Computational protocol: Prevalence and molecular characterizations of enterovirus D68 among children with acute respiratory infection in China between 2012 and 2014

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Protocol publication

[…] Sequence data for each clinical strain were formatted and assembled by the Seqman program of DNASTAR Software (v5.0). The sequences of EV-D68 strains that were newly obtained in Chongqing have been deposited in GenBank under the accession numbers KT803582–KT803606. To study the distribution and diversity of EV-D68 identified in this study compared to other EV-D68 strains, multiple sequence alignments were made using the ClustalW function of the BioEdit program (v7.0.9). Phylogenetic trees were constructed using the MEGA neighbor-joining algorithm (5.05). The statistical significances of the tree topologies were tested via bootstrapping (1000 replicates). Only bootstrap values >70% are shown in each tree. A phylogenetic tree that was constructed with 369 bp of VP1 gene nucleotide sequences showed that modern EV-D68 strains were divided into three primary clades (A, B and C) according to the classification previously described by Tokarz (). Nearly full-length nucleotide sequences that correspond to nt 145–7203 of the EV-D68 prototype strain (GenBank accession no. AY426531) were obtained from 13 strains of EV-D68 in the current study. A phylogenetic tree was constructed based on this region of nucleotide sequences with the 13 strains from Chongqing (Ten strains from 2014, two strains from 2013, and one strain from 2012), seven strains from the 2014 US outbreak and available EV-D68 sequences that were long enough (). […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Homo sapiens
Diseases Asthma, Respiratory Tract Infections