Multiplex real-time RT-PCR for simultaneous detection of GI/GII noroviruses and murine norovirus 1

Development and validation of a duplex RT-qPCR assay for norovirus quantification in wastewater samples

Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.

A multiplex TaqMan real-time RT-PCR assay for the simultaneous detection of H4, H6, and H10 avian influenza viruses

Avian influenza viruses (AIVs) have caused a large number of epidemics in domestic and wild birds, and even posed a health challenge to humans. Highly pathogenic AIVs have attracted the most public attention. However, low pathogenic AIVs, including H4, H6, and H10 subtype AIVs, have spread covertly in domestic poultry, without obvious clinical signs. The emergence of human infections with H6 and H10 AIVs and the evidence of seropositivity of H4 AIV in poultry-exposed individuals indicated that these AIVs sporadically infect humans and could cause a potential pandemic. Therefore, a rapid and sensitive diagnostic method to simultaneously detect Eurasian lineage H4, H6, and H10 subtype AIVs is urgently required. Four singleplex real-time RT-PCR (RRT-PCR) assays were established based on carefully designed primers and probes of the conserved regions of the matrix, H4, H6, and H10 genes and combined into a multiplex RRT-PCR method to simultaneously detect H4, H6, and H10 AIVs in one reaction. The detection limit of the multiplex RRT-PCR method was 1-10 copies per reaction when detecting standard plasmids, and showed no cross-reaction against other subtype AIVs and other common avian viruses. Additionally, this method was suitable to detect the AIVs in samples from different sources, the results of which showed high consistency with virus isolation and a commercial influenza detection kit. In summary, this rapid, convenient, and practical multiplex RRT-PCR method could be applied in laboratory testing and clinical screening to detect AIVs.

The Role of Histo-Blood Group Antigens and Microbiota in Human Norovirus Replication in Zebrafish Larvae

Human norovirus (HuNoV) is the major agent for viral gastroenteritis, causing >700 million infections yearly. Fucose-containing carbohydrates named histo-blood group antigens (HBGAs) are known (co)receptors for HuNoV. Moreover, bacteria of the gut microbiota expressing HBGA-like structures have shown an enhancing effect on HuNoV replication in an in vitro model. Here, we studied the role of HBGAs and the host microbiota during HuNoV infection in zebrafish larvae. Using whole-mount immunohistochemistry, we visualized the fucose expression in the zebrafish gut for the HBGA Lewis X [Le^X, α(1,3)-fucose] and core fucose [α(1,6)-fucose]. Costaining of HuNoV-infected larvae proved colocalization of Le^X and to a lower extent core fucose with the viral capsid protein VP1, indicating the presence of fucose residues on infected cells. Upon blocking of fucose expression by a fluorinated fucose analogue, HuNoV replication was strongly reduced. Furthermore, by comparing HuNoV replication in conventional and germfree zebrafish larvae, we found that the natural zebrafish microbiome does not have an effect on HuNoV replication, contrary to earlier reports about the human gut microbiome. Interestingly, monoassociation with the HBGA-expressing Enterobacter cloacae resulted in a minor decrease in HuNoV replication, which was not triggered by a stronger innate immune response. Overall, we show here that fucose has an essential role for HuNoV infection in zebrafish larvae, as in the human host, but their natural gut microbiome does not affect viral replication. IMPORTANCE Despite causing over 700 million infections yearly, many gaps remain in the knowledge of human norovirus (HuNoV) biology due to an historical lack of efficient cultivation systems. Fucose-containing carbohydrate structures, named histo-blood group antigens, are known to be important (co)receptors for viral entry in humans, while the natural gut microbiota is suggested to enhance viral replication. This study shows a conserved mechanism of entry for HuNoV in the novel zebrafish infection model, highlighting the pivotal opportunity this model represents to study entry mechanisms and identify the cellular receptor of HuNoV. Our results shed light on the interaction of HuNoV with the zebrafish microbiota, contributing to the understanding of the interplay between gut microbiota and enteric viruses. The ease of generating germfree animals that can be colonized with human gut bacteria is an additional advantage of using zebrafish larvae in virology. This small animal model constitutes an innovative alternative to high-severity animal models.

The Identification and Genetic Characterization of Parechovirus Infection Among Pediatric Patients With Wide Clinical Spectrum in Chongqing, China

Human parechoviruses (HPeVs) are important causes of infection in children. However, without a comprehensive and persistent surveillance, the epidemiology and clinical features of HPeV infection remain ambiguous. We performed a hospital-based surveillance study among three groups of pediatric patients with acute respiratory infection (Group 1), acute diarrhea (Group 2), and hand, foot and mouth disease (Group 3) in Chongqing, China, from 2009 to 2015. Among 10,212 tested patients, 707 (6.92%) were positive for HPeV, with the positive rates differing significantly among three groups (Group 1, 3.43%; Group 2, 14.94%; Group 3, 3.55%; P < 0.001). The co-infection with other pathogens was detected in 75.2% (531/707) of HPeV-positive patients. Significant negative interaction between HPeV and Parainfluenza virus (PIV) (P = 0.046, OR = 0.59, 95% CI = 0.34–0.98) and positive interactions between HPeV and Enterovirus (EV) (P = 0.015, OR = 2.28, 95% CI = 1.23–4.73) were identified. Among 707 HPeV-positive patients, 592 (83.73%) were successfully sequenced, and 10 genotypes were identified, with HPeV1 (n = 396), HPeV4 (n = 86), and HPeV3 (n = 46) as the most frequently seen. The proportion of genotypes differed among three groups (P < 0.001), with HPeV1 and HPeV4 overrepresented in Group 2 and HPeV6 overrepresented in Group 3. The spatial patterns of HPeV genotypes disclosed more close clustering of the currently sequenced strains than those from other countries/regions, although they were indeed mixed. Three main genotypes (HPeV1, HPeV3, and HPeV4) had shown distinct seasonal peaks, highlighting a bi-annual cycle of all HpeV and two genotypes (HPeV 1 and HPeV 4) with peaks in odd-numbered years and with peaks in even-numbered years HPeV3. Significantly higher HPeV1 viral loads were associated with severe diarrhea in Group 2 (P = 0.044), while associated with HPeV single infection than HPeV-EV coinfection among HFMD patients (P = 0.001). It’s concluded that HPeV infection was correlated with wide clinical spectrum in pediatric patients with a high variety of genotypes determined. Still no clinical significance can be confirmed, which warranted more molecular surveillance in the future.

