A Metagenomic Survey of Virological Hazards in Market-Ready Oysters

Abstract

Viral contamination of bivalve molluscs, such as oysters, is a well-recognized food safety risk. The aim of this study was to assess virological hazards in market-ready oysters on the Dutch market. Non-targeted metagenome analysis was first performed on norovirus spiked-in samples showing linear and sensitive detection of norovirus GI.2 and GII.4 down to 14 and 5 genome copies per reaction, respectively. Subsequently, metagenomic measurements were performed to detect vertebrate viral genomes present in 24 undepurated B-area samples and 144 market-ready oyster samples taken in November up to and including February of the years 2015-2021. Genome sequences from fifteen viral species were identified in market-ready oysters which are associated with infections in humans and were detected above the genomic coverage threshold (5%) applied. Among these, the two genera from the Caliciviridae family, norovirus and sapovirus were detected at high prevalence (44 and 30%). Additionally, adeno-associated dependoparvovirus A and B as well as Aichi virus A and B (ribo)nucleic acids were detected (42, 33, 6, and 11%). Nucleic acids from virus species in oysters included potentially hazardous Picobirnavirus, Anellovirus, and multiple Circoviridae and Genomoviridae species. By integrating metagenome analysis into the monitoring process, researchers, food producers and regulatory bodies can gain valuable insights into the viral communities present in the food chain. This allows for the detection of potential pathogenic hazards at an early stage, providing an opportunity for tailored monitoring programs and targeted interventions to maintain the sanitary quality of the production area and safeguard public health.

Keywords: Food safety; Metagenome; Oyster; Shellfish; Viral contamination; Virome.

Fig. 1

Linearity and pearson correlation between human norovirus genome copies and metagenome sequencing results. Results are shown for norovirus GI.2 (left) and norovirus GII.4 (right), with RT-dPCR measurements on the X axis and sequencing reads as ‘counts per million’ (cpm) on the Y axis

Fig. 2

Ratio of viral genome copies or cpm after metagenomics. Mixture (gc) = gc of each virus as % of total viral gc as determined by RT-dPCR in the mixture without shellfish matrix; Mixture (cpm) = metagenome cpm for each virus as % of total cpm for virus spiked-in mixture; Mixture in proteinase K-treated digestive oyster tissue (cpm) = metagenome cpm for each virus as % of total retrieved from virus spiked oyster digested gastrointestinal tissue