Computational protocol: Adenoviruses Associated with Acute Diarrhea in Children in Beijing, China

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Protocol publication

[…] Nucleic acid was extracted from fecal specimens using DNAzol (Molecular Research Center, Inc., Cincinnati, Ohio, USA) and the method that we have previously published . Ad DNA was detected with conventional polymerase chain reactions (PCRs) using the universal primers for all types of Ad , and followed by PCR with specific primers for the identification of Ad group F (Ad 40 and Ad 41) (). PCR was performed under conditions identical to those described previously , . The PCR products were verified by sequencing and then analyzed at the NCBI website (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi). The specimens were also tested for rotavirus using the Rota/Adenoscreen Dipstick (Microgen Bioproducts Ltd., Camberley, Surrey, UK). The sequences of Ad 41 that were amplified from fecal specimens were aligned with CLUSTAL W software. The neighbor-joining (NJ) algorithm in MEGA4 was used for phylogenetic analyses. Genetic distances were calculated by the Jukescantor parameter, and the reliabilities of phylogenetic trees were examined with bootstrap tests with 1,000 replications. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases MicroGen
Application Phylogenetics
Organisms Homo sapiens, unidentified adenovirus
Diseases Incontinentia Pigmenti