Infection of zebrafish larvae with human norovirus and evaluation of the in vivo efficacy of small-molecule inhibitors

We have recently established that human norovirus (HuNoV) replicates efficiently in zebrafish larvae after inoculation of a clinical sample into the yolk, providing a simple and robust in vivo system in which to study HuNoV. In this Protocol Extension, we present a detailed description of virus inoculation by microinjection, subsequent daily monitoring and harvesting of larvae, followed by viral RNA quantification. This protocol can be used to study viral replication of genogroup (G)I and GII HuNoVs in vivo within 3-4 d. Additionally, we describe how to evaluate the in vivo antiviral effect and toxicity of small molecules using HuNoV-infected zebrafish larvae, in multi-well plates and without the need for specific formulations. This constitutes a great advantage for drug discovery efforts, as no specific antivirals or vaccines currently exist to treat or prevent norovirus gastroenteritis.

Evaluation of Copper Alloy Surfaces for Inactivation of Tulane Virus and Human Noroviruses

ABSTRACT

This study evaluated the efficacy of copper alloy surfaces for inactivation of Tulane virus (TV), assessed by plaque assay and porcine gastric mucin-conjugated magnetic bead (PGM-MB) binding assay, followed by quantitative reverse transcription PCR (PGM-MB-RT-qPCR assay). In addition, the efficacy of a copper surface for inactivation of human norovirus (HuNoV) GII.4 Sydney and GI.3B Potsdam strains was evaluated by PGM-MB-RT-qPCR assay. Results of time-dependent inactivation of viruses on copper, bronze, and brass coupons revealed that 15 min of surface treatments of each of the copper and copper alloys achieved >4-log reduction of purified TV, as assessed by plaque assay, while up to 20 min of copper alloy surface treatments only achieved ∼2-log reduction, as assessed by PGM-MB-RT-qPCR assay. As assessed by PGM-MB-RT-qPCR assay, 10 min of copper surface treatments achieved reductions of 3 and 4 log units for HuNoVs GII.4 Sydney and GI.3B Potsdam, respectively. Results from this study suggest that even though PGM-MB-RT-qPCR assay underestimated the efficacy of copper alloy surface inactivation of TV, copper alloy surfaces were able to effectively inactivate TV and HuNoVs. Therefore, copper alloys can be used as a preventive measure to prevent HuNoV infection and are an effective surface treatment for HuNoVs.

HIGHLIGHTS

A Survey of Analytical Techniques for Noroviruses

As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses.

Two rapid and sensitive methods based on TaqMan qPCR and droplet digital PCR assay for quantitative detection of Bacillus subtilis in rhizosphere

AIMS

Bacillus subtilis, a typical plant growth-promoting rhizobacteria, can benefit plant through promoting growth and reducing disease. The colonization intensity of B. subtilis in rhizosphere is a key factor for improving their effectiveness of field application. In this study, we developed a rapid and sensitive method for detecting B. subtilis in rhizosphere via TaqMan qPCR and droplet digital PCR (ddPCR) methods.

METHODS AND RESULTS

The primers/probe set targeting gyrB gene could successfully distinguish B. subtilis from its close-related species. Both the TaqMan qPCR and ddPCR methods exhibited a good linear relationship in the sensitivity assay, suggesting the developed method was specific, effective and reliable. Finally, the two methods were used to detect the colonization dynamic of B. subtilis within Arabidopsis rhizosphere. Both of them showed a consistent trend compared with the traditional cultivation-based and microscopy-based methods.

CONCLUSIONS

The TaqMan qPCR and droplet digital PCR (ddPCR) methods we developed could be used to rapidly detect B. subtilis in rhizosphere.

SIGNIFICANCE AND IMPACT OF THE STUDY

The TaqMan qPCR and ddPCR methods developed in this study can be applied to rapid quantitative detection of B. subtilis populations, and will be helpful to evaluate their effectiveness of field application.

A robust human norovirus replication model in zebrafish larvae

Human noroviruses (HuNoVs) are the most common cause of foodborne illness, with a societal cost of $60 billion and 219,000 deaths/year. The lack of robust small animal models has significantly hindered the understanding of norovirus biology and the development of effective therapeutics. Here we report that HuNoV GI and GII replicate to high titers in zebrafish (Danio rerio) larvae; replication peaks at day 2 post infection and is detectable for at least 6 days. The virus (HuNoV GII.4) could be passaged from larva to larva two consecutive times. HuNoV is detected in cells of the hematopoietic lineage and the intestine, supporting the notion of a dual tropism. Antiviral treatment reduces HuNoV replication by >2 log10, showing that this model is suited for antiviral studies. Zebrafish larvae constitute a simple and robust replication model that will largely facilitate studies of HuNoV biology and the development of antiviral strategies.

