Computational protocol: Intergenogroup Recombination in Sapoviruses

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Protocol publication

[…] We compared the complete genome sequences of 11 SaV strains to analyze suspected novel recombinant SaV strains. For this study, we sequenced the complete genomes of 4 SaV strains (Mc2, SK15, Ehime1107, and SW278). The Mc2 strain was isolated from a child with gastroenteritis in Chiang Mai, Thailand, in 2000 (); SK15 was isolated from an adult with gastroenteritis in Sakai, Japan, in 2001 (unpub. data); Ehime1107 was isolated from an adult with gastroenteritis in Matsuyama, Japan, in 2002 (unpub. data); and SW278 was isolated from an adult with gastroenteritis in Solna, Sweden, in 2003 (). The complete genome sequences were amplified and sequenced as described earlier (). Phylogenetic analysis was performed by using the Genetyx program (Genetyx for the Macintosh version 13.0.5, Genetyx Corp., Tokyo, Japan) and ClustalX (Version 1.82; available from http://www.embl.de/~chenna/clustal/darwin/). Trees were drawn by using njplot (for the Macintosh; available from http://pbil.univ-lyon1.fr/software/njplot.html). […]

Pipeline specifications

Software tools Clustal W, NJplot
Application Phylogenetics
Organisms Homo sapiens, Sus scrofa
Diseases Gastroenteritis