Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
Lopes R., Pham K., Klaassen F., Chitwood MH., Hahn AM., Redmond S., Swartwood NA., Salomon JA., Menzies NA., Cohen T., Grubaugh ND.
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.