A review on recent progress in the detection methods and prevalence of human enteric viruses in water

Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.

Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA

Human astroviruses are a major cause of pediatric gastroenteritis, especially in immunocompromised children. We conducted a retrospective study to demonstrate that diverse astrovirus genotypes can co-circulate in pediatric oncology patients. A subset of cases is associated with long-term virus shedding (range 17–183 days).

Evaluation of Chlorine Treatment Levels for Inactivation of Human Norovirus and MS2 Bacteriophage during Sewage Treatment

This study examined the inactivation of human norovirus (HuNoV) GI.1 and GII.4 by chlorine under conditions mimicking sewage treatment. Using a porcine gastric mucin-magnetic bead (PGM-MB) assay, no statistically significant loss in HuNoV binding (inactivation) was observed for secondary effluent treatments of ≤25 ppm total chlorine; for both strains, 50 and 100 ppm treatments resulted in ≤0.8-log₁₀ unit and ≥3.9-log₁₀ unit reductions, respectively. Treatments of 10, 25, 50, and 100 ppm chlorine inactivated 0.31, 1.35, >5, and >5 log₁₀ units, respectively, of the norovirus indicator MS2 bacteriophage. Evaluation of treatment time indicated that the vast majority of MS2 and HuNoV inactivation occurred in the first 5 min for 0.2-μm-filtered, prechlorinated secondary effluent. Free chlorine measurements of secondary effluent seeded with MS2 and HuNoV demonstrated substantial oxidative burdens. With 25, 50, and 100 ppm treatments, free chlorine levels after 5 min of exposure ranged from 0.21 to 0.58 ppm, from 0.28 to 16.7 ppm, and from 11.6 to 53 ppm, respectively. At chlorine treatment levels of >50 ppm, statistically significant differences were observed between reductions for PGM-MB-bound HuNoV (potentially infectious) particles and those for unbound (noninfectious) HuNoV particles or total norovirus particles. While results suggested that MS2 and HuNoV (measured as PGM-MB binding) behave similarly, although not identically, both have limited susceptibility to chlorine treatments of ≤25 ppm total chlorine. Since sewage treatment is performed at ≤25 ppm total chlorine, targeting free chlorine levels of 0.5 to 1.0 ppm, these results suggest that traditional chlorine-based sewage treatment does not inactivate HuNoV efficiently.IMPORTANCE HuNoV is ubiquitous in sewage. A receptor binding assay was used to assess inactivation of HuNoV by chlorine-based sewage treatment, given that the virus cannot be routinely propagated in vitro Results reported here indicate that chlorine treatment of sewage is not effective for inactivating HuNoV unless chlorine levels are above those routinely used for sewage treatment.

Evaluation of Assays to Quantify Infectious Human Norovirus for Heat and High-Pressure Inactivation Studies Using Tulane Virus

We compared the heat and high hydrostatic pressure (HHP) inactivation results of Tulane virus (TV), a human norovirus (HuNoV) surrogate, obtained by plaque assay, direct quantitative reverse transcription PCR (RT-qPCR), porcine gastric mucin magnetic beads (PGM-MBs) binding assay followed by RT-qPCR (PGM/PCR), and propidium monoazide (PMA) assay followed by RT-qPCR (PMA/PCR). Heat and HHP inactivation of a HuNoV genotype I.1 (GI.1) strain and a genotype II.4 (GII.4) strain was also evaluated using those molecular assays. Viruses were heat treated at 50-90 °C for 2 min and HHP treated at 100-550 MPa at initial temperatures of 4 or 21 °C for 2 min. For heat treatment, the three molecular methods significantly underestimated the inactivation of TV. It could be logically concluded that the PGM/PCR assay was better than the PMA/PCR and direct RT-qPCR assays in estimating the inactivation of HuNoV GI.1. The three molecular methods were comparable in estimating the heat inactivation of GII.4. For HHP treatment, both PGM/PCR and PMA/PCR assays were able to estimate inactivation of TV at ≤~2-log reduction levels, but significantly underestimated its inactivation at >~2-log reduction levels. The direct RT-qPCR assay was the worst method for estimating HHP inactivation of TV. It could be logically concluded that the PGM/PCR and PMA/PCR assays were comparable in estimating the HHP inactivation of GI.1 and both were significantly better than the direct RT-qPCR assay. Among the three molecular methods, the PGM/PCR assay was the best in estimating the HHP inactivation of GII.4. These results demonstrated that the PGM/PCR assay was probably the method of choice in estimating the inactivation of HuNoV GI.1 and GII.4 for heat and HHP treatments, but this method would likely result in underestimation of HuNoV inactivation.

Prevalence of Rotavirus Genogroup A and Norovirus Genogroup II in Bassaseachic Falls National Park Surface Waters in Chihuahua, Mexico

In areas lacking potable water treatment, drinking contaminated water may represent a public health threat. In addition to enteropathogenic bacteria and parasites, fecal contamination in water environments is associated with the transmission of enteric viruses and other causal agents of infectious disease. Rotavirus and norovirus are the main enteric viral agents responsible for diarrheic outbreaks. The aim of the present study was to detect seasonal variation of rotavirus and norovirus in the surface water at Bassaseachic Falls National Park during 2013. Rivers and streams within and nearby this park were sampled once in each season during 2013. Viral concentration was carried out by a handmade filtration equipment, using a commercial electropositive membrane coupled with the virus absortion elution technique (VIRADEL©). Detection of rotavirus and norovirus was performed by SYBR Green reverse transcription-real time polymerase chain reaction (SYBR GREEN© RT-qPCR) analyses. Norovirus genogroup II was detected in samples collected in June and October 2013. In the case of rotavirus, genogroup A was detected in March and June. The presence of rotavirus and norovirus was related to viral acute diarrhea in children less than five years of age, who were inhabiting the sampled areas. This may indicates that the contaminated water was potentially a risk factor for regional diarrheic outbreaks.

