Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern

S. Wesley Long, Randall J. Olsen, Paul A. Christensen, Sishir Subedi, Robert Olson, James J. Davis, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Kristina Reppond, Madison N. Shyer, Jessica Cambric, Ilya J. Finkelstein, Jimmy Gollihar, James M. Musser(* co-first authors) († co-corresponding) , American Journal of Pathology (2021).

Abstract

Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic,there has been international concern about the emergence of virus variants with mutations thatincrease transmissibility, enhance escape from the human immune response, or otherwise alter bio-logically important phenotypes. In late 2020, several variants of concern emerged globally, includingthe UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and tworelated California variants of interest (B.1.429 and B.1.427). These variants are believed to haveenhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations inspike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On thebasis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patientsamples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greatermetropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%)in the population, they are geographically widespread. Houston is thefirst city in the United States inwhich active circulation of all six current variants of concern has been documented by genomesequencing. As vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 isessential to understanding the presence, frequency, and medical impact of consequential variants andtheir patterns and trajectory of dissemination.