Computational protocol: Mumps Epidemiology and Mumps Virus Genotypes Circulating in Mainland China during 2013-2015

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Protocol publication

[…] The entire SH gene of the MuV strains, including the noncoding region (316 nt), was aligned to the WHO reference strains using Bioedit software (Version 7.0). Representative genotype F strains isolated in China from 1995–2012 [], the WHO reference strains [], and the MuCV strains (Jeryl Lynn strain) were downloaded from GenBank and selected for phylogenetic analysis in this study. The representative SH gene sequences of genotype G collected from other countries throughout the world were downloaded from GenBank. The phylogenetic trees for genotype F () and genotype G () were drawn on the basis of the SH gene using the neighbor-joining method in MEGA software (version 5.03) with bootstrapping (500 replicates). The substitution model was the Kimura 2-parameter for nucleotides.In addition, a BSP (a retrospective model of population genetics) was used under both strict and relaxed clock conditions to estimate the demographic history with the 316-nt sequence window of the MuV sequences isolated from 1995–2015. This allowed for estimates of the effective population size over time with credibility intervals at every time point depending on errors due to the phylogeny reconstruction and the stochastic nature of the coalescent process []. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms , Homo sapiens
Diseases HIV Infections