Modeling human enteric dysbiosis and rotavirus immunity in gnotobiotic pigs

Background

Rotavirus vaccines have poor efficacy in infants from low- and middle-income countries. Gut microbiota is thought to influence the immune response to oral vaccines. Thus, we developed a gnotobiotic (Gn) pig model of enteric dysbiosis to study the effects of human gut microbiota (HGM) on immune responses to rotavirus vaccination, and the effects of rotavirus challenge on the HGM by colonizing Gn pigs with healthy HGM (HHGM) or unhealthy HGM (UHGM). The UHGM was from a Nicaraguan infant with a high enteropathy score (ES) and no seroconversion following administration of oral rotavirus vaccine, while the converse was characteristic of the HHGM. Pigs were vaccinated, a subset was challenged, and immune responses and gut microbiota were evaluated.

Results

Significantly more rotavirus-specific IFN-γ producing T cells were in the ileum, spleen, and blood of HHGM than those in UHGM pigs after three vaccine doses, suggesting HHGM induces stronger cell-mediated immunity than UHGM. There were significant correlations between multiple Operational Taxonomic Units (OTUs) and frequencies of IFN-γ producing T cells at the time of challenge. There were significant positive correlations between Collinsella and CD8+ T cells in blood and ileum, as well as CD4+ T cells in blood, whereas significant negative correlations between Clostridium and Anaerococcus, and ileal CD8+ and CD4+ T cells. Differences in alpha diversity and relative abundances of OTUs were detected between the groups both before and after rotavirus challenge.

Conclusion

Alterations in microbiome diversity and composition along with correlations between certain microbial taxa and T cell responses warrant further investigation into the role of the gut microbiota and certain microbial species on enteric immunity. Our results support the use of HGM transplanted Gn pigs as a model of human dysbiosis during enteric infection, and oral vaccine responses.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0136-y) contains supplementary material, which is available to authorized users.

Arc discharge-mediated disassembly of viral particles in water

In this study, we investigated the inactivation effects on murine norovirus (MNV-1) with/without purification in water using a submerged plasma reactor of arc discharge (underwater arc), which produced a shockwave, UV light, reactive oxygen species and reactive nitrogen species. Underwater arc treatments of 3 and 6 Hz at 12 kV resulted in 2.6- and 4.2-log reductions in the virus titer of non-purified MNV-1 after 1 min of treatment, respectively. The reduction of purified MNV-1 was higher than that of non-purified MNV-1 after underwater arc treatment for all applied conditions (12 or 15 kV and 3 or 6 Hz). One of the viral capsid proteins (VP1) was not detectable after underwater arc treatment, when its integrity was assessed by western blot analysis. Transmission electron microscopy analysis also revealed that MNV-1 particles were completely dissembled by the treatment. This study demonstrates that underwater arc treatment, which was capable of disintegrating the MNV-1 virion structure and the viral capsid protein, can be an effective disinfection process for the inactivation of water-borne noroviruses.

Geographical and temporal variation of E. coli and norovirus in mussels

Bivalve shellfish may accumulate contaminants of public health concern including pathogenic bacteria and viruses. Microbiological monitoring of production areas is based on faecal coliforms in water in the USA and Escherichia coli in bivalve molluscs in the European Union. E. coli is known to reflect contamination with Salmonella enterica but not necessarily with other human pathogens such as enteric viruses. A structured field study was undertaken at three locations in order to investigate the geographical and temporal variability of E. coli and norovirus (NoV). Total norovirus concentration differed significantly by both sampling site and sampling date. A significant correlation was found between total NoV concentration and E. coli concentration by sample, but not with E. coli in seawater. The results have implications for the establishment of sampling plans for NoV in harvesting areas and potentially also for the approach taken to classification based on faecal indicator bacteria.

Comparison of Quantitative PCR and Droplet Digital PCR Multiplex Assays for Two Genera of Bloom-Forming Cyanobacteria, Cylindrospermopsis and Microcystis

The increasing occurrence of harmful cyanobacterial blooms, often linked to deteriorated water quality and adverse public health effects, has become a worldwide concern in recent decades. The use of molecular techniques such as real-time quantitative PCR (qPCR) has become increasingly popular in the detection and monitoring of harmful cyanobacterial species. Multiplex qPCR assays that quantify several toxigenic cyanobacterial species have been established previously; however, there is no molecular assay that detects several bloom-forming species simultaneously. Microcystis and Cylindrospermopsis are the two most commonly found genera and are known to be able to produce microcystin and cylindrospermopsin hepatotoxins. In this study, we designed primers and probes which enable quantification of these genera based on the RNA polymerase C1 gene for Cylindrospermopsis species and the c-phycocyanin beta subunit-like gene for Microcystis species. Duplex assays were developed for two molecular techniques-qPCR and droplet digital PCR (ddPCR). After optimization, both qPCR and ddPCR assays have high linearity and quantitative correlations for standards. Comparisons of the two techniques showed that qPCR has higher sensitivity, a wider linear dynamic range, and shorter analysis time and that it was more cost-effective, making it a suitable method for initial screening. However, the ddPCR approach has lower variability and was able to handle the PCR inhibition and competitive effects found in duplex assays, thus providing more precise and accurate analysis for bloom samples.

