Computational protocol: Viral Gastroenteritis Associated with Genogroup II Norovirus among U.S. Military Personnel in Turkey, 2009

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Protocol publication

[…] Viral RNA was extracted from 140 µl of a 10% fecal suspension in vertrel/water solution using a QIAamp Viral RNA Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s protocol. Identification of NoV was performed by RT-PCR as previously described . Genogroup II NoV was identified using primers targeting GII-specific regions in the 5′ capsid gene as described . PCR amplicons from NoV-positive specimens were sequenced using the ABI Prism Big Dye Terminator cycle sequencing kit and an ABI Prism 3100 DNA sequence (Applied Biosystems, Foster City, CA, USA). Sequences were aligned against NoV capsid sequences obtained from Genbank using BioEdit software, version 5.1. Phylogenetic analysis was carried out using MEGA 5.0 and a dendrogram was constructed using the neighbor-joining method with genetic distance modeled using the Kimura 2-parameter model . Statistical confidence for the phylogenetic branches was assessed by bootstrap analysis (2,000 replicates) . The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree . […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms Meleagris gallopavo, Homo sapiens, Bacteria
Diseases Virus Diseases