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

Abstract

SARS-CoV-2 Omicron surged as a variant of concern (VOC) in late 2021. Subsequently, several distinct Omicron variants have appeared and overtaken each other. We combined variant frequencies from GISAID 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 between late 2021 and early 2022 before it was replaced by BA.2. We estimate that BA.5, despite a slower takeoff than BA.1, also infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other Omicron variants - BA.2, BA.4, or XBB - infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability. Our findings reveal the complex interplay between viral evolution, population susceptibility, and social factors since Omicron emerged in the US.One-Sentence SummaryFor each US state, we estimate Omicron variant-specific infections, attack rates, and effective reproduction numbers.

The effect of circulating neutralizing antibodies on the replication of SARS-CoV-2 variants following post-vaccination infections

“…In contrast to the effect of vaccination, infection with Omicron BA.1 was associated, in both univariate and multivariable analyses, with reduced maximum RNA titers compared to pre-Delta, Delta and BA.5 infection, as previously suggested 18 . The mechanisms by which BA.1 remained infectious at low viral loads 19 , achieving attack rates that exceeded those of other variants 20 with lower peak viral titers remains to be fully understood, although there is evidence that mutations accumulated in Spike reduce the barrier to infection through accelerated early infection kinetics and evasion of innate immunity compared to Delta and pre-Delta variants 21,22 .…”