Laboratory diagnosis of noroviruses: present and future

Norovirus is an important cause of gastroenteritis outbreaks globally and the most prevalent cause of sporadic gastroenteritis in many regions. Rapid and accurate identification of causative viral agents is critical for outbreak investigation, disease surveillance, and management. Because norovirus is not cultivable and has a highly diversified and variable genome, it is difficult to develop diagnostic assays. Detection methods have evolved from electron microscopy to conventional end-point reverse transcription polymerase chain reaction (RT-PCR), immunoassay, real-time RT-PCR, other molecular technologies, and nanotechnology array-based assays. The status and features of various testing methods are summarized in this review.

Prevalence and genetic characteristics of Saffold cardiovirus in China from 2009 to 2012

The epidemiology and clinical features of the Saffold cardiovirus (SAFV) remain ambiguous. The present study was designed to systematically and intensively investigate the epidemiological features of SAFV in pediatric patients in China. Three cohorts of pediatric patients were recruited from 2009 to 2012. Cohort 1 comprised patients with acute respiratory tract infections. Cohort 2 comprised patients with diarrhea. Cohort 3 comprised hand, foot, and mouth disease (HFMD) patients. A total of 115 patients (1.6%) among 6052 (17/1647, 12/2013, and 86/2392 in cohorts 1, 2, and 3, respectively) were SAFV-positive. The samples from 82 SAFV-positive patients were successfully sequenced, and four genotypes were identified: 8 SAFV-1, 41 SAFV-2, 29 SAFV-3, and 4 SAFV-6. A significantly higher detection rate was found in the HFMD patients than in other two cohorts (both P <0.001). A higher frequency of severe clinical outcome and nervous system manifestation were also observed in the SAFV-positive HFMD patients. Additionally, 6 (3.5%) cerebrospinal fluid and 7 (2.2%) serum samples from the HFMD-associated encephalitis patients were SAFV-positive. Based on the VP1 sequences, all four genotypes displayed distinct geographical clustering. SAFV infection might be associated with a wide clinical spectrum and contribute to HFMD.

Evaluation of the porcine gastric mucin binding assay for high-pressure-inactivation studies using murine norovirus and tulane virus

We compared the results of high-hydrostatic-pressure (HHP) inactivation of murine norovirus type 1 (MNV-1) and Tulane virus (TV) obtained by a porcine gastric mucin binding assay followed by quantitative reverse transcription-PCR (referred to here as the PGM-MB/PCR assay) and a plaque assay and evaluated HHP inactivation of a human norovirus (HuNoV) genogroup I genotype 1 (GI.1) strain and a HuNoV GII.4 strain by using the PGM-MB/PCR assay. Viruses were treated at different pressure levels for 2 min at 4 or 21°C in culture medium of neutral pH and in culture medium of pH 4 at 21°C. The log reductions of infectious MNV-1 and TV particles caused by HHP were assessed using the PGM-MB/PCR and plaque assays, while the log reductions of HuNoVs were assessed by the PGM-MB/PCR assay only. For TV and MNV-1, the two pressure inactivation curves obtained using the plaque and PGM-MB/PCR assays were almost identical at ≤2-log-reduction levels regardless of the treatment temperature and pH. Further increasing the pressure over the 2-log-reduction level resulted in higher log reductions of TV and MNV-1, as assessed by the plaque assay, but did not increase the log reductions, as assessed by the PGM-MB/PCR assay. HHP treatments could achieve maximum reductions of ∼3 and 3.5 log units for GI.1 and GII.4, respectively, as assessed by the PGM-MB/PCR assay. On the basis of these results, it can reasonably be concluded that the PGM-MB/PCR assay would very likely be able to estimate HHP inactivation of HuNoV at ≤2-log-reduction levels. It would also likely conservatively quantify HHP inactivation of the GI.1 strain at 2- to 3-log-reduction levels and the GII.4 strain at 2- to 3.5-log-reduction levels.

Application of long-range and binding reverse transcription-quantitative PCR to indicate the viral integrities of noroviruses

This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60°C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60°C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm(2), no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles.

Batch testing for noroviruses in frozen raspberries

Berries, in particular raspberries, have been associated with multiple recalls due to norovirus contamination and were linked to a number of norovirus (NoV) outbreaks. In the present study a total of 130 samples of frozen raspberries were collected from 26 batches in four different raspberry processing companies. In two companies the samples consisted of bulk frozen raspberries serving as raw material for the production of raspberry puree (an intermediate food product in a business to business setting). In two other companies, the samples consisted of bulk individually quick frozen (IQF) raspberries serving as raw material for the production of frozen fruit mixes (as a final food product for consumer). Enumeration of Escherichia coli and coliforms was performed as well as real-time reverse transcription PCR (RT-qPCR) detection of GI and GII NoV (in 2 × 10 g). In addition, in cases where positive NoV GI or GII RT-qPCR signals were obtained, an attempt to sequence the amplicons was undertaken. Six out of 70 samples taken from the 14 batches of frozen raspberries serving raspberry puree production provided a NoV RT-qPCR signal confirmed by sequencing. Four of these six positive samples clustered in one batch whereas the other two positive samples clustered in another batch from the same company. All six positive samples showed NoV RT-qPCR signals above the limit of quantification of the RT-qPCR assay. These two positive batches of frozen raspberries can be classified as being of insufficient sanitary quality. The mean NoV level in 20 g of these raspberry samples was 4.3 log genomic copies NoV GI/20 g. The concern for public health is uncertain as NoV RT-qPCR detection is unable to discriminate between infectious and non-infectious virus particles. For the IQF raspberries, one batch out of 12 tested NoV positive, but only 1 out of the 5 samples analyzed in this batch showed a positive RT-qPCR GI NoV signal confirmed by sequencing. The RT-qPCR signal was below the limit of quantification of the assay used (<3.7 log genomic copies/20g). It was shown that the applied protocol for sequencing of the amplicon to confirm the specificity of the RT-qPCR signal was successful for GI NoV amplicons but often failed and provided an inconclusive result for GII NoV amplicons.

