Digital RT-PCR method for hepatitis A virus and norovirus quantification in soft berries

An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue

An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.

Evaluation of a new automated viral RNA extraction platform for hepatitis A virus and human norovirus in testing of berries, lettuce, and oysters

Fruits, vegetables, and shellfish are often associated with outbreaks of illness caused particularly by human norovirus (HuNoV) and hepatitis A virus (HAV), the leading causative agents of foodborne illness worldwide. The aim of this study was to evaluate a new automated nucleic acid extraction platform (EGENE-UP EASYPREP) for enteric viruses in several at-risk food matrices and to test its limit of detection in comparison to a semi-automated method (EGENE-UP) using Boom methodology for nucleic acid extraction as suggested in the reference method ISO 15216-2:2019. Fresh and frozen raspberries, frozen blackberries, romaine lettuce and oyster digestive glands were artificially contaminated with HAV, HuNoV GII.4 or HuNoV GI.7 at 102, 103 or 104 genome copies/sample. Virus was then recovered from the food matrix using the ISO method. Viral RNA extracted from frozen berry samples by the automated system was purified on a column for additional removal of RT-qPCR inhibitors. For fresh raspberry, oysters, and romaine lettuce, the two extraction platforms were deemed equivalent. For frozen raspberry, the automated platform appeared to be more efficient for viral recovery, particularly for HAV and HuNoV GI at lower concentrations. With frozen blackberries, the two platforms may be considered equivalent for all targeted viruses. However, the automated method led to less sample-associated inhibition of the PCR, 56.5 % of samples versus 95.0 % for the semi-automated. We thus found that the automated extraction can be performed easily by users while obtaining equivalent or even superior results to the ISO 15216-2:2019 method, and therefore appears to be suitable for routine sanitary monitoring in food processing and for tracing outbreaks of illness.

Concentration of foodborne viruses eluted from fresh and frozen produce: Applicability of ultrafiltration

Foodborne illnesses involving raw and minimally processed foods are often caused by human noroviruses (HuNoV) and hepatitis A virus (HAV). Since food is contaminated usually with small numbers of virions, these must be eluted from the food surface and then concentrated for detection. The objective of this study was to optimize an ultrafiltration (UF) concentration method for HAV and HuNoVs present on various fresh and frozen produce. The detection range of the optimized method and its applicability to different food matrices was compared to the reference method ISO 15216-1:2017. Strawberry, raspberry, blackberry, lettuce, and green onion (25 g) were contaminated with HAV, HuNoV GI.7 and HuNoV GII.4 and then recovered therefrom by elution. A commercial benchtop UF device was used for the concentration step. Viral RNA was extracted and detected by RT-qPCR. From fresh strawberries, recovery of HAV loaded at 104 genome copies per sample was 30 ± 13 %, elution time had no significant impact, and UF membrane with an 80-100 kDa cut-off in combination with Tris-glycine elution buffer at pH 9.5 was found optimal. At lower copy numbers on fresh strawberry, at least 1 log lower numbers of HuNoV were detectable by the UF method (103 vs 104 GII.4 copies/sample and 101 vs 103 GI.7 copies/sample), while HAV was detected at 101 genome copies/sample by both methods. Except on raspberry, the UF method was usually equivalent to the ISO method regardless of the virus tested. The UF method makes rapid viral concentration possible, while supporting the filtration of large volume of sample. With fewer steps and shorter analysis time than the ISO method, this method could be suitable for routine analysis of viruses throughout the food production and surveillance chain.

A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques

Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.

Risk assessment of norovirus and hepatitis A virus in strawberries imported into China

Norovirus (NoV) and hepatitis A virus (HAV) pose a considerable health risk worldwide. In recent years, many cases of virus infection caused by virus-contaminated strawberries have occurred worldwide. This study applied a critical control point system to analyze the main hazards during the production and marketing of strawberries imported into China and explore the key control points in the whole process. To further evaluate the risks in the supply chain, the established quantitative microbial risk assessment (QMRA) was used to determine the probability that residents would be infected with viruses after consuming imported strawberries. It was found that the risk of virus contamination from imported strawberries was low, and the virus contamination mainly results from water resources and personnel. This research helps the regulatory authorities formulate strategies to ensure the long-term microbial safety of imported strawberries. In addition, the methods may prove useful in evaluating the risks of other agricultural produce.

