Computational protocol: Frequent Detection of Human Adenovirus from the Lower Gastrointestinal Tract in Men Who Have Sex with Men

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Protocol publication

[…] An aliquot of DNA from all episodes of HAdV was designated for molecular typing based on nested PCR amplification and sequencing of a partial region of the HAdV hexon gene , ; 116 such samples were submitted to the Centers for Disease Control and Prevention laboratory performing these assays. Predicted amino acid sequences of the hexon hypervariable regions 1–6 (corresponding to amino acid position 192–332 of HAdV type 1 [accession number AP_000512]) were aligned with HAdV prototype sequences (accession numbers DQ115407- DQ115457) using Clustal X ver. 1.83 implemented in BioEdit ver. 7.0.9.0 . Phylogenetic trees were constructed using neighbor-joining method in MEGA version 4.0.2 and midpoint-rooted using minimum F-value optimization. Evolutionary distances were computed using the JTT matrix-based method with all positions containing alignment gaps and missing data eliminated in pair-wise sequence comparisons. For the purpose of this study, HAdVs were typed based on the reference prototype strain that showed the highest sequence identity score at ≥90% and phylogenetic association with ≥90% bootstrap support. HAdV sequences with identity scores <90% were classified by species, but not assigned a type , . Sequence submission to GenBank pending manuscript acceptance. […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Homo sapiens, Human immunodeficiency virus 2, Human alphaherpesvirus 2, Viruses, Human immunodeficiency virus 1
Diseases Adenoviridae Infections, Infection, HIV Infections