Computational protocol: Epidemics and Frequent Recombination within Species in Outbreaks of Human Enterovirus B-Associated Hand, Foot and Mouth Disease in Shandong China in 2010 and 2011

Similar protocols

Protocol publication

[…] The amplicons of cDNA sequence fragments were evaluated and assembled manually. The full-length genome sequences of CVB1SD, E6SD, E25SD and E30SD were aligned using Clustal W (http://www.clustal.org/). All sequences were deposited in the GenBank sequence database (18 HEV-B strains accession numbers: KC411818–KC411825, JQ713883–JQ713888, JX976769–JX976773). The resulting alignments were analyzed using SimPlot software version 3.5.1 (http://sray.med.som.jhmi.edu/SCRoftware/simplot/) with a sliding window of 400 nucleotides (nt) moving in steps of 50 nt, with each strain as a query in each run. Phylogenetic trees for 3 distinct genomic regions were constructed with the Molecular Evolutionary Genetics Analysis (MEGA) version 5.0 software package (NJ algorithm and Kimura evolution model) , . Recombination analyses were implemented via the Genetic Algorithms for Recombination Detection program in the DataMonkey software package (http://www.datamonkey.org). Multiple breakpoint detection between the non-recombinant and recombinant models was assessed by comparing the corrected Akaike's Information Criterion (AICC) scores. The Kishino-Hasegawa (KH) test was applied to verify whether the adjacent sequence fragments yielded significant topological incongruence. Ancestral-state reconstruction was performed using the neighbor-joining-tree method with DataMonkey software. […]

Pipeline specifications

Software tools Clustal W, SimPlot, MEGA, RDP4, Datamonkey
Applications Phylogenetics, Population genetic analysis
Organisms Enterovirus B, Hendra henipavirus, Homo sapiens, Viruses
Diseases Foot-and-Mouth Disease, Hand, Foot and Mouth Disease, Myotonic Dystrophy