Computational protocol: A large outbreak of acute gastroenteritis caused by the human norovirus GII.17 strain at a university in Henan Province, China

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Protocol publication

[…] The full norovirus genomes were compiled using the SeqMan program in the Lasergene software package (DNASTAR, Version 2.0, Madison, WI, USA). The percentage similarities of nucleotide identity or amino acid identity were calculated using the ClustalX software, [Version 2.0, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK]. Molecular phylogenetic analysis was conducted using the maximum likelihood method based on the Kimura 2-parameter model with MEGA 5 software (available at: http://mega.software.informer.com/5.0/) []. The tree with the highest log-likelihood was shown. The percentage of trees in which the associated taxa clustered together was shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows: when the number of common sites was < 100 or < 1/4 of the total number of sites, the maximum parsimony method was used; otherwise the Neighbor-Joining (NJ) method with maximum likelihood (ML) distance matrix was used. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. Complete norovirus genomes from GenBank were used as a reference, and phylogenetic trees were constructed to type and to understand the molecular epidemiology of the outbreak strain. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Homo sapiens, Norovirus GII