Detection of noroviruses in shellfish and semiprocessed fishery products from a Belgian seafood company

Shellfish have been implicated in norovirus (NoV) infection outbreaks worldwide. This study presents data obtained from various batches of shellfish and fishery products from a Belgian seafood company over a 6-month period. For the intact shellfish (oysters, mussels, and clams), 21 of 65 samples from 12 of 34 batches were positive for NoVs; 9 samples contained quantitative NoV levels at 3,300 to 14,300 genomic copies per g. For the semiprocessed fishery products (scallops and common sole rolls with scallop fragments), 29 of 36 samples from all eight batches were positive for NoVs; 17 samples contained quantitative NoV levels at 200 to 1,800 copies per g. This convenience study demonstrated the performance and robustness of the reverse transcription quantitative PCR detection and interpretation method and the added value of NoV testing in the framework of periodic control of seafood products bought internationally and distributed by a Belgian seafood processing company to Belgian food markets.

Semi-direct lysis of swabs and evaluation of their efficiencies to recover human noroviruses GI and GII from surfaces

Enteric viruses such as noroviruses (NoVs) continue to be the cause of widespread viral outbreaks due to person-to-person transmission, contaminated food, and contaminated surfaces. In order to optimize swabbing methodology for the detection of viruses on (food) contact surfaces, three swab elution/extraction strategies were compared in part one of this study, out of which, one strategy was based on the recently launched ISO protocol (ISO/TS 15216-1) for the determination of hepatitis A virus and NoV in food using real-time RT-PCR (RT-qPCR). These three swab elution/extraction strategies were tested for the detection of GI.4 and GII.4 NoV on high-density polyethylene (HD-PE) surfaces with the use of cotton swabs. For detection of GI.4 and GII.4, the sample recovery efficiency (SRE) obtained with the direct lysis strategy (based on ISO/TS 15216-1) was significantly lower than the SRE obtained with both other strategies. The semi-direct lysis strategy was chosen to assess the SRE of two common swabs (cotton swab and polyester swab) versus the biowipe (Biomérieux, Lyon, France) on three surfaces (HD-PE, neoprene rubber (NR), and nitrile gloves (GL)). For both surfaces, HD-PE and GL, no significant differences in SREs of GI.4 and GII.4 NoVs were detected between the three different swabs. For the coarser NR, biowipes turned out to be the best option for detecting both GI.4 and GII.4 NoV.

Simultaneous detection of five enteric viruses associated with gastroenteritis by use of a PCR assay: a single real-time multiplex reaction and its clinical application

We developed a highly sensitive reverse transcription and multiplex real-time PCR (rtPCR) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups I and II; sapovirus genogroups I, II, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. In comparison to monoplex rtPCR assays, the sensitivities and specificities of the multiplex rtPCR ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clinical stool specimens.

Standardized multiplex one-step qRT-PCR for hepatitis A virus, norovirus GI and GII quantification in bivalve mollusks and water

A quadruplex Real-Time RT-PCR assay for the simultaneous quantitative detection of hepatitis A virus (HAV), norovirus (NoV) GI and GII, and mengovirus (used as process control for determination of the virus/nucleic acid extraction efficiency) has been developed. This multiplex assay has been comparatively evaluated with the individual monoplex assays and showed to be slightly less sensitive, with average ΔCq values of 0.90, 0.28 and 0.44 for HAV, NoV GI and NoV GII, respectively, in standard curves of viral RNA, or 0.32, 0.37 and 0.51 for the same viruses respectively, in naturally-contaminated samples. These ΔCq values were mostly negligible since it represented, in the worst case scenario, a loss of 0.43 log in genome copy numbers. The quadruplex assay shows similar theoretical detection limits than the monoplex assay for NoV GII, and 10 times higher for HAV and NoV GI. However, when naturally-contaminated food and water samples were tested, these theoretical detection thresholds were often exceeded and very low genome copy numbers (below the limit of detection) could be quantified. The quadruplex assay fulfills the requirements of the method developed by the European Committee on Standardization (CEN) for virus detection in selected foodstuffs with significant advantages in labor and reagent costs.

Environmental detection of genogroup I, II, and IV noroviruses by using a generic real-time reverse transcription-PCR assay

Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups.

