Fig. 3: Alpha was introduced into Connecticut at a similar frequency as Iota but was associated with larger cluster sizes.
a, b Discrete phylogeography of Alpha (a) and Iota (b). Tips and nodes were assigned one of four possible locations: Connecticut, New York/New Jersey, domestic, and international. The phylogeographic analysis was performed in BEAST23 using a time-resolved tree as the fixed topology24. Bootstrap values for each clade are shown at each ancestral node (right) and were obtained by constructing individual maximum likelihood trees with 1000 ultrafast bootstraps in IQTree26. Clades without a support value were part of polytomies. c We summed the number of sustained introductions for each variant by week. We defined sustained introductions as Connecticut-only clades containing at least 3 tips related by a non-Connecticut ancestor with at least 0.7 posterior probability for the inferred location. Bar colors indicate the source of introduction. Error bars show the range of the five replicates per variant. d There were more sustained introductions of Iota than Alpha into Connecticut. The horiztonal bars show the median and 95% CI over five replicates per variant. e The size of Alpha clades in Connecticut was on average larger than Iota clades in Connecticut. We calculated the log10 size of Connecticut clades shown in a, b. The horizontal lines denote the median and 95% CI log cluster size.
