Application of virome capture sequencing in shellfish sold at retail level in Singapore
2021
Tan, M.T.H. | Ho, S.X. | Chu, J.J.H. | Li, D.
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.
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