Use of Human Intestinal Enteroids for Recovery of Infectious Human Norovirus from Berries and Lettuce

Norovirus (NoV) is the leading cause of viral foodborne gastroenteritis globally. Currently, the gold standard for detecting NoV in clinical, food, and environmental samples is via molecular-based methods, primarily RT-PCR. Nevertheless, there is a great need for confirmatory assays that can determine the infectivity of viral particles recovered from contaminated matrices. The use of the human intestinal enteroids system (HIEs) has allowed for the expansion of norovirus replication, although it still suffers from limitations of strain preferences and the requirement of high titer stocks for infection. In this study, we wanted to explore the feasibility of using the HIEs to support the replication of NoV that had been recovered from representative food matrices that have been associated with foodborne illness. We first confirmed that HIEs can support the replication of several strains of NoV as measured by RT-qPCR. We subsequently chose two of those strains that reproducibly replicated, GII.4 and GII.6, to evaluate in a TCID50 assay and for future experiments. Infectious NoV could be recovered and quantified in the HIEs from lettuce, frozen raspberries, or frozen strawberries seeded with high titers of either of these strains. While many experimental challenges still remain to be overcome, the results of this study represent an important step toward the detection of infectious norovirus from representative produce items.

A Review of Modern Methods for the Detection of Foodborne Pathogens

Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to foodborne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. Although extensive reviews of methods for foodborne pathogens detection exist, most are skewed towards bacteria despite the increasing relevance of other pathogens such as viruses. Therefore, this review of foodborne pathogen detection methods is holistic, focusing on pathogenic bacteria, fungi, and viruses. This review has shown that culture-based methods allied with new approaches are beneficial for the detection of foodborne pathogens. The current application of immunoassay methods, especially for bacterial and fungal toxins detection in foods, are reviewed. The use and benefits of nucleic acid-based PCR methods and next-generation sequencing-based methods for bacterial, fungal, and viral pathogens' detection and their toxins in foods are also reviewed. This review has, therefore, shown that different modern methods exist for the detection of current and emerging foodborne bacterial, fungal, and viral pathogens. It provides further evidence that the full utilization of these tools can lead to early detection and control of foodborne diseases, enhancing public health and reducing the frequency of disease outbreaks.

Evaluation of a Proteinase K-Based Extraction Method to Detect Hepatitis A Virus, Hepatitis E Virus and Norovirus in Artificially Contaminated Dairy Products

Human norovirus and hepatitis viruses (hepatitis A (HAV) and hepatitis E (HEV)) are leading causes of foodborne disease worldwide. Among the various food products, different types of dairy products can be implicated in viral foodborne outbreaks and contamination can occur at different stages, such as preparation, contact with contaminated equipment or via other foods. The aim of this study was to characterise a proteinase K method adapted from the ISO 15216 method for the detection of HAV, HEV and norovirus in artificially contaminated dairy products, based on the recent international standard of ISO 16140-4. Results showed that the recovery yields obtained from pure RNA in dairy products ranged from 5.76% to 76.40% for HAV, from 35.09% to 100.00% for HEV, from 25.09% to 100.00% for norovirus GI and from 47.83% to 100.00% for norovirus GII. The process control MNV-1 was detected in all RNA extracts, with recovery yields between 36.83% and 100.00%. The limit of detection (LOD) of the method was between 184 and 642 genome copies/mL (or/g) for the LOD50 and 802 and 2800 genome copies/mL or/g for the LOD95 according to the virus analysed. This method proved to be suitable for detecting viruses in dairy products for routine diagnostic needs.

Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform

Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.

Crystal digital RT-PCR for the detection and quantification of norovirus and hepatitis A virus RNA in frozen raspberries

Berries are important vehicles for norovirus (NoV) and hepatitis A virus (HAV) foodborne outbreaks. Sensitive and quantitative detection of these viruses in food samples currently relies on RT-qPCR, but remains challenging due to their low concentration and the presence of RT-qPCR inhibitors. Moreover, quantification requires a standard curve. In this study, crystal digital RT-PCR (RT-cdPCR) assays were adapted from RT-qPCR sets of primers and probe currently used in our diagnostic laboratory for the detection and precise quantification of norovirus genogroups I and II (NoV GI, GII) and hepatitis A virus (HAV) RNA in frozen raspberry samples. We selected assay conditions based on optimal separation of positive and negative droplets, and peak resolution. Using virus-specific in vitro RNA transcripts diluted in raspberry RNA extracts, we showed that all three RT-cdPCR assays were sensitive, and we estimated the 95 % detection limit at 9 copies per RT-cdPCR reaction for NoV GI, 3 for NoV GII, and 14 for HAV. Serial dilutions of the RNA transcripts showed excellent linearity over a range of four orders of magnitude. We achieved precise quantification (CV ≤ 35 %) of the RNA transcripts between runs down to 15-145 copies per reaction for NoV GI, <20 for NoV GII, and < 15 for HAV. The three RT-cdPCR assays also proved to be tolerant to inhibitors from frozen raspberries, although not as tolerant as the RT-qPCR assays in the case of NoV GI and HAV. We further evaluated the assays with inoculated frozen raspberry samples and compared their performance to that of the RT-qPCR assays. As compared to the corresponding RT-qPCR assays, the NoV GI and HAV RT-cdPCR assays showed a decreased qualitative sensitivity, while the NoV GII RT-cdPCR assay had an increased sensitivity. As for quantification, the NoV GI and NoV GII RT-cdPCR assays produced similar estimates of RNA copy number than their respective RT-qPCR assays, whereas for HAV, the RT-cdPCR assay produced lower estimates than the RT-qPCR assay. However, all the RT-cdPCR assays provided more precise quantitative measurements at low levels of contamination than the RT-qPCR assays. In conclusion, the potential of the RT-cdPCR assays in this study to detect viral RNA from frozen raspberries varied according to assay, but these RT-cdPCR assays should be considered for precise absolute quantification in difficult matrices such as frozen raspberries.

