Fig. 6

Repeat mutations, cocirculation, and occasional gene flow. a Number of coinfected individuals within major vANI95 clusters. b Mantel tests and partial Mantel tests comparing host genetic distance, geographic distance, and structure of virome dissimilarity with P values adjusted by the Benjamini and Hochberg methods. c Population genetic statistics (Pi, Fst, Tajima’s D, and number of geographic sites) of major vANI95 clusters across the sampling sites. d Geographic connection (> 200 km) of most similar viral pairs within the same vANI95 cluster. e Impact of recombination on the genome-wide population structure of CoV-3A