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2 results on '"Rambo-Martin BL"'

1. Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.

Author

Ma KC, Shirk P, Lambrou AS, Hassell N, Zheng XY, Payne AB, Ali AR, Batra D, Caravas J, Chau R, Cook PW, Howard D, Kovacs NA, Lacek KA, Lee JS, MacCannell DR, Malapati L, Mathew S, Mittal N, Nagilla RR, Parikh R, Paul P, Rambo-Martin BL, Shepard SS, Sheth M, Wentworth DE, Winn A, Hall AJ, Silk BJ, Thornburg N, Kondor R, Scobie HM, and Paden CR

Subjects
Humans, Pandemics, Genomics, SARS-CoV-2 genetics, COVID-19 epidemiology
Abstract

CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023. During this period, the Omicron variant remained predominant, with various descendant lineages reaching national predominance (>50% prevalence). During the first half of 2022, BA.1.1 reached predominance by the week ending January 8, 2022, followed by BA.2 (March 26), BA.2.12.1 (May 14), and BA.5 (July 2); the predominance of each variant coincided with surges in COVID-19 cases. The latter half of 2022 was characterized by the circulation of sublineages of BA.2, BA.4, and BA.5 (e.g., BQ.1 and BQ.1.1), some of which independently acquired similar spike protein substitutions associated with immune evasion. By the end of January 2023, XBB.1.5 became predominant. As of May 13, 2023, the most common circulating lineages were XBB.1.5 (61.5%), XBB.1.9.1 (10.0%), and XBB.1.16 (9.4%); XBB.1.16 and XBB.1.16.1 (2.4%), containing the K478R substitution, and XBB.2.3 (3.2%), containing the P521S substitution, had the fastest doubling times at that point. Analytic methods for estimating variant proportions have been updated as the availability of sequencing specimens has declined. The continued evolution of Omicron lineages highlights the importance of genomic surveillance to monitor emerging variants and help guide vaccine development and use of therapeutics., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Published
2023
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2. Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.

Author

Lambrou AS, Shirk P, Steele MK, Paul P, Paden CR, Cadwell B, Reese HE, Aoki Y, Hassell N, Zheng XY, Talarico S, Chen JC, Oberste MS, Batra D, McMullan LK, Halpin AL, Galloway SE, MacCannell DR, Kondor R, Barnes J, MacNeil A, Silk BJ, Dugan VG, Scobie HM, Wentworth DE, Caravas J, Kovacs NA, Gerhart JG, Jia Ng H, Beck A, Chau R, Cintron R, Cook PW, Gulvik CA, Howard D, Jang Y, Knipe K, Lacek KA, Moser KA, Paskey AC, Rambo-Martin BL, Nagilla RR, Retchless AC, Schmerer MW, Seby S, Shepard SS, Stanton RA, Stark TJ, Uehara A, Unoarumhi Y, Bentz ML, Burgin A, Burroughs M, Davis ML, Keller MW, Keong LM, Le SS, Lee JS, Madden Jr JC, Nobles S, Owuor DC, Padilla J, Sheth M, and Wilson MM

Subjects
Centers for Disease Control and Prevention, U.S., Genomics, Humans, Prevalence, Public Health Surveillance methods, United States epidemiology, COVID-19 epidemiology, COVID-19 virology, SARS-CoV-2 genetics
Abstract

Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune escape. During June 2021-January 2022, CDC expanded genomic surveillance data sources to incorporate sequence data from public repositories to produce weighted estimates of variant proportions at the jurisdiction level and refined analytic methods to enhance the timeliness and accuracy of national and regional variant proportion estimates. These changes also allowed for more comprehensive variant proportion estimation at the jurisdictional level (i.e., U.S. state, district, territory, and freely associated state). The data in this report are a summary of findings of recent proportions of circulating variants that are updated weekly on CDC's COVID Data Tracker website to enable timely public health action. † The SARS-CoV-2 Delta (B.1.617.2 and AY sublineages) variant rose from 1% to >50% of viral lineages circulating nationally during 8 weeks, from May 1-June 26, 2021. Delta-associated infections remained predominant until being rapidly overtaken by infections associated with the Omicron (B.1.1.529 and BA sublineages) variant in December 2021, when Omicron increased from 1% to >50% of circulating viral lineages during a 2-week period. As of the week ending January 22, 2022, Omicron was estimated to account for 99.2% (95% CI = 99.0%-99.5%) of SARS-CoV-2 infections nationwide, and Delta for 0.7% (95% CI = 0.5%-1.0%). The dynamic landscape of SARS-CoV-2 variants in 2021, including Delta- and Omicron-driven resurgences of SARS-CoV-2 transmission across the United States, underscores the importance of robust genomic surveillance efforts to inform public health planning and practice., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Published
2022
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