Detection and Sequencing of Multiple Human Norovirus Genotypes from Imported Frozen Raspberries Linked to Outbreaks in the Province of Quebec, Canada, in 2017

Human noroviruses are among the main causes of acute gastroenteritis worldwide. Frozen raspberries have been linked to several norovirus food-related outbreaks. However, the extraction of norovirus RNA from frozen raspberries remains challenging. Recovery yields are low and PCR inhibitors limit the sensitivity of the detection methodologies. In 2017, 724 people from various regions of the Province of Quebec, Canada, were infected by noroviruses and the outbreak investigation pointed to frozen raspberries as a putative source. A new magnetic silica bead approach was used for the extraction of viruses from different outbreak samples. The RNA extracts were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and five samples were confirmed positive for norovirus by RT-qPCR amplicon sequencing. A multiplex long-range two-step RT-PCR approach was developed to amplify norovirus ORF2 and ORF3 capsid genes from the positive frozen raspberry RNA extracts and other sequencing strategies were also explored. These capsid genes were sequenced by Next-Generation Sequencing. Phylogenetic analyses confirmed the presence of multiple genotypes (GI.3, GI.6, and GII.17) and intra-genotype variants in some of the frozen raspberry samples. Variants of genotype GI.3 and GI.6 had 100% homology with sequences from patient samples. Similar strains were also reported in previous outbreaks. Confirmation approaches based on sequencing the norovirus capsid genes using Next-Generation Sequencing can be applied at trace level contaminations and could be useful to assess risk and assist in source tracking.

Application of Lab-on-Chip for Detection of Microbial Nucleic Acid in Food and Environment

Various diseases caused by food-borne or environmental pathogenic microorganisms have been a persistent threat to public health and global economies. It is necessary to regularly detect microorganisms in food and environment to prevent infection of pathogenic microorganisms. However, most traditional detection methods are expensive, time-consuming, and unfeasible in practice in the absence of sophisticated instruments and trained operators. Point-of-care testing (POCT) can be used to detect microorganisms rapidly on site and greatly improve the efficiency of microbial detection. Lab-on-chip (LOC) is an emerging POCT technology with great potential by integrating most of the experimental steps carried out in the laboratory into a single monolithic device. This review will primarily focus on principles and techniques of LOC for detection of microbial nucleic acid in food and environment, including sample preparation, nucleic acid amplification and sample detection.

Extraction of human noroviruses from leafy greens and fresh herbs using magnetic silica beads

Consumption of leafy greens and to a lesser extent fresh herbs has been associated with several foodborne outbreaks including human norovirus (HuNoV). However, the extraction and detection of viruses from these matrices present multiple challenges such as low recovery yields and relatively high PCR inhibition. A new magnetic silica bead based (MSB) extraction protocol was developed and used to recover norovirus from leafy greens and fresh herbs. The performance results were compared to the ISO 15216-1:2017 standard. The HuNoV GII.4 and GI.5 recovery yields from spiked lettuce using the MSB extraction protocol range from 33 to 82%. There was a good correlation between murine norovirus (MNV) and HuNoV recovery yields from fresh herbs and leafy greens. No reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) inhibition was detected from leafy green extracts using the MSB methodology. The selected commercial RT-qPCR detection kit had a major impact on RT-qPCR inhibition levels detected in the ISO 15216-1:2017 RNA extracts. RNase treatment was used to estimate genome recovery from HuNoV with intact capsids. This treatment resulted in similar HuNoV and MNV recovery yields. Between 2019 and 2020, the MSB protocol was used to conduct a survey of HuNoV in domestic and imported leafy greens and fresh herbs sold at retail in Canada. All of the 280 samples tested were negative. Overall, the use of MSB was shown to be an efficient approach to recover HuNoV from leafy greens and certain types of fresh herbs and to conduct surveys.

