Computational protocol: An outbreak of coxsackievirus A6 hand, foot, and mouth disease associated with onychomadesis in Taiwan, 2010

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Protocol publication

[…] Patients diagnosed with HFMD with positive enterovirus isolation results in the virology reference laboratories network database from July through December, 2010 were eligible for analysis in the study. Demographic data, including gender and age, and the virus isolation information were obtained from the virology reference laboratories network database. After obtaining approval from the Institutional Review Board of the TCDC and informed consent for participation in the study from the patients or their guardians, we performed a telephone interview with eligible patients or their caregivers to collect information concerning symptoms, treatments, the presence of desquamation within 2 weeks of the HFMD episode, and the presence of nail abnormalities within 8 weeks of the HFMD episode. Nail abnormalities included Beau's line, defined as transverse ridging of the nail plate, or onychomadesis, defined as nail separation starting at the matrix, which may extend distally to the proximal portion of the nail bed.The serotypes of the enterovirus isolates were determined using an in-house indirect immunofluorescence assay (IFA) kit [] and a commercial IFA kit (Chemicon International, Temecula, CA, USA). For the sequencing of the VP1 (viral protein 1) gene, viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Santa Clara, CA). One-step RT-PCR of the VP1 gene was performed as described previously []. The products were confirmed by agarose electrophoresis and were then sequenced using a BigDye Terminator Ready Reaction Cycle Sequencing Kit and an automated sequencer ABI 3730 (Applied Biosystems, Foster City, CA, USA). Obtained sequences were compared with reference EV sequences in GenBank using BLAST [] and confirmed by phylogenetic analysis. All sequences were prepared and aligned by BioEdit (version 7.0.9.0) with the Clustal W program []. The phylogenetic tree for the current CA6 strains in 2010, 52 previous CA6 strains isolated in Taiwan from 1998 through 2009, along with 8 reference sequences from other countries was constructed using the neighbor-joining command in MEGA software (version 4) in order to perform bootstrap analysis with 1,000 replications [].Stata software, version 10 (Stata Corp LP, College Station, Texas, USA), was used for statistical analyses. The Fisher's exact test or chi-square test was used to compare categorical variables, and the Mann-Whitney U test was used to compare continuous variables. A p value of less than 0.05 was considered significant. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Application Phylogenetics
Organisms Homo sapiens
Diseases Drug Eruptions, Hand, Foot and Mouth Disease, Infection, Mouth Diseases, Skin Diseases