Computational protocol: Evolution of DS-1-like G1P[8] double-gene reassortant rotavirus A strains causing gastroenteritis in children in Vietnam in 2012/2013

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Protocol publication

[…] Nucleotide sequences were aligned using the SeqMan programme in the Lasergene 11 software package (DNASTAR, Inc. Madison, WI, USA). The genotype of each genome segment was determined by using the RotaC 2.0 automated genotyping tool for RVA [].Multiple sequence alignment was carried out using the MUSCLE programme, and the genetic distances were calculated by the p-distance method implemented in MEGA ver. 6.06 []. Nucleotide substitution model testing was carried out in MEGA ver. 6.06, and the best-fit evolutionary model for each gene was selected based on the lowest Bayesian information criterion score. Maximum-likelihood phylogenetic trees were constructed using MEGA ver. 6.06 []. Trees were analysed by bootstrapping with 1000 replicates, and inferred by using the general time-reversible model (GTR) with gamma distribution (G) and invariant sites (I) for VP3; GTR+ I for VP1 and VP2; the Tamura-Nei model (TN93) + I for NSP3; the Tamura 3-parameter (T92) +G for VP7, VP4, VP6, NSP2, NSP4 and NSP5; and T92+I for NSP1 []. […]

Pipeline specifications

Software tools RotaC, MEGA
Application Phylogenetics
Organisms Rotavirus A, Homo sapiens
Diseases Gastroenteritis