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.

FIG 1

Phylogenetic analysis showing the genetic relatedness of partial viral protein 1 (VP1) nucleotide sequences for human parechovirus type 3 identified in New Zealand (shown in boldface and indicated by a triangle) with known human parechoviruses. Evolutionary history was inferred for a total of 479 nucleotide sites by using a maximum likelihood method based on the Tamura-Nei model, with gamma distribution and invariant sites in MEGA5 software. Bootstrap values were calculated from 1,000 trees (only bootstrap values of >50% are shown). Scale bar indicates nucleotide substitutions per site.