Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US

• Published in: Cell reports (Cambridge) Vol. 43; no. 7; p. 114451
• Main Authors: Lopes, Rafael, Pham, Kien, Klaassen, Fayette, Chitwood, Melanie H., Hahn, Anne M., Redmond, Seth, Swartwood, Nicole A., Salomon, Joshua A., Menzies, Nicolas A., Cohen, Ted, Grubaugh, Nathan D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 23.07.2024; Elsevier
• Subjects: CP: Microbiology; CP: Microbiology
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2024.114451

Omicron surged as a variant of concern in late 2021. Several distinct Omicron variants appeared and overtook each other. We combined variant frequencies and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population before it was replaced by BA.2. We estimate that BA.5 infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other variants—BA.2, BA.4, and XBB—together infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability and a negative correlation between the BA.1 and BA.2 attack rates. Our findings illustrate the complex interplay between viral evolution, population susceptibility, and social factors during the Omicron emergence in the US. [Display omitted] •Combining genomic data with infection estimates shows virus lineage dynamics•∼48% of the US population was infected with Omicron BA.1•BA.1 and BA.5 attack rates were correlated with the social vulnerability index Lopes et al. combine genomic sequence data and infection estimates to show the dynamics of SARS-CoV-2 Omicron lineages in the US from 2022 to 2023. Estimating lineage-specific infections and attack rates reveals the public health impact of virus evolution during a pandemic.