The influence of temperature, pH, and water immersion on the high hydrostatic pressure inactivation of GI.1 and GII.4 human noroviruses

Detection of human norovirus (HuNoV) usually relies on molecular biology techniques, such as qRT-PCR. Since histo-blood group antigens (HBGAs) are the functional receptors for HuNoV, HuNoV can bind to porcine gastric mucin (PGM), which contains HBGA-like antigens. In this study, PGM-conjugated magnetic beads were used to collect and quantify potentially infectious HuNoV strains GI.1 and GII.4 treated by high hydrostatic pressure (HHP). Both GI.1 and GII.4 strains used in this study showed increasing pressure sensitivity as judged by loss of PGM binding with decreasing temperature over a range of 1 to 35 °C. Both GI.1 and GII.4 were more resistant to pressure at pH4 than at neutral pH. Because GI.1 was significantly more resistant to pressure than GII.4, it was used to evaluate HuNoV pressure inactivation in blueberries. GI.1 on dry blueberries was very resistant to pressure while immersion of blueberries in water during pressure treatments substantially enhanced the inactivation. For example, a 2 min-600 MPa treatment of dry blueberries at 1 and 21 °C resulted in <1-log reductions while a 2.7-log reduction of GI.1 was achieved by a treatment at 500 MPa for 2 min at 1 °C when blueberries were immersed in water. In total, this novel study provides unique information for designing pressure processing parameters (pressure, temperature, and time) and product formulations (such as pH) to inactivate HuNoV in high-risk foods such as berries.

Norovirus transfer between foods and food contact materials

Human infective noroviruses (NoVs) are a worldwide leading cause of foodborne illness and are frequently spread via infected food handlers preparing and manipulating food products such as deli sandwiches. The objective of the current study was to determine the efficiencies whereby NoV could be transferred between surfaces associated with the preparation of manually prepared foods such as deli sandwiches. Nonfood surfaces included gloves and stainless steel discs, and boiled ham, lettuce, and a sandwich bun were the ingredients of the deli sandwich. Both NoV GII.4 and the murine NoV 1 (MNV-1, a cultivable human NoV surrogate) were included in the presented study. Transfer of NoV GII.4 and MNV-1 between surfaces was performed by pressing an inoculated donor surface against an acceptor surface. To evaluate the effect of subsequent contact, donor surfaces were pressed a second time to an identical acceptor surface. Subsequently, NoV GII.4 and MNV-1 were detected using real-time reverse transcription PCR assays and plaque assays, respectively. Transfer of both viruses from gloves to stainless steel was inefficient, and virus transfer from food products to stainless steel occurred with more variability for NoV GII.4 than for MNV-1. Virus transfer from the stainless steel discs to the gloves was substantially more efficient than from the gloves to the stainless steel. NoV GII.4 and MNV-1 transfer from food products to the gloves occurred with varying efficiencies, although this variation was more evident for NoV GII.4. The MNV-1 inoculum was significantly less efficiently transferred to the acceptor surface at the second contact, which was not the case for NoV GII.4. The obtained transfer efficiency data may provide insights into the transfer of NoV during preparation of foods and can be included in risk assessment models describing the transmission of NoVs in this context.

Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients

BACKGROUND

Noroviruses are a highly transmissible and major cause of nosocomial gastroenteritis resulting in bed and hospital-ward closures. Where hospital outbreaks are suspected, it is important to determine the routes of spread so that appropriate infection-control procedures can be implemented. To investigate a cluster of norovirus cases occurring in children undergoing bone marrow transplant, we undertook norovirus genome sequencing by next-generation methods. Detailed comparison of sequence data from 2 linked cases enabled us to identify the likely direction of spread.

METHODS

Norovirus complementary DNA was amplified by overlapping polymerase chain reaction (PCR) from 13 stool samples from 5 diagnostic real-time PCR-positive patients. The amplicons were sequenced by Roche 454, the genomes assembled by de novo assembly, and the data analyzed phylogenetically.

RESULTS

Phylogenetic analysis indicated that patients were infected by viruses similar to 4 distinct GII.4 subtypes and 2 patients were linked by the same virus. Of the 14 sites at which there were differences between the consensus sequences of the 2 linked viral genomes, 9 had minor variants present within one or the other patient. Further analysis confirmed that minor variants at all 9 sites in patient B w ere present as the consensus sequence in patient A.

CONCLUSIONS

Phylogenetic analysis excluded a common source of infection in this apparent outbreak. Two of 3 patients on the same ward had closely related viruses, raising the possibility of cross-infection despite protective isolation. Analysis of deep sequencing data enabled us to establish the likely direction of nosocomial transmission.

P2 domain profiles and shedding dynamics in prospectively monitored norovirus outbreaks

BACKGROUND

Norovirus P2 domain is commonly used to extrapolate transmission within an outbreak (OB) setting. The current definition is that transmission among cases is considered to be proven when no sequence variation is found.

OBJECTIVES

Previous studies have shown a high mutation rate and errors during replication of the norovirus genome, therefore the validity of this criterion must be evaluated.

STUDY DESIGN

Sequences of the P2 domain were obtained from patients and health care workers sampled during 4 prospectively GII.4 outbreaks. Fecal samples were tested by RT-PCR for presence of norovirus RNA against a standard control preparation to allow quantification. Estimated time of onset of shedding was derived from shedding kinetics modeled on data from sequential sampling. Thereby P2 sequence variation could be linked to estimated total virus excretion in individual subjects.

RESULTS

In all the outbreaks, P2 domain variation was found that resulted in unique codon changes in some patients. Mutations were found in 14% of initial samples and >50% of follow-up samples taken from patients involved in an outbreak. In three patients, aa mutations was observed in or near sites involved in host or antigen binding.

CONCLUSIONS

We concluded that P2 domain variation increases with duration of virus shedding, but was unrelated to total amounts of virus shed. Therefore, we propose that cluster identification based on identical sequences should be relaxed to accommodate minor sequence variation. When using sequence data to support outbreak investigations, sequence diversity should be interpreted in relation to timing of sampling since onset of illness.

