Phylogenetic analysis and genetic diversity
A phylogenetic tree was produced with MEGA 6
software15 using the maximum likelihood method
(options: Tamura-Nei 93 + G model, 1,000 replicates). For ease of
representation, only one representative sequence was for each pattern of
mutation. The sequences produced were compared to pre-epidemic and
epidemic sequences retrieved on GenBank (Supplementary Methods
S1).