Application of virome capture sequencing in shellfish sold at retail level in Singapore

During the period from late 2019 to early 2020, we performed a foodborne virus detection from shellfish collected in Singapore at retail level. Multiple human enteric viruses were included as our targets including human noroviruses (NoVs) GI and GII, hepatitis A virus, hepatitis E virus and rotavirus. Out of the 60 shellfish samples, 23 (38·3%) were detected to be positive by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with human enteric viruses. Six samples were selected to proceed with virome capture sequencing with positive control samples spiked with serially diluted NoV GII clinical samples in oyster extract. As a result, the natural sample with comparable Ct values (34·0-35·0) of the spiked sample as detected by RT-qPCR generated much lower read counts (>7-log₂ cumulative sum scaling difference) and genome coverage (406 nt. vs 3715 nt.), suggesting that the RT-qPCR positive signals detected from the shellfish samples collected at the retail market were likely from degraded RNA derived from inactive virus particles.