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

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.

FIGURE 1

National estimates of weekly proportions of SARS-CoV-2 variants (A) and estimated number of variant-attributed cases (B) — United States, January 2, 2022–May 13, 2023 Abbreviations: CELR = COVID-19 electronic laboratory reporting; NS3 = National SARS-CoV-2 Strain Surveillance Program. * Sequences are reported to CDC through NS3, contract laboratories, public health laboratories, and other U.S. institutions. Variant proportion estimation methods use a complex survey design and statistical weights to account for the probability that a specimen is sequenced. https://covid.cdc.gov/covid-data-tracker/#variant-proportions ^† Lineages reaching a prevalence of ≥1% with spike protein substitutions of potential therapeutic relevance and separated out on the COVID Data Tracker website. ^§ Estimated numbers of COVID-19 cases attributable to variants were calculated by multiplying weekly numbers of reported positive nucleic acid amplification tests from CELR with estimated variant proportions.

FIGURE 2

Omicron XBB.1.5 predominance, by U.S. Department of Health and Human Services Region and week that the variant became predominant — United States, December 25, 2022–February 11, 2023 Abbreviation: HHS = U.S. Department of Health and Human Services. * The timing of XBB.1.5 predominance was defined as the week ending date during which the variant proportion estimate exceeded 50% in each HHS region. https://covid.cdc.gov/covid-data-tracker/#variant-proportions ^† HHS Region 2 includes data from Puerto Rico and the U.S. Virgin Islands. HHS Region 3 includes data from the District of Columbia. HHS Region 9 includes data from American Samoa, Guam, and the Northern Mariana Islands. https://www.hhs.gov/about/agencies/iea/regional-offices/index.html