Computational protocol: Genetic diversity of PRRSV 1 in Central Eastern Europe in 1994–2014: origin and evolution of the virus in the region

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Protocol publication

[…] The ORF5 sequences from Central Eastern Europe were analyzed together with the ORF5 of PRRSV 1 Subtype 1 representing the full range of genetic diversity of this Subtype. Altogether 607 sequences were analyzed in the study (Supplementary Table). Sequence alignment was performed based on ClustalW (Geneious 10.1.3, Biomatters) and phylogenetic analysis using a Bayesian Markov chain Monte Carlo method in MrBayes v3.2. Detailed parameter settings and the principles of lineage definitions were identical to those described previously. A general time-reversible nucleotide substitution model with 4 categories of gamma-distributed rate heterogeneity and a proportion of invariant sites GTR (GTR + Г4 + I) was used. The posterior distribution of trees and model parameters were summarized from Markov chain Monte Carlo sampling over 1.1 million generations, during which trees were sampled every 250 generations. The initial 10% of samples were discarded as burn-in. […]

Pipeline specifications

Software tools Clustal W, Geneious, MrBayes
Application Phylogenetics
Organisms Porcine reproductive and respiratory syndrome virus, Human poliovirus 1 Mahoney, Sus scrofa, Salem virus