Fig. 2: Alpha and Iota had a larger effective reproduction number (Rt) than other circulating lineages in the first half of 2021.
a, d Daily incidence and full vaccination rates (2 weeks post last dose) of Alpha, Iota, and other circulating lineages in New Haven County (a) and New York City (d). Estimated daily infections were assigned to one of three lineage categories (‘Alpha’, ‘Iota’, and ‘other’) according to the 7-day rolling average of variant frequency among sequenced cases. ‘Iota’ includes the sublineages B.1.526, B.1.526.1, and B.1.526.2. b, e Time-varying effective reproduction numbers (Rt) were calculated using the R package EpiEstim. An Rt value above 1 indicates that an infected individual will, on average, infect more than 1 additional person. We assumed a serial interval of mean 5.2 days and standard deviation of 4 days for all lineages. 0.025 and 0.975 quantiles are shown as dotted lines. c, f Ratios of estimated Rt between January 24 and April 24, 2021. The mean and 95% CI for the scatter plots are shown in black.
