Trajectory of Growth of SARS-CoV-2 Variants in Houston, Texas, January through May 2021 Based on 12,476 Genome Sequences

Randall J. Olsen, Paul A. Christensen*, S. Wesley Long*, Sishir Subedi*, Parsa Hodjat, Robert Olson, Marcus Nguyen, James J. Davis, Prasanti Yerramilli, Matthew Odeja Saavedra, Lanye Pruitt, Kristina Reppond, Madison N. Shyer, Jessica Cambric, Ryan Gaad, Rashi M. Thakur, Akanksha Batajoo, Ilya J. Finkelstein, Jimmy Gollihar, and James M. Musser (* co-authors), American Journal of Pathology (2021).

Abstract

‘Certain genetic variants of SARS-CoV-2 are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. We report SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist healthcare system diagnosed from January 1 through May 31, 2021. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63%-90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants (e.g., B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1) also increased rapidly, although the magnitude was less than B.1.1.7. We identified 22 patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants; these patients had a high rate of hospitalization. Breakthrough cases (n=207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many that are not currently designated variants of interest or concern. In the aggregate, our study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, and heralds the arrival of B.1.617 variants in the metroplex.’