Computational protocol: A Food Handler-Associated, Foodborne Norovirus GII.4 Sydney 2012-Outbreak Following a Wedding Dinner, Austria, October 2012

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Protocol publication

[…] Stool specimens from two wedding guests, who fell sick with gastroenteritis within 48 h following the wedding dinner and from all 14 kitchen workers and 2 hotel employees were tested for bacterial enteric pathogens as described elsewhere (Huhulescu et al. ) and for NV by using realtime RT-PCR (Bernard et al. ). Genotyping was performed on NV RNA from the two positive wedding guests and the six kitchen workers by the German Consultant Laboratory for NV. Processing, amplification and sequencing of region A [(RNA-dependent RNA polymerase gene (ORF1))] and region C in the 5′-terminal part of the capsid gene (ORF2) were performed as described elsewhere (Felsenstein ). Sequences were aligned to prototype sequences drawn from GenBank with use of CLUSTAL W, version 1.6, and phylogenetic trees were produced using the neighbour joining and DNADIST program of the Phylogeny Interference Package (PHYLIP), version 3.57c (Felsenstein ). In addition, NV strains from previous Austrian outbreaks, which indicated the genotype NV GII.4 Sydney 2012 by routine genotyping performed by the Austrian Reference Laboratory, as described elsewhere (Oh et al. ), were selected for re-genotyping by the German Consultant Laboratory for NV. […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Norovirus GII, Homo sapiens
Diseases Infection