Computational protocol: Dengue virus type 1 clade replacement in recurring homotypic outbreaks

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Protocol publication

[…] The DENV-1 E gene dataset for phylogenetic analysis comprised of 44 isolates from Malaysia and 121 global sequences representing the 6 distinct DENV-1 genotypes as previously reported [,]. The maximum clade credibility tree (MCC) was inferred by using the Bayesian Markov Chain Monte Carlo (MCMC) method implemented in BEAST version 1.6.2 []. The best-fit model of nucleotide substitution was selected by Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) as implemented in jModelTest 0.1.1 []. Both AIC and BIC approaches found the TN93 + G4 + I model as the best-fit model for the dataset. Two independent MCMC analyses (100 million steps) were performed utilizing relaxed uncorrelated lognormal molecular clock with Bayesian skyline as coalescent prior. The convergence of the chain was evaluated by using Tracer 1.5 []. The effective sample size (ESS) values of >200 indicated sufficient level of sampling. The MCC tree was generated and visualized by using TreeAnnotator program and FigTree 1.2.3, respectively. The degree of uncertainty in each parameter estimate is provided by the 95% highest posterior density (HPD) values. [...] The selection pressure analysis was performed by using the online facility of Datamonkey web server (http://www.datamonkey.org) based on the neighbor joining tree []. Four datasets were included, one containing only Malaysian isolates (n = 44) and the other three containing isolates belonged to the three different virus groups, genotype I (n = 63), genotype II (n = 36) and genotype III (n = 57). Five likelihood-based algorithms: SLAC, FEL, IFEL, REL and PARRIS methods were used to identify the existence of positive selection pressure at individual codon sites in the DENV-1 E gene. Sites were considered to be under positive selection if the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (ratio dN/dS) indicated with high statistical significance (P <0.1 / Bayes factor >50). […]

Pipeline specifications

Software tools BEAST, jModelTest, FigTree, Datamonkey
Applications Phylogenetics, Population genetic analysis
Organisms Dengue virus 1, Ilomantsi virus, Homo sapiens
Diseases HIV Infections