2018 Volume 35 Issue 2 Pages 81-87
In some sporadic cases and outbreaks of gastroenteritis at Toyama Institute of Health, the causative pathogens have not been identified using standard methods such as RT-PCR. Here, we performed metagenomics using next-generation sequencing (NGS) to investigate a suspected case of foodborne gastroenteritis that occurred in Toyama Prefecture in April 2013, the pathogen of which had not been identified. Approximately 2–3 million reads were obtained from each specimen, and 18–845 reads of the nucleotide sequence of sapovirus (SaV) were identified in all specimens. These SaV reads were similar to a part of the genome sequence of sapovirus strain Hu/Nagoya/NGY-1/2012/JPN (SaV NGY-1), belonging to genotype GV.2, first reported in a foodborne gastroenteritis outbreak that occurred in Aichi Prefecture in April 2012. We generated specific primers for SaV NGY-1 and performed a nested RT-PCR. The amplicons were obtained from all six samples, and their sequences were identical and revealed to be 99.8% identical to that of SaV NGY-1. We thus concluded that SaV GV.2 was the causative agent in the present case. SaV GV.2 strains were detected in raw sewage but not clinical specimens collected during the corresponding period of the outbreak in Toyama, suggesting that the SaV GV.2 strains had circulated among inhabitants with subclinical infections. In conclusion, our findings demonstrated that NGS is useful for the detection of a causative virus in fecal specimens collected from a gastroenteritis outbreak.
