Computational protocol: Seroepidemiology and Molecular Epidemiology of Enterovirus 71 in Russia

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Protocol publication

[…] Complete VP1 genome region sequences (891 nt) of EV71 isolates were identified by Sanger sequencing after PCR with oligonucleotides VP3F (GCG CCC AAY ACA GCY TAY ATA ATA GCA) and 2AR (TGG CGA GRT GRC GRT TRA CCA CTC T). Out of over 3000 EV71 VP1 sequences available in Genbank, we selected all sequences of genotype C that differed by at least 1% of nucleotide sequence (330 sequences) Phylogenetic analysis was done using Bayesian likelihood-based algorithm implemented in Beast version 1.7.5 . The SRD06 substitution model optimized for coding sequences was used with a relaxed exponential clock setting, which was better than the strict clock and the relaxed lognormal clock upon Bayes factor test (Log10 Bayes factors >10). The population prior had no significant effect on the analysis; therefore the constant population prior was used. Each analysis was run over 100 million generations and trees were sampled every 10,000 generations, resulting in 10,000 trees. Trees were annotated with TreeAnnotator v.1.4.8 using a burn-in of 1,000 trees and visualized with FigTree v.1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).Genbank accession numbers of Russian EV71 isolates are JQ973699-05, KJ645794-814, KC879485-527. […]

Pipeline specifications

Software tools BEAST, FigTree
Application Phylogenetics
Organisms Homo sapiens
Diseases Hand, Foot and Mouth Disease, Nervous System Diseases