Norovirus Extraction from Frozen Raspberries Using Magnetic Silica Beads

Human noroviruses (HuNoV) are among the main causes of acute gastroenteritis worldwide. Frozen raspberries have been linked to several HuNoV food-related outbreaks. However, the extraction of HuNoV RNA from frozen raspberries remains challenging. Recovery yields are low, and real-time quantitative reverse transcriptase PCR (RT-qPCR) inhibitors limit the sensitivity of the detection methodologies. A new approach using fine magnetic silica beads was developed for the extraction of HuNoV spiked on frozen raspberries. Relatively low recovery yields were observed with both the magnetic silica bead and the reference ISO 15216-1:2017 methods. High RT-qPCR inhibition was observed with the ISO 15216-1:2017 recommended amplification kit but could be reduced by using an alternative kit. Reducing RT-qPCR inhibition is important to limit the number of inconclusive HuNoV assays thus increasing the capacity to assess the HuNoV prevalence in frozen raspberries.

A Rapid and Sensitive Europium Nanoparticle-Based Lateral Flow Immunoassay Combined with Recombinase Polymerase Amplification for Simultaneous Detection of Three Food-Borne Pathogens

Food-borne pathogens have become an important public threat to human health. There are many kinds of pathogenic bacteria in food consumed daily. A rapid and sensitive testing method for multiple food-borne pathogens is essential. Europium nanoparticles (EuNPs) are used as fluorescent probes in lateral flow immunoassays (LFIAs) to improve sensitivity. Here, recombinase polymerase amplification (RPA) combined with fluorescent LFIA was established for the simultaneous and quantitative detection of Listeria monocytogenes, Vibrio parahaemolyticus, and Escherichia coliO157:H7. In this work, the entire experimental process could be completed in 20 min at 37 °C. The limits of detection (LODs) of EuNP-based LFIA–RPA were 9.0 colony-forming units (CFU)/mL for Listeria monocytogenes, 7.0 CFU/mL for Vibrio parahaemolyticus, and 4.0 CFU/mL for Escherichia coliO157:H7. No cross-reaction could be observed in 22 bacterial strains. The fluorescent LFIA–RPA assay exhibits high sensitivity and good specificity. Moreover, the average recovery of the three food-borne pathogens spiked in food samples was 90.9–114.2%. The experiments indicate the accuracy and reliability of the multiple fluorescent test strips. Our developed EuNP-based LFIA–RPA assay is a promising analytical tool for the rapid and simultaneous detection of multiple low concentrations of food-borne pathogens.

One-step duplex RT-droplet digital PCR assay for the detection of norovirus GI and GII in lettuce and strawberry

The study was designed to develop a sensitive one-step duplex reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) to detect norovirus genogroup I and II (NoV GI and GII) in lettuce and strawberry. The specificity, sensitivity, repeatability and robustness of the assay was compared with RT-qPCR. The lowest concentration detected by RT-ddPCR for NoV GI and NoV GII were 4.68 and 8.47 copies/μL respectively, much lower than that of RT-qPCR with a number of 46.8 and 84.7 copies/μL, respectively. Lettuce and strawberry samples were artificially contaminated with NoV GI and GII suspensions, with inoculum size of 3.00 × 106 to 1.70 × 108 copies and 4.80 × 105 to 2.50 × 107 copies, respectively. Strawberry spiked with low inoculum size revealed positive results by RT-ddPCR, while recorded negative by RT-qPCR. Meanwhile, RT-ddPCR also showed a higher average recovery rate for NoV in lettuce and strawberry than RT-qPCR.The limit of detection (LoDs) of RT-ddPCR for NoVs in lettuce was 2.32 × 104 copies/25g (NoV GI) and 2.36 × 104 ciopies/25g (NoV GII), and that in strawberry was 2.56 × 104 copies/25g (NoV GI) and 2.64 × 104 ciopies/25g (NoV GII), which were 10 folds lower than that of RT-qPCR. The developed duplex RT-ddPCR assay exhibited stability and increased capacity to resist inhibitors in food samples with low concentration of NoV, making it a reliable method to avoid false negative result as opposed to RT-qPCR. In conclusion, one-step RT-ddPCR method developed in this study is pertinent in detecting foodborne virus such as NoV.

Foodborne transmission of hepatitis A and hepatitis E viruses: A literature review

Foodborne viruses have been recognized as a growing concern to the food industry and a serious public health problem. Hepatitis A virus (HAV) is responsible for the majority of viral outbreaks of food origin worldwide, while hepatitis E virus (HEV) has also been gaining prominence as a foodborne viral agent in the last years, due to its zoonotic transmission through the consumption of uncooked or undercooked infected meat or derivatives. However, there is a lack of scientific reports that gather all the updated information about HAV and HEV as foodborne viruses. A search of all scientific articles about HAV and HEV in food until March 2020 was carried out, using the keywords "HAV", "HEV", "foodborne", "outbreak" and "detection in food". Foodborne outbreaks due to HAV have been reported since 1956, mainly in the USA, and in Europe in recent years, where the number of outbreaks has been increasing throughout time, and nowadays it has become the continent with the highest foodborne HAV outbreak report. Investigation and detection of HAV in food is more recent, and the first detections were performed in the 1990s decade, most of them carried out on seafood, first, and frozen food, later. On the other hand, HEV has been mainly looked for and detected in food derived from reservoir animals, such as meat, sausages and pate of pigs and wild boars. For this virus, only isolated cases and small outbreaks of foodborne transmission have been recorded, most of them in industrialized countries, due to HEV genotype 3 or 4. Virus detection in food matrices requires special processing of the food matrix, followed by RNA detection by molecular techniques. For HAV, a real-time PCR has been agreed as the standard method for virus detection in food; in the case of HEV, a consensus assay for its detection in food has not been reached yet. Our investigation shows that there is still little data about HAV and HEV prevalence and frequency of contamination in food, prevalent viral strains, and sources of contamination, mainly in developing countries, where there is no research and legislation in this regard. Studies on these issues are needed to get a better understanding of foodborne viruses, their maintenance and their potential to cause diseases.

