Computational protocol: Complex Epidemiology of a Zoonotic Disease in a Culturally Diverse Region: Phylogeography of Rabies Virus in the Middle East

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Protocol publication

[…] Sequences generated in this study were combined with selected published RABV sequences to include, as far as possible, comprehensive cover of the Middle East, and representative sequences from surrounding regions. Sequences were aligned using ClustalX2 (version 1.2). The length of sequence available for analysis varied among isolates, but a 400 base pair region of the nucleoprotein gene was chosen for further analyses as it was common to 171 of the selected sequences. A phylogenetic analysis of all these 171 virus sequences was implemented using Bayesian Markov Chain Monte Carlo simulation in the BEAST packagev1.8.0 []. A TN93 nucleotide substitution model with rate variation and a proportion of invariant sites (Gamma+I) were determined to best fit the data using Akaike Information Criterion in MEGA 6.0. A relaxed and strict molecular clock model with either constant or Bayesian skyline population prior were used in Markov Chain Monte Carlo (MCMC) simulation for 100,000,000 iterations, sampling every 10,000 states to give effective sample sizes of over 200. Molecular clock and population coalescent models were compared using a modified Akaike information criterion (AICM) in Tracer v1.5 on a subset of 137 sequences, as described previously [] (), and maximum clade credibility trees were annotated using TreeAnnotator (v1.8.0) after 10% of trees were discarded. The maximum clade credibility (MCC) trees were then visualised using Fig Tree (v1.4.0) (). A strict molecular clock and Bayesian skyline population prior gave the lowest AICM and were therefore used for the estimates of divergence dates. Neighbour-joining and maximum likelihood phylogenetic reconstructions were also undertaken on the data set in MEGA6 [] for comparison with Bayesian reconstructions. A neighbour joining tree was derived from p-distances with 1000 bootstrap replicates and a maximum likelihood tree using the same TN93 +G +I evolutionary model as used in the Bayesian analyses, the Nearest-neighbour inference heuristic and 100 bootstrap replicates. NJ and ML trees were visualized in FigTree (v1.4.0).An additional Bayesian MCMC phylogenetic analysis, with the same model parameters as above, was undertaken on a set of 59 sequences of 380 base pairs in length. These included 12 sequences from Oman and the United Arab Emirates which had only a 380 base pair region common to the other sequences, and were therefore not represented in the larger 400 base pair data set. These 12 were combined with 47 related sequences from the larger data set that were trimmed to 380 base pairs. […]

Pipeline specifications

Software tools Clustal W, MEGA, BEAST, FigTree
Application Phylogenetics
Organisms Rabies lyssavirus, Human poliovirus 1 Mahoney, Viruses
Diseases Zoonoses