Bayesian phylogenetic analysis of partial CHIKV E1 gene sequences.
<p>(A) Bayesian MCC tree of 249 Asian lineage strains calibrated to the sampling date and built using the HKY+G nucleotide substitution model, a lognormal relaxed clock and a Bayesian Skygrid coalescent model. Nodes with posterior probabilities (clade-credibility values) ≥0.9 have 95% HPD intervals for node heights shown. The two main epidemic Asian lineage clades (CL) are also shown. (B) A subtree of the American and Caribbean sublineage showing posterior probabilities and calibrated tMRCA and 95% HPD intervals for statistically supported monophyletic groups. For clarity, node bars with 95% HPD intervals are not shown, only relevant strains are labelled, and the colour code is as in section a).</p
Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Cancer, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, dynamic, lineage E 1 sequences, Illumina MiSeq platform, CHIKV, non-synonymous consensus mutations, envelope glycoprotein 1 gene, Bayesian phylogenetic analysis, Chikungunya virus epidemic, understanding, intra-host level, Latin American clusters, introduction, Americas, intra-envelope spike interactions, hotspot, III, nucleotide substitution rates, II, South, E 1 protein, E 1
DOI identifier: 10.1371/journal.pone.0209292.g003
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