Microfluidic devices for detection of RNA viruses

There is a long way to go before the coronavirus disease 2019 (Covid-19) outbreak comes under control. qRT-PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Covid-19, but it is expensive, time-consuming, and not as sensitive as it should be. Finding a rapid, easy-to-use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT-PCR, RT-LAMP, nested-PCR, nucleic acid hybridization, ELISA, fluorescence-Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol-gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy-to-use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS-CoV-2.

Detection of norovirus, hepatitis A and hepatitis E viruses in multicomponent foodstuffs

Among the enteric viruses implicated in foodborne outbreaks, the human norovirus and hepatitis viruses A and E (HAV and HEV) represent a serious public health concern. International standard ISO 15216 proposes methods for detecting HAV and norovirus (genogroups I and II) RNA from soft fruit, leaf, stem and bulb vegetables, bottled water or food surfaces. These methods had not previously been validated for detecting the targeted viruses in other foodstuffs such as multicomponent foods, nor for detecting other viruses in foodstuffs. The aim of this study was to characterise a method derived from the vegetable method described in ISO 15216 to detect HAV, HEV and norovirus in artificially-contaminated multicomponent foodstuffs according to the recent international standard ISO 16140-4. Results showed that the mean recovery rates for all settings did not differ according to the operator. The mean extraction yields ranged from 0.35% to 40.44% for HAV, 5.19% to 100% for HEV, 0.10% to 40.61% for norovirus GI and 0.88% to 69.16% for norovirus GII. The LOD₉₅ was 10² genome copies/g for HAV, HEV and norovirus GII and 10³ genome copies/g for norovirus GI. The LOQ was 2.90 × 10⁴, 1.40 × 10³, 1.60 × 10⁴ and 1.30 × 10⁴ genome copies/g for HAV, HEV, norovirus GI and norovirus GII respectively. The MNV-1 process control was detected in 120 out of 128 RNA extracts analysed and was recovered with an efficiency of between 3.83% and 50.22%. The mean inhibition rates of quantitative real-time RT-PCR reaction ranged from 3.25% to 28.70% and varied significantly with the type of food matrix. The described method could be used to detect viruses in composite food products for routine diagnosis needs.

Application of an Optimized Direct Lysis Method for Viral RNA Extraction Linking Contaminated Dates to Infection With Hepatitis A Virus

Consumption of dates has not been considered a common risk of hepatitis A virus (HAV) infection. In January 2018, an outbreak of hepatitis was identified with cases resident in all regions of Denmark. All the detected strains belonged to HAV genotype 3A. Epidemiological investigations through patients’ interviews, case-control and trace-back studies pointed toward different batches of dates from a single producer as the vehicle of infection. Boxes of dates from suspected batches were collected from homes of patients and healthy families and analyzed using a recently reported optimized direct lysis method, consisting of simultaneous viral RNA elution and extraction from dates followed by purification of the nucleic acids. Extracts were analyzed for HAV and norovirus (NoV) RNA using RT-qPCR, while detected HAV were genotyped by Sanger sequencing. Among 20 nucleic acid extracts representing eight batches of dates, RNA of HAV (9.3 × 10² genome copies/g) and NoV genogroup (G)II (trace amounts) were detected in one batch, while NoV GII RNA (trace amounts) was detected in another. Average extraction efficiency of spiked process control murine norovirus was 20 ± 13% and the inhibitions of RT-qPCR detection of NoV GI, NoV GII, and HAV were 31 ± 34, 9 ± 9, and 3 ± 7%, respectively. The HAV genome detected in the dates matched by sequence 100% to the HAV genotype 3A detected in stool samples from cases implicated in the outbreak. This confirmed, to our knowledge, for the first time a sequence link between HAV infection and consumption of contaminated dates, suggesting dates to be an important vehicle of HAV transmission.

