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.
Randall J. Olsen,Randall J. Olsen,Paul A. Christensen,S. Wesley Long,S. Wesley Long,Sishir Subedi,Parsa Hodjat,Robert Olson,Robert Olson,Marcus Nguyen,Marcus Nguyen,James J. Davis,James J. Davis,Prasanti Yerramilli,Matthew Ojeda Saavedra,Layne Pruitt,Kristina Reppond,Madison N. Shyer,Jessica Cambric,Ryan Gadd,Rashi M. Thakur,Akanksha Batajoo,Ilya J. Finkelstein,Jimmy Gollihar,Jimmy Gollihar,James M. Musser,James M. Musser +26 more
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In this article, the trajectory of SARS-CoV2 variants circulating in a major metropolitan area, documents B.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.617 variants in the metroplex.Abstract:
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.read more
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Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas
Paul A. Christensen,Randall J. Olsen,S. Wesley Long,R. D. Snehal,James J. Davis,Matthew Ojeda Saavedra,K. Reppond,Madison N. Shyer,Jessica E. Cambric,Ryan D. H. Gadd,R. M. Thakur,A. Batajoo,R. Mangham,S Silva Peña,Tri Quang Trinh,Jacob C. Kinskey,Guy Williams,Robert Olson,Jimmy Gollihar,James M. Musser +19 more
TL;DR: In this article , a genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron (B.1.529) from late November 2021 through January 5, 2022.
Journal ArticleDOI
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer
Suresh V. Kuchipudi,Meera Surendran-Nair,Rachel Ruden,Michèle Gan Yon,Ruth H. Nissly,Kurt J. Vandegrift,Rahul K. Nelli,Lingling Li,Bhushan M. Jayarao,Costas D. Maranas,Nicole Levine,Katriina Willgert,Andrew J. K. Conlan,Randall J. Olsen,James J. Davis,James M. Musser,Peter J. Hudson,Vivek Kapur +17 more
TL;DR: The discovery of widespread infection of white-tailed deer indicates their establishment as potential reservoir hosts for SARS-CoV-2, a finding with important implications for the ecology, long-term persistence, and evolution of the virus, including the potential for spillback to humans.
Journal ArticleDOI
Delta variants of SARS-CoV-2 cause significantly increased vaccine breakthrough COVID-19 cases in Houston, Texas.
Paul A. Christensen,Randall J. Olsen,S. Wesley Long,Sishir Subedi,James J. Davis,Parsa Hodjat,Debbie R. Walley,Jacob C. Kinskey,Matthew Ojeda Saavedra,Layne Pruitt,Kristina Reppond,Madison N. Shyer,Jessica Cambric,Ryan Gadd,Rashi M. Thakur,Akanksha Batajoo,Regan Mangham,Sindy Pena,Trina Trinh,Prasanti Yerramilli,Marcus Nguyen,Robert Olson,Richard Snehal,Jimmy Gollihar,James M. Musser +24 more
TL;DR: In this paper, the authors sequenced the genomes of 16,965 SARS-CoV-2 from samples acquired March 15, 2021 through September 20, 2021 in the Houston Methodist hospital system.
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Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas
TL;DR: The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe acute respiratory syndrome coronavirus disease 2019 (COVID-19) pandemic, hospitalizations, and deaths as mentioned in this paper .
Journal ArticleDOI
Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines
TL;DR: In 2019, the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) separately developed a categorization system for differentiating new strains of SARS-CoV-2 into variants of concern and variants of interest as mentioned in this paper .
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TL;DR: Using a variety of statistical and dynamic modeling approaches, the authors estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants, and a fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases.
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