title: Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans.
abstract: The etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ∼25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased high-throughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected for de novo metagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, and Dientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen.
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand.
authors.forename: Nicole E
authors.initials: NE
authors.lastname: Moore
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Norovirus Reference Laboratory, Institute of Environmental Science & Research, Kenepuru Science Centre, Porirua, New Zealand.
authors.forename: Joanne
authors.initials: J
authors.lastname: Hewitt
authors.affiliation: Norovirus Reference Laboratory, Institute of Environmental Science & Research, Kenepuru Science Centre, Porirua, New Zealand.
authors.forename: Dawn
authors.initials: D
authors.lastname: Croucher
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Williamson
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand.
authors.forename: Shevaun
authors.initials: S
authors.lastname: Paine
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand.
authors.forename: Seiha
authors.initials: S
authors.lastname: Yen
authors.affiliation: Norovirus Reference Laboratory, Institute of Environmental Science & Research, Kenepuru Science Centre, Porirua, New Zealand.
authors.forename: Gail E
authors.initials: GE
authors.lastname: Greening
authors.affiliation: Health Programme, Institute of Environmental Science & Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand richard.hall@esr.cri.nz.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Hall
mesh_terms: D019295:Computational Biology; D004196:Disease Outbreaks; D005243:Feces / Q000821:virology*; D005759:Gastroenteritis / Q000453:epidemiology* / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054892:Metagenome; D064307:Microbiota; D009520:New Zealand / Q000453:epidemiology; D010802:Phylogeny; D014780:Viruses / Q000145:classification* / Q000235:genetics*