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/).