Figure 2.

Variant logistic growth rates during their respective emergence periods in the context of infections and vaccination

(A) Estimated infections per 100,000 population (gray bars, left axis) and percentage of the population fully vaccinated (black lines, right axis) (7 day rolling average), with the colored rectangles indicating the 90 day emergence periods for each variant.

(B) Predicted probability of a given sequence belonging to each variant category over time determined by a binomial logistic regression for the variant category as the outcome and the number of days since the first detection as the predictor, estimating the logistic growth rate for Alpha versus Delta. Shown with 95% confidence intervals. The analysis is restricted to the first 90 days of emergence in each state as shown in (A). During the Alpha emergence period, we had the following number of Alpha genomes for each state: Connecticut, n = 1;221; Maine, n = 508; Massachusetts, n = 2;062; New Hampshire, n = 298; Rhode Island, n = 641; and Vermont, n = 466. During the Delta emergence period, we had the following number of Delta genomes for each state: Connecticut, n = 301; Maine, n = 108; Massachusetts, n = 268; New Hampshire, n = 30; Rhode Island, n = 136; and Vermont, n = 82.

(C) The regression coefficients (slopes) of the logistic growth rate from (B) with 95% confidence intervals. A sensitivity analysis varying the emergence periods by ±30 days is presented in Figure S1 and Table S4.