Norovirus is the principal agent of bivalve shellfish-associated gastroenteric illness worldwide. Numerous studies using PCR have demonstrated norovirus contamination in a significant proportion of both oyster and other bivalve shellfish production areas and ready-to-eat products. By comparison, the number of epidemiologically confirmed shellfish-associated outbreaks is relatively low. This study attempts to compare norovirus RNA detection in Pacific oysters (Crassostrea gigas) by quantitative real-time reverse transcription PCR (RT-PCR) and human health risk. Self-reported customer complaints of illness in a restaurant setting (screened for credible norovirus symptoms) were compared with presence and levels of norovirus as determined by real-time RT-PCR for the batch of oysters consumed. No illness was reported for batches consistently negative for norovirus by real-time RT-PCR. However, norovirus was detected in some batches for which no illness was reported. Overall presence or absence of norovirus showed a significant association with illness complaints. In addition, the batch with the highest norovirus RNA levels also resulted in the highest rate of reported illness, suggesting a linkage between virus RNA levels and health risks. This study suggests that detection of high levels of norovirus RNA in oysters is indicative of a significantly elevated health risk. However, illness may not necessarily be reported after detection of norovirus RNA at low levels.

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The efficacy of an activated sludge (modified Ludzack-Ettinger (MLE)) UV disinfection processes in removing human noroviruses and E. coli from sewage were compared with the prevalence of these microorganisms in a settled storm discharge from the same sewage treatment works. Both discharges impacted a designated oyster production area. The treatment process delivered average NoV and E. coli reductions of 2.9log 10 and 5.2log 10 , respectively. Most E. coli reductions occurred during the UV disinfection process whereas the MLE process was comparatively more important in reducing NoV levels. A positive relationship was found between NoV removal and measured applied UV dose. The average levels of total NoV in the settled storm tank were of the same order of magnitude of those in screened raw influent at the works. These results highlight the importance of measures to reduce the impact of stormwater discharges to minimise the risk of NoV gastroenteritis associated with the consumption of oysters.

Knowledge of the fate of human noroviruses (NoV) in the marine environment is key to better controlling shellfish-related NoV gastroenteritis. We quantified NoV and Escherichia coli in sewage from storm tank discharges and treated effluent processed by a UV-disinfection plant following activated sludge treatment and studied the fate of these microorganisms in an oyster harvesting area impacted by frequent stormwater discharges and infrequent freshwater discharges. Oyster monitoring sites were positioned at intervals downstream from the wastewater treatment works (WwTW) outfall impacting the harvesting area. The decay rates of NoV in oysters as a function of the distance from the outfall were less rapid than those for E. coli that had concentrations of NoV of the same order of magnitude and were over 7 km away from the outfall. Levels of E. coli in oysters from more tidally influenced areas of the estuary were higher around high water than around low water, whereas tidal flows had no influence on NoV contamination in the oysters. The study provides comparative data on the contamination profiles and loadings of NoV and E. coli in a commercial oyster fishery impacted by a WwTW.

White spot disease in penaeid shrimp is caused by the white spot syndrome virus (WSSV). It is the most economically important disease of farmed warm‐water shrimp, causing extensive economic losses estimated from $8 to $15 billion since its emergence in the 1990s. Early diagnosis of disease is critical in the management of outbreaks and to avoid crop losses. Diagnosis of white spot disease is generally carried out in centralized laboratory settings using molecular biology approaches. However, this mode of testing can be expensive and time consuming, requiring laboratory equipment, highly trained laboratory personnel, dedicated laboratory space, and long‐distance transportation of samples from field to lab. In‐field diagnostics are gaining credence as tools for rapid and early animal disease detection, allowing diagnosticians and farmers to potentially manage disease outbreaks from the pond side. In the present study, we describe the development and application of a new in‐field point‐of‐need diagnostic test and platform for the diagnosis of WSSV in remote settings (shrimp farms). We report its performance in laboratory and field settings and compare it with current gold‐standard diagnostic approaches. We discuss the potential benefits (and barriers to uptake) of applying such testing in the global shrimp farming sector.

Aims:  To investigate the potential for LENTICULES™ to act as reference materials (RMs) for noroviruses (NoV) [genogroups I (GI) and II (GII)] by determining their homogeneity and stability characteristics. Methods and Results:  NoV used in this study originated from human faecal material, screened for the absence of other faecally transmitted pathogens. The norovirus strains present in the faecal material were characterized by sequencing, and samples containing GI and GII strains representative of genotypes commonly circulating in the community were selected. RMs were produced utilizing modified lenticulating technology. A batch comprising 500 LENTICULES™ containing both norovirus genogroups was produced according to ISO Guide 34. The batch was tested and quantified using an ISO 17025 accredited quantitative real‐time RT‐PCR assay. Sufficient homogeneity was established using procedures described by Fearn and Thompson (2010), while stability at less than −15°C and ambient temperature (17–22°C) was assessed over 52 weeks and 7 days, respectively. Conclusions:  Lenticulation was shown to be an effective means of preservation of detectable NoV. LENTICULES™ were sufficiently homogeneous and stable throughout medium‐term frozen and short‐term storage at room temperature to serve as RMs. Virus LENTICULES™ have the advantages of being easy to manipulate, provide assigned values and do not require the manipulation of high titre clinical material. Significance and Impact of the Study:  The results of this study show that norovirus LENTICULES™ can be used as stable RMs for quantitative real‐time RT‐PCR assays. They can be utilized as in‐run positive extraction controls and potentially for method calibration and to enable more easy comparison of data generated by the variety of differing norovirus determination methods that have emerged in recent years. LENTICULES™ have the potential to provide essential elements of laboratory quality assurance systems for laboratories implementing these new methods for virus testing in foodstuffs and for those running routine analyses.

Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae, found at depths between 70 and 2,500 meters on the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. Genomic sequence data for this species is limited. Here, we report a high-quality assembly and annotation of the D. eleginoides genome, generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. The high-quality genome assembly of the Patagonian toothfish will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.