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
Anastasia S. Lambrou, Philip Shirk, Molly Steele, Prabasaj Paul, Clinton R. Paden, Betsy L. Cadwell, Heather E. Reese, Yutaka Aoki, Norman Hassell, Xiaoyu Zheng, Sarah Talarico, Jessica C. Chen, M. Steven Oberste, Dhwani Batra, Laura K. McMullan, Alison Laufer Halpin, Summer E. Galloway, Duncan MacCannell, Rebecca Kondor, John Barnes, Adam MacNeil, Benjamin J. Silk, Vivien G. Dugan, Heather M. Scobie, David E. Wentworth, Strain Surveillance and Emerging Variants Bioinformatic Working Group, Strain Surveillance and Emerging Variants NS3 Working Group
Abstract
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.