Phylogeography and Bayesian Skyride analysis
Phylogenetic trees were generated by Bayasian inference through Markov chain Monte Carlo (MCMC) implemented in BEAST version 2.5. To reconstruct the ancestral-state phylogeographic transmission across countries, the discrete-trait model implemented in BEAST version 2.516 . The coding genes were partitioned into first+second and third codon positions and applied a separate Hasegawa-Kishino-Yano (HKY+G) substitution model with gamma-distributed rate heterogeneity among sites to each partition17 .The relaxed clock with Gausian Markov Random Field Skyride plot (GMRF) coalescent prior was selected for the final analysis. The MCMC was set at 100, 000, 000 states with10% as burn in. Results were visualized using Tracer version 1.8. (http://tree.bio.ed.ac.uk/software/tracer/) all effective sampling size ESS values were >200 indicating sufficient sampling. Bayesian Skyride analysis was carried out to visualize the epidemic evolutionary history using Tracer v 1.8. (http://tree.bio.ed.ac.uk/software/tracer/).