Development of a method for direct extraction of viral RNA from bivalve molluscs

Application Research on the Triplex RT-ddPCR Assay for the Simultaneous Detection of Human Astrovirus and Sapovirus in Bivalve Shellfish

Human astrovirus (HAstV) and sapovirus (SaV) are significant pathogens associated with acute gastroenteritis in humans. This study established a triple reverse transcription-droplet digital polymerase chain reaction (PCR) (RT-ddPCR) assay incorporating MS2 phage as a process control virus for the simultaneous quantification of HAstV and SaV. The assay was validated using 240 bivalve samples, comprising five shellfish species: Ostreidae (n = 43), Ruditapes philippinarum (n = 84), Sinonovacula constricta (n = 27), Scapharca subcrenata (n = 23), and Pectinidae (n = 63). The results indicated that the developed RT-ddPCR assay had a good exclusivity, with detection limits of 5.15 copies/reaction for HAstV, 7.71 copies/reaction for SaV, and 6.13 copies/reaction for MS2 RNA. Viral screening revealed HAstV in 1.25% (3/240) of samples, with a maximum load of 22,140 copies/2 g, while SaV exhibited a higher prevalence of 13.33% (32/240) and a peak concentration of 68,700 copies/2 g. Different species of bivalve shellfish exhibited varying detection rates; the highest SaV detection rate was found in Ostreidaes at 20.93% (9/43), followed by Ruditapes philippinarums at 14.29% (12/84), Scapharca subcrenatas at 13.04% (3/23), Pectinidaes at 11.11% (7/63), and Sinonovacula constrictas at 3.70% (1/27). HAstV was only detected in R. philippinarums and Pectinidaes, with detection rates of 1.19% (1/84) and 3.17% (2/63), respectively. Additionally, both HAstV and SaV were detected in a single Pectinidae sample (0.42%, 1/240). The triple RT-ddPCR assay developed in this study is reliable, accurate, and highly sensitive, providing effective technical support for the quantitative detection of HAstV and SaV in bivalve shellfish.

Development and Application of a Multiplex Reverse Transcription-Droplet Digital PCR Assay for Simultaneous Detection of Hepatitis A Virus and Hepatitis E Virus in Bivalve Shellfish

Foodborne viruses are significant contributors to global food safety incidents, posing a serious burden on human health and food safety. In this study, a multiplex reverse transcription-droplet digital PCR (RT-ddPCR) assay based on the MS2 phage as a process control virus (PCV) was developed to achieve the simultaneous detection of hepatitis A virus (HAV) and hepatitis E virus (HEV) in bivalve shellfish. By optimizing the reaction system and procedures, the best reaction conditions were selected, and the specificity, sensitivity, and reproducibility of the method were assessed. Additionally, the MS2 phage's recovery rate was utilized as an indicator to evaluate the optimal sample nucleic acid enrichment method. The results indicated that the RT-ddPCR assay exhibited optimal amplification efficiency with primer concentrations of 900 nmol/L, probe concentrations of 350 nmol/L for HAV and HEV, and 500 nmol/L for MS2, an annealing temperature of 53.1 °C, an extension time of 90 s, and 45 cycles. Additionally, the developed multiplex RT-ddPCR assay demonstrated high specificity, with quantitation limits of 12.6, 8.9, and 7.8 copies/reaction being observed for HAV, HEV, and the MS2 phage, respectively. A total of 240 bivalve samples were analyzed, of which 4 were positive for HAV and 12 for HEV. The viral loads for HAV ranged from 3048 to 6528 copies/2 g, while those for HEV ranged from 3312 to 20,350 copies/2 g. This assay provides a vital tool for enhancing food safety monitoring.

Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models

Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.

