TY - JOUR
T1 - Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences
AU - Olsen, Randall J.
AU - Christensen, Paul A.
AU - Long, S. Wesley
AU - Subedi, Sishir
AU - Hodjat, Parsa
AU - Olson, Robert
AU - Nguyen, Marcus
AU - Davis, James J.
AU - Yerramilli, Prasanti
AU - Saavedra, Matthew O.
AU - Pruitt, Layne
AU - Reppond, Kristina
AU - Shyer, Madison N.
AU - Cambric, Jessica
AU - Gadd, Ryan
AU - Thakur, Rashi M.
AU - Batajoo, Akanksha
AU - Finkelstein, Ilya J.
AU - Gollihar, Jimmy
AU - Musser, James M.
N1 - Funding Information:
Supported by the Houston Methodist Academic Institute Infectious Diseases Fund ; and the National Institute of Allergy and Infectious Diseases , NIH , Department of Health and Human Services contract 75N93019C00076 (J.J.D. and R.O.).
Publisher Copyright:
© 2021 American Society for Investigative Pathology
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
Copyright © 2021 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
PY - 2021/10
Y1 - 2021/10
N2 - Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (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. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 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 [eg, 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 that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants 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 not currently designated variants of interest or concern. In the aggregate, this 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, TX, and heralds the arrival of B.1.617 variants in the metroplex.
AB - Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (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. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 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 [eg, 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 that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants 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 not currently designated variants of interest or concern. In the aggregate, this 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, TX, and heralds the arrival of B.1.617 variants in the metroplex.
KW - COVID-19/epidemiology
KW - Female
KW - Genome, Viral
KW - Humans
KW - Male
KW - Middle Aged
KW - Mutation
KW - SARS-CoV-2/genetics
KW - Texas/epidemiology
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U2 - 10.1016/j.ajpath.2021.07.002
DO - 10.1016/j.ajpath.2021.07.002
M3 - Article
C2 - 34303698
AN - SCOPUS:85115125537
VL - 191
SP - 1754
EP - 1773
JO - American Journal of Pathology
JF - American Journal of Pathology
SN - 0002-9440
IS - 10
ER -