Extended Data Fig. 1: The magnitude of the relative risk of observing sequences at a given genetic distance within the same county is impacted by transmission intensity.

A. Relative risk of observing sequences at a given genetic distance within the same county across multiple epidemic waves. We defined waves as: March 2021-June 2021 (Wave 4), July 2021-November 2021 (Wave 5), December 2021-February 2022 (Wave 6) and March 2022-August 2022 (Wave 7). In A, circular points correspond to individuals counties and triangles correspond to the median across counties. B. Median relative risk of observing pairs sequences within the same county (with IQR) as a function of genetic distance stratified by variant during Wave 6. C. A higher transmission intensity results in larger clusters of identical sequences that tend to be more mixed across groups. In C, the two clusters are simulated using a branching process with mutation¹³ by assuming the probability for an infector and an infectee to have the same consensus sequence equal to 0.69 and a probability for an infectee of being in the same groups as its infector of 0.7. We consider a reproduction number of 1.2 for the lower transmission intensity scenario and of 2.0 in the higher transmission intensity scenario.