Computational protocol: Genotypes of the Enterovirus Causing Hand Foot and Mouth Disease in Shanghai, China, 2012-2013

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Protocol publication

[…] The genetic identity of each PCR product was first determined by comparison with the standard strains in GenBank (US National Center for Biotechnology Information, NCBI). All the sequences obtained in this study were then deposited to GenBank with the given accession numbers KP717564-KP717665 for CA6, KP717666-KP717683 for CA10, KP717684-KP717686 for CA16 and KP717687-KP717759 for EV71. Multiple sequence alignment was conducted using ClustalW. Phylogenetic trees based on partial VP1 genes were built using the neighbor-joining method in the Molecular Evolutionary Genetics Analysis program, version 5.0 (MEGA 5.0). Gaps were treated as a complete deletion. Statistical support for each clade was assessed using bootstrap analysis with 1000 replicates. Genetic distances were calculated with the P-distance model. All the reference strains used were retrieved from Genbank database, which shared the highest identity with our sequences. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Homo sapiens
Diseases Central Nervous System Diseases, Encephalitis, Hand, Foot and Mouth Disease, Meningitis, Meningoencephalitis