily mutated during its spread to more than 300 million people. Certain mutations may have higher infectivity or resist neutralization by antibodies of vaccinated individuals and convalescent patients. The World Health Organization calls these mutations “variants of concern.”
The UTMB researchers applied cluster and network analysis to more than 1.2 million sequences of the SARS-CoV-2 spike protein from 36 countries. They identified some regionally specific groups of variants. Strains circulating in each country contained different sets of high-frequency mutations, many of which were known variants of concern. Mutations within clusters increased in frequency simultaneously.
Low frequency, but highly correlated mutations detected by this method could signal emerging variant of concern, especially if they occur at higher frequencies in other regions.
Using this new computational analysis, the researchers reported several instances where the results of the correlated mutation patterns over several countries or over time coincide with signature mutations of emerging variants of concern in Brazil, India, the United Kingdom and the United States.
They also detected mutations that may be future variants of concern.
“Our tool could be also useful for other researchers wishing to detect specific mutation patterns in other areas of the SARS-CoV-2 proteome,” the researchers concluded in the paper.
The other study authors are Drs. Surendra S. Negi and Catherine H. Schein, who like Braun are also researchers with the Sealy Center for Structural Biology and Biophysics and the Institute for Human Infections and Immunity at UTMB.
ABOUT THE UNIVERSITY OF TEXAS MEDICAL BRANCH: Texas' first academic health center opened its doors in 1891 and today has four campuses, four health sciences schools, four institutes for advanced study, a research enterprise that includes one of only two national laboratories dedicated to the safe study of infectious threats to human health, a Level 1 Trauma Center and a health system offering a full range of primary and specialized medical services throughout the Texas Gulf Coast region. UTMB is an institution in the University of Texas System and a member of the Texas Medical Center.