Evaluation of three different filters and two methods for recovering viruses from drinking water

Among the enteric viruses implicated in waterborne outbreaks, human norovirus and hepatitis A virus (HAV) are a serious public health issue. Most foodborne viruses are difficult or currently unlikely to cultivate. Because of the lack of a cell culture method, real-time reverse transcriptase PCR is commonly used for the detection of norovirus in foodstuffs and environmental samples. Due to low infectious doses in humans and low virus concentration in water sample, filter adsorption methods were used for concentrating viruses from water. The ISO (Anonymous, ISO 15216-1, 2017) describes standardized molecular methods for detecting HAV and norovirus in bottled water. This method includes a two-step procedure: concentrating the virus using a microporous electropositive filter (47 mm diameter, 0.45 μm pore size) then molecular detection. The Zetapor filter, which had a charged membrane with a pore size of 0.45 μm, was commonly used in the past to concentrate viruses from water or from salad leaves following virus elution. But, unfortunately, the Zetapor filter is no longer marketed and it is therefore necessary to assess an alternative filter. The aim of this study was to compare the ability of two electropositive filters with a pore size of 0.45 μm or 0.22 μm and one uncharged filter (0.45 μm) to recover norovirus and HAV from two different types of drinking water (bottled water and tap water) with the adsorption-elution method proposed by ISO (Anonymous, ISO 15216-1, 2017) (method A) and with direct viral extraction using filters (method B). The mean extraction yields for norovirus and HAV calculated with RNA extracts ranged from 0.2 % - 4.81 % with method A and from 5.05 % - 53.58 % with method B, and did not differ significantly between the two types of drinking water tested. For method B, the mean extraction yields for HAV and norovirus were evaluated according to results from the three filters used. The recovery rate of HAV and norovirus ranged between 3.47 % and 62.41 % with the 0.45 μm electropositive filter and were higher than the other filters. The 0.45 μm electropositive filter could be used to concentrate viruses for routine viral monitoring of drinking water for researchers who want to adopt the method in their lab routine.

Development of a Digital RT-PCR Method for Absolute Quantification of Bluetongue Virus in Field Samples

Bluetongue (BT) is a major Office International des Epizooties (OIE)-listed disease of wild and domestic ruminants caused by several serotypes of Bluetongue virus (BTV), a virus with a segmented dsRNA genome belonging to the family Reoviridae, genus Orbivirus. BTV is transmitted through the bites of Culicoides midges. The aim of this study was to develop a new method for quantification of BTV Seg-10 by droplet digital RT-PCR (RTdd-PCR), using nucleic acids purified from complex matrices such as blood, tissues, and midges, that notoriously contain strong PCR inhibitors. First, RTdd-PCR was optimized by using RNAs purified from serially 10-fold dilutions of a BTV-1 isolate (10^5.43TCID₅₀/ml up to 10^−0.57 TCID₅₀/ml) and from the same dilutions spiked into fresh ovine EDTA-blood and spleen homogenate. The method showed a good degree of linearity (R² ≥ 0.995). The limit of detection (LoD) and the limit of quantification (LoQ) established were 10^−0.67TCID₅₀/ml (0.72 copies/μl) and 10^0.03TCID₅₀/ml (3.05 copies/μl) of BTV-1, respectively. Second, the newly developed test was compared, using the same set of biological samples, to the quantitative RT-PCR (RT-qPCR) detecting Seg-10 assay widely used for the molecular diagnosis of BTV from field samples. Results showed a difference mean of 0.30 log between the two assays with these samples (p < 0.05). Anyway, the analysis of correlation demonstrated that both assays provided similar measurements with a very close agreement between the systems.

Virological analyses in collective catering outbreaks in France between 2012 and 2017

Enteric viruses cause the majority of foodborne illnesses and common symptoms of many foodborne illnesses include vomiting, diarrhea, abdominal pain, and fever. Among the enteric viruses, human Norovirus (NoV) and hepatitis virus (HAV and HEV) are the main viruses suspected to cause foodborne outbreaks and represent a serious public health. The study presents survey tools of viruses in a wide variety of foodstuffs and results obtained during 56 foodborne outbreaks investigation in France between 2012 and 2017. 246 suspected foods were examined for the presence of four human enteric viruses (NoV GI and NoV GII, HAV or HEV) either using methods described in the EN ISO 15216-1 or in house methods. All viral analysis of food samples were performed with the implementation of process control and an external amplification controls. Eighteen of 56 foodborne outbreaks investigated included at least one positive food sample (16/18 NoV, 1/18 HAV and 1/18 HEV). The genomic levels of four viruses detected ranged from < 10² to 10⁷ genome copies per g or per L. This study showed the interest to develop methods for the extraction of viruses in different foodstuffs to increase the possibility to identify the association between viral illness and food consumption.