The transcriptomic and biochemical responses of blood clams (Tegillarca granosa) to prolonged intermittent hypoxia

The blood clam (Tegillarca granosa), a marine bivalve of ecological and economic significance, often encounters intermittent hypoxia in mudflats and aquatic environments. To study the response of blood clam foot to prolonged intermittent hypoxia, the clams were exposed to intermittent hypoxia conditions (0.5 mg/L dissolved oxygen, with a 12-h interval) for 31 days. Initially, transcriptomic analysis was performed, uncovering a total of 698 differentially expressed genes (DEGs), with 236 upregulated and 462 downregulated. These genes show enrichments in signaling pathways related to glucose metabolism, sugar synthesis and responses to oxidative stress. Furthermore, the activity of the enzyme glutathione peroxidase (GPx) and the levels of gpx1 mRNA showed gradual increases, reaching their peak on the 13th day of intermittent hypoxia exposure. This observation suggests an indirect protective role of GPx against oxidative stress. The results of this study make a significantly contribute to our broader comprehensive of the physiological, biochemical responses, and molecular reactions governing the organization of foot muscle tissue in marine bivalves exposed to prolonged intermittent hypoxic conditions.

Spatial Distribution and Enrichment Dynamics of Foodborne Norovirus in Oyster Tissues

The prevalence of norovirus in oysters poses a significant threat to food safety, necessitating a comprehensive understanding of contamination patterns. This study explores the temporal dynamics of norovirus distribution in various oyster tissues over a contamination period ranging from 6 to 96 h. Four tissues-the gill, palp, digestive gland, and stomach-were subjected to systematic monitoring using RT-qPCR for absolute quantification. Results revealed rapid norovirus detection in all tissues six hours post-contamination, with subsequent variations in detection rates. Gill and digestive gland tissues exhibited a peak in detection at 12-24 h, aligning with the oyster's gastrointestinal circulatory system. The digestive gland, distinguished by specific enrichment and adsorption capabilities, demonstrated the highest virus concentration at 48 h. In contrast, the stomach displayed a reemergence of norovirus. Beyond 72 h, detection remained exclusive to the digestive gland, with Ct values comparable to earlier time points. At 96 h, a limited amount of norovirus was detected in the digestive gland, emphasizing the importance for timely monitoring. In addition to providing critical insights into optimal detection strategies, these findings highlight the time-related characteristics of norovirus contamination in oysters. The study identifies the digestive gland as a key target for reliable monitoring, providing valuable data to improve protocols for reducing hazards associated with oyster consumption and foodborne norovirus infections. This research contributes to the understanding of norovirus dynamics in oyster tissues and reinforces current efforts aimed at ensuring food safety and public health.

Development of an RNA Extraction Protocol for Norovirus from Raw Oysters and Detection by qRT-PCR and Droplet-Digital RT-PCR

Foodborne viruses such as norovirus and hepatitis A virus cause frequent outbreaks associated with the consumption of raw or undercooked oysters. Viral particles are bioaccumulated in the oyster's digestive glands, making RNA extraction and RT-PCR detection difficult due to the complex nature of the food matrix and the presence of RT-PCR inhibitors. Herein, we have developed a viral RNA extraction protocol from raw oysters using murine norovirus (MNV) as a surrogate for human noroviruses. The method combines lysis in Tri-Reagent reagent, followed by RNA extraction using Direct-Zol purification columns and lithium chloride precipitation. Viral load quantification was performed by both qRT-PCR and droplet-digital RT-PCR. We have demonstrated that this method can efficiently remove RT-PCR inhibitors, and is sensitive enough to reliably detect viral contamination at 25 PFU/0.2 g. We have also compared the efficiency of this method with the ISO 15216-1:2017 method and Method E developed by Quang and colleagues, and observed significantly higher efficiency compared with the ISO 15216-1 method and comparable efficiency with Method E, with less steps, and shorter hands-on time.

