ABSTRACT
BackgroundRecently emerged variants of SARS-CoV-2 have shown greater potential to cause vaccine breakthrough infections. MethodsA matched cohort analysis used a genomic sequence dataset linked with demographic and vaccination information from New York State (NYS). Two sets of conditional logistic regression analyses were performed, one during the emergence of Delta and another during the emergence of Omicron. For each set, cases were defined as individuals with the emerging lineage, and controls were individuals infected with any other lineage. The adjusted associations of vaccination status, vaccine type, time since vaccination, and age with lineage were assessed using odds ratios (OR) and 95% confidence intervals (CI). ResultsFully vaccinated status (OR: 3, 95% CI: 2.0 - 4.9) and Boosted status (OR 6.7, 95% CI: 3.4 - 13.0) were significantly associated with having the Omicron lineage during the Omicron emergence period. Risk of Omicron infection relative to Delta generally decreased with increasing age (OR: 0.964, 95% CI 0.950 - 0.978). The Delta emergence analysis had low statistical power for the observed effect size. ConclusionsVaccines offered less protection against Omicron, thereby increasing the number of potential hosts for the emerging variant. Lay SummaryThere are different variants, or types, of the virus that causes COVID-19. These variants may differ in their ability to infect a person, cause severe disease, or evade vaccine protection. From previous studies, we know that vaccines provide substantial protection against the original COVID-19 virus. In this study, we wanted to know how some of the new variants compare to one another in this regard. We found that the Omicron variant could break through vaccine protection more effectively than the Delta variant. The data suggested that Delta may be better able to break through vaccines compared to previous variants, including Alpha, but our sample sizes were low, so this pattern was not statistically significant. Individuals with a booster shot had much stronger protection against Delta compared to their protection against Omicron. We also found that younger people were more likely to be infected with Omicron than Delta.
ABSTRACT
The emergence of novel SARS-CoV-2 variants in late 2020 and early 2021 raised alarm worldwide and prompted reassessment of the management, surveillance, and projected future of COVID-19. Mutations that confer competitive advantages by increasing transmissibility or immune evasion have been associated with the localized dominance of single variants. Thus, elucidating the evolutionary and epidemiological dynamics among novel variants is essential for understanding the trajectory of the COVID-19 pandemic. Here we show the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) in New York (NY) from December 2020 to April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 likely evolved in the Bronx in late 2020, providing opportunity for an initial foothold in the heavily interconnected New York City (NYC) region, as evidenced by numerous exportations to surrounding locations. In contrast, B.1.1.7 became dominant in regions of upstate NY where B.1.526 had limited presence, suggesting that B.1.1.7 was able to spread more efficiently in the absence of B.1.526. Clusters discovered from the spatial-time scan analysis supported the role of competition between B.1.526 and B.1.1.7 in NYC in March 2021 and the outsized presence of B.1.1.7 in upstate NY in April 2021. Although B.1.526 likely delayed the rise of B.1.1.7 in NYC, B.1.1.7 became the dominant variant in the Metro region by the end of the study period. These results reveal the advantages endemicity may grant to a variant (founder effect), despite the higher fitness of an introduced lineage. Our research highlights the dynamics of inter-variant competition at a time when B.1.617.2 (Delta) is overtaking B.1.1.7 as the dominant lineage worldwide. We believe our combined spatiotemporal methodologies can disentangle the complexities of shifting SARS-CoV-2 variant landscapes at a time when the evolution of variants with additional fitness advantages is impending.