Efficiency of PEG secondary concentration and PCR for the simultaneous concentration and quantification of foodborne bacteria, viruses and protozoa

Fresh fruits are a potential source of many different pathogens, including bacteria, enteric viruses and protozoa that may pose serious health risks. The consumption of raspberries has been widely associated with large foodborne outbreaks and because of the low concentration at which most of these pathogens are found, sensitive and accurate detection methods are required. Methods that would allow for an accurate and sensitive simultaneous elution and concentration of the different classes of pathogens would decrease the time for analysis, the costs associated and the expertise necessary. In this study we explored the use of polyethylene glycol (PEG) secondary concentration to simultaneously concentrate bacteria, enteric viruses and protozoa from raspberries. PEG secondary concentration showed good recovery rates for all the organisms tested. This work indicates that PEG secondary concentration followed by quantitative (Reverse Transcription) Polymerase Chain Reaction (q(RT)PCR) may be a relevant alternative to standardized methods for the simultaneous concentration of bacteria, enteric viruses and protozoa.

Evaluation of Bead-Based Assays for the Isolation of Foodborne Viruses from Low-Moisture Foods

ABSTRACT

Foodborne viruses such as norovirus and hepatitis A virus (HAV) are highly transmissible, persistent in the environment, and resistant to many conventional inactivation methods. Foods can become contaminated with these viruses either at the source of harvest or during food handling and processing. Multiple lines of evidence suggest that foodborne viruses can survive desiccation and dry conditions. Several foodborne virus outbreaks have been linked to low-moisture foods (LMFs), indicating that these foods can be vehicles of virus transmission. However, the efficiencies of common virus extraction methodologies have not been examined with LMFs. We adapted the International Organization for Standardization (ISO) 15216-1:2017 method for virus recovery for use with chocolate, pistachios, and cornflakes. We also developed a magnetic bead assay for the recovery of HAV from LMFs and used the porcine gastric mucin-coated magnetic beads (PGM-MBs) to extract norovirus surrogates, feline calicivirus (FCV), and murine norovirus (MNV) from the same LMFs. The efficiency of virus recovery using the bead-based assay was then compared with that of the ISO 15216-1:2017 method. In chocolate and pistachios, the recovery rates with the PGM-MB method were 5.6- and 21.3-fold higher, respectively, for FCV and 1.65- and 18-fold higher, respectively, for MNV than those with the ISO 15216-1:2017 method. However, the PGM-MB method failed to recover MNV and FCV from cornflakes. The recovery rates for HAV in chocolate, pistachios, and corn flakes with the magnetic bead method were 11.5-, 3-, and 5.6-fold higher, respectively, than those with the ISO 15216-1:2017 method. Thus, depending upon the food matrix and the target virus, the bead-based assays can be used to efficiently and rapidly extract viruses from LMFs.

HIGHLIGHTS

Critical issues in application of molecular methods to environmental virology

Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.

Development of a novel digital RT-PCR method for detection of human sapovirus in different matrices

A new nanofluidic digital RT-PCR method was developed for sapovirus (SaV) using control material obtained according to standards for enteric viruses. Primers employed amplify a fragment of 112 bp of the polymerase capsid junction, allowing the detection of human genogroups I, II and IV. Analytical validation was performed in clinical, shellfish and environmental water samples. This novel protocol rendered great effectiveness and repetitiveness, as well as higher sensitivity than real time RT-PCR assay, with differences in quantification ranging from 0.1 to 2.6 log-units. The method described here can constitute a promising tool for standardizing SaV quantification.

Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR

Virus-contaminated frozen berries have been frequently identified as cause of foodborne disease outbreaks. To provide new tools for virus detection and characterization in berries, next generation sequencing (NGS) and reverse transcription-digital PCR (RT-dPCR) techniques were tested here with strawberries previously involved in a large-scale norovirus (NoV) gastroenteritis outbreak in Germany. By NGS, about 29 million sequence reads were generated, which mainly showed identities to sequences from the plant matrix and from the bacterial flora. Most abundant virus sequences originated from plant-specific viruses, whereas sequences with high identity to human viruses were rare. Only two sequence reads showed homologies to human NoV. They were identical to GII.P16/GII.13 NoV sequences from patients and a strawberry sample independently analyzed during the outbreak. Quantification of the GII NoV RNA of the berries using RT-dPCR confirmed a low mean virus amount of 185 copies/25 g, which is similar to independently assessed RT-qPCR results (257 copies/25 g). The study shows that identification of human-pathogenic viruses in naturally contaminated frozen berries is possible using NGS technologies. However, the method needs to be further optimized in order to enable convenient and reproducible detection of a low amount of human-pathogenic virus sequences in a background of highly abundant nucleic acids of other sources.