Contamination, bioaccumulation mechanism, detection, and control of human norovirus in bivalve shellfish: A review

Human norovirus (HuNoV) is a major foodborne pathogen that causes acute viral gastroenteritis, and bivalve shellfish are one of the main carriers of HuNoV transmission. A comprehensive understanding of bivalve shellfish-related HuNoV outbreaks focusing on contamination factors, bioaccumulation mechanisms, and pre- and post-harvest interventions is essential for the development of effective strategies to prevent contamination of shellfish. This review comprehensively surveys the current knowledge on global contamination and non-thermal treatment of HuNoV in bivalve shellfish. HuNoV contamination in bivalve shellfish is significantly related to the season and water. While evaluating the water quality of shellfish-inhabited waters is a key intervention, the development of non-heat treatment technology to effectively inactivate the HuNoV in bivalve shellfish while maintaining the flavor and nutrition of the shellfish is also an important direction for further research. Additionally, this review explores the bioaccumulation mechanisms of HuNoV in bivalve shellfish, especially the mechanism underlying the binding of histo-blood group antigen-like molecules and HuNoV. The detection methods for infectious HuNoV are also discussed. The establishment of effective methods to rapidly detect infectious HuNoV and development of biological components to inactivate or prevent HuNoV contamination in shellfish also need to be studied further.

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

Norovirus Monitoring in Oysters Using Two Different Extraction Methods

Detection of noroviruses in bivalve shellfish is difficult because of the low concentration of norovirus and the presence of reverse transcription (RT)-PCR inhibitors. This study aimed to assess the presence of noroviruses in oysters extracted using a proteinase K extraction (ISO 15216 method) and an adsorption-elution method. Seventy oyster samples were extracted using the two extraction methods and evaluated using RT-nested PCR. The results showed norovirus detection rates at an equal frequency of 28.6%, of which a total of 48 (68.6%) samples had corresponding positive or negative results, while there were 22 (31.4%) samples with discrepant results. Norovirus genogroup (G)I, GII, and mixed GI and GII were detected in 20%, 4.3%, and 4.3% of samples, respectively, by the proteinase K extraction method, which comprised of GI.2, GI.5b, GI.6b, GII.4, and GII.17 genotypes. With the adsorption-elution method noroviruses were detected in 17.1%, 8.6%, and 2.9% of samples, respectively, which comprised of GI.2, GII.2, GII.4, and GII.17 genotypes. All norovirus-positive oyster samples were further estimated for genome copy number using RT-quantitative PCR. The oyster samples processed using the adsorption-elution method contained norovirus GI of 3.36 × 10¹-1.06 × 10⁵ RNA copies/g of digestive tissues and GII of 1.29 × 10³-1.62 × 10⁴ RNA copies/g. Only GII (2.20 × 10¹ and 7.83 × 10¹ RNA copies/g) could be quantified in samples prepared using the proteinase K extraction method. The results demonstrate the different performance of the two sample-processing methods, and suggest the use of either extraction method in combination with RT-nested PCR for molecular surveillance of norovirus genotypes in oysters.

Cockles and mussels, alive, alive, oh-The role of bivalve molluscs as transmission vehicles for human norovirus infections

Human noroviruses are recognized as the leading worldwide cause of sporadic and epidemic viral gastroenteritis, causing morbidity and mortality in impoverished developing countries and engendering enormous economic losses in developed countries. Transmitted faecal-orally, either via person-to-person contact, or by consumption of contaminated foods or water, norovirus outbreaks are often reported in institutional settings or in the context of communal dining. Bivalve molluscs, which accumulate noroviruses via filter feeding and are often eaten raw or insufficiently cooked, are a common food vehicle implicated in gastroenteritis outbreaks. The involvement of bivalve molluscs in norovirus outbreaks and epidemiology over the past two decades are reviewed. The authors describe how their physiology of filter feeding can render them concentrated vehicles of norovirus contamination in polluted environments and how high viral loads persist in molluscs even after application of depuration practices and typical food preparation steps. The global prevalence of noroviruses in bivalve molluscs as detected by different monitoring efforts is determined and the various methods currently utilized for norovirus extraction and detection from bivalve matrices described. An overview of gastroenteritis outbreaks affirmatively associated with norovirus-contaminated bivalve molluscs as reported in the past 18 years is also provided. Strategies for risk reduction in shellfish contamination and subsequent human infection are discussed.