Rapid Detection of Human Norovirus in Frozen Raspberries

Raspberries have lately caused several human norovirus (HuNoV) outbreaks in Europe. In this study, we developed and evaluated for HuNoV reverse transcription (RT)-PCR detection in frozen raspberries extraction methods that have equal sensitivity but are less time-consuming than widely used methods based on polyethylene glycol (PEG) precipitation and chloroform-butanol purification. One method was applied to stored frozen raspberries linked to previous HuNoV outbreaks and berries on sale. In the virus elution-based Method 1, sparkling water eluted viruses most efficiently from the berries. Method 2, based on direct nucleic acid extraction with minor PEG supplement, yielded the highest number of positive findings (4 out of 9) at low virus concentration level of 100 genome copies HuNoV genogroup II per 25 g raspberries. Both methods showed approximately equal sensitivity to a method including PEG precipitation and chloroform-butanol purification. Two naturally contaminated berry samples linked to HuNoV outbreaks in 2006 and 2009 were still positive for HuNoV genogroup I, but all berry products purchased from a local store remained negative for HuNoV. In conclusion, this study presents two efficient and rapid methods which can be used in urgent HuNoV outbreak investigations, since the results of the virus analysis are available in a few hours.

Foodborne Norovirus State of Affairs in the EU Rapid Alert System for Food and Feed

The European Union Rapid Alert System for Food and Feed (EU RASFF) database is an invaluable instrument for analyzing notifications involving norovirus in food. The aim of this work was to carry out a thorough research of the alert and border rejection notifications submitted in the RASFF database from its onset until 31 August 2017. Some conclusions of interest were: (i) Denmark, France, Italy, the Netherlands and Norway have contributed the majority of alert notifications as notifying countries, (ii) France and Serbia have been cited more often in alert notifications as countries of origin, (iii) Italy and Spain have submitted the majority of border rejection notifications, (iv) Third Countries implicated more frequently in border rejection notifications for norovirus in bivalve molluscs were Vietnam and Tunisia, whereas in fruits and vegetables were China and Serbia, (v) "risk dispersion" from norovirus-contaminated food was narrow since, in just over half of all alert notifications and all of the border rejection notifications, only up to three countries were involved, and (vi) both raw (oysters and berries) and cooked (mussels) food products can present a health risk to consumers. The information retrieved from the RASFF database on norovirus-contaminated food could prove helpful in the planning of future norovirus risk analysis endeavors.

Binary Nanoparticle Graphene Hybrid Structure-Based Highly Sensitive Biosensing Platform for Norovirus-Like Particle Detection

Nanoparticle (NP)-decorated carbon nanotubes or graphenes (GRPs) have attracted attention because of their synergic properties such as enhanced electrical conductivity, magneto-optical effect, and plasmon resonance energy transfer. These hybrid carbon nanomaterials are widely used in sensing platforms to monitor target biomolecules, gases, and chemicals. In this study, binary nanoparticles, specifically gold (Au)/magnetic nanoparticle (MNP)-decorated graphenes (GRPs), were applied in a virus-sensing platform. This hybrid material exhibited multiple functionalities, including magnetic, plasmonic, and enhanced electrical properties. The Au/MNP-GRPs were synthesized in two steps at room temperature under mild conditions and magnetically deposited on a Pt-interdigitated electrode as electrical-sensing channels. After deposition onto the electrode, the surface of Au/MNP-GRPs was conjugated with norovirus antibody to produce a norovirus-like particle (NoV-LP)-sensing platform. NoV-LPs were successfully detected by the hybrid nanomaterial-sensing platform, exhibiting high sensitivity and specificity in a concentration range from 0.01 pg to 1 ng. In this case, the limit of detection was calculated as 1.16 pg/mL. Thus, the binary nanoparticle-decorated graphene shows excellent potential as an electrical-sensing platform for biomolecules.

Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment

The accurate detection of pathogens in environmental matrices, such as sediment, is critical in understanding pathogen fate and behavior in the environment. In this study, we assessed the usefulness of methods for the detection and quantification of Vibrio spp. and norovirus (NoV) nucleic acids in sediment. For bacteria, a commonly used direct method using hexadecyltrimethylammonium bromide (CTAB) and phenol-chloroform-isoamyl alcohol (PCI) extraction was optimized, whereas for NoV, direct and indirect (virus elution-concentration) methods were evaluated. For quantification, commercially available quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR) kits were tested alongside a digital PCR (dPCR) approach. CTAB-based extraction combined with 16 h polyethylene glycol 6000 (PEG6000) precipitation was found to be suitable for the direct extraction of high abundance bacterial and viral nucleic acids. For the indirect extraction of viral RNA, beef extract-based elution followed by PEG6000 precipitation and extraction using the NucliSENS® MiniMag® Nucleic Acid Purification System and the PowerViral® Environmental RNA/DNA Isolation Kit and qRT-PCR resulted in 83-112 and 63-69% recoveries of NoV, respectively. dPCR resulted in lower viral recoveries (47 and 9%) and ~4 orders of magnitude lower Vibrio concentrations (3.6-4.6 log10 gc/100 g sediment) than was observed using qPCR. The use of internal controls during viral quantification revealed that the RT step was more affected by inhibitors than the amplification. The methods described here are suitable for the enumeration of viral and/or bacterial pathogens in sediment, however the use of internal controls to assess efficiency is recommended.