New approaches in microbial pathogen detection

Viruses are common causes of foodborne outbreaks. Viral diseases have low fatality rates but transmission to humans via food is important due to the high probability of consuming fecally contaminated food or water because of poor food handling. Because of the low infectious doses of some foodborne viruses, there is a need for standardization and the development of new sensitive methods for detecting viruses. The focus is on molecular and non-molecular approaches, and emerging methods for the detection of foodborne viruses. The detection of noroviruses, hepatitis A and E viruses, rotaviruses and adenoviruses will be discussed. The chapter will conclude with insights into future research directions.

Molecular detection and genotyping of noroviruses

Noroviruses (NoVs) are a major cause of gastroenteritis worldwide in humans and animals and are known as very infectious viral agents. They are spread through feces and vomit via several transmission routes involving person-to-person contact, food, and water. Investigation of these transmission routes requires sensitive methods for detection of NoVs. As NoVs cannot be cultivated to date, detection of these viruses relies on the use of molecular methods such as (real-time) reverse transcriptase polymerase chain reaction (RT-PCR). Regardless of the matrix, detection of NoVs generally requires three subsequent steps: a virus extraction step, RNA purification, and molecular detection of the purified RNA, occasionally followed by molecular genotyping. The current review mainly focused on the molecular detection and genotyping of NoVs. The most conserved region in the genome of human infective NoVs is the ORF1/ORF2 junction and has been used as a preferred target region for molecular detection of NoVs by methods such as (real-time) RT-PCR, NASBA, and LAMP. In case of animal NoVs, broad range molecular assays have most frequently been applied for molecular detection. Regarding genotyping of NoVs, five regions situated in the polymerase and capsid genes have been used for conventional RT-PCR amplification and sequencing. As the expected levels of NoVs on food and in water are very low and inhibition of molecular methods can occur in these matrices, quality control including adequate positive and negative controls is an essential part of NoV detection. Although the development of molecular methods for NoV detection has certainly aided in the understanding of NoV transmission, it has also led to new problems such as the question whether low levels of human NoV detected on fresh produce and shellfish could pose a threat to public health.

Evaluation of viral concentration methods from irrigation and processing water

Four viral concentration methods were evaluated for their efficiency in recovering murine norovirus-1 (MNV-1) (surrogate for human noroviruses (NoV)) and MS2 bacteriophages from processing water (1L) and four different types of irrigation water (bore hole water, rain water, open well and river water) (2-5L). Three methods were based on the viral adsorption and elution principle, two methods using an electronegative HA-membrane (Katayama et al., 2002), one method using an electropositive Zetapor membrane according to CEN/TC275/WG6/TAG4 and the fourth method was based on size exclusion using a tangential flow filtration system. Detection of MNV-1 was achieved by real-time RT-PCR and detection of MS2 by double-layer plaque assay. For the recovery of MNV-1, the method using an electronegative HA-filter in combination with an elution buffer earlier optimized by Hamza et al. (2009) (Method 1) performed best for all types of water (recovery: 5.8-21.9%). In case of MS2 detection, the best method depended upon the type of water although Method 1 provided the most consistent recovery. To complete this evaluation, the Method 1 was evaluated further for the concentration of human enteric viruses (GI and GII NoV, hepatitis A virus (HAV) and rotaviruses) in the same five types of water. Although detection of rotaviruses (RV) was somewhat less efficient, Method 1 proved reliable for the detection of NoV and HAV in all water types. Mean recovery efficiencies ranging from 4.8% for detection of GI NoV in open well water to 32.1% for detection of HAV in bore hole water, depending on the water type and the viral pathogen analyzed.

Effect of grape seed extract on human norovirus GII.4 and murine norovirus 1 in viral suspensions, on stainless steel discs, and in lettuce wash water

The anti-norovirus (anti-NoV) effect of grape seed extract (GSE) was examined by plaque assay for murine norovirus 1 (MNV-1), cell-binding reverse transcription-PCR for human NoV GII.4, and saliva-binding enzyme-linked immunosorbent assay for human NoV GII.4 P particles, with or without the presence of interfering substances (dried milk and lettuce extract). GSE at 0.2 and 2 mg/ml was shown to reduce the infectivity of MNV-1 (>3-log PFU/ml) and the specific binding ability of NoV GII.4 to Caco-2 cells (>1-log genomic copies/ml), as well as of its P particles to salivary human histo-blood group antigen receptors (optical density at 450 nm of >0.8). These effects were decreased as increasing concentrations of dried milk (0.02 and 0.2%) or lettuce extract were added. Under an electron microscope, human NoV GII.4 virus-like particles showed inflation and deformation after treatment with GSE. Under conditions that simulated applications in the food industry, the anti-NoV effect of GSE using MNV-1 as a target organism was shown to be limited in surface disinfection (<1-log PFU/ml, analyzed in accordance with EN 13697:2001). However, a 1.5- to 2-log PFU/ml reduction in MNV-1 infectivity was noted when 2 mg of GSE/ml was used to sanitize water in the washing bath of fresh-cut lettuce, and this occurred regardless of the chemical oxygen demand (0 to 1,500 mg/ml) of the processing water.

Co-detection in the pathogenesis of severe hand-foot-mouth disease

It still needs to be elucidated whether co-detection of EV71 with other intestinal tract viruses plays a role in the pathogenesis of severe hand-foot-mouth disease (HFMD). A total of 680 stool specimens collected from clinically diagnosed mild and severe-HFMD patients were tested for EV71, CA16, norovirus, bocavirus and rotavirus. The results showed that EV71 was significantly associated with severe-HFMD patients. Co-detection of EV71 with norovirus and rotavirus was also significantly associated with severe-HFMD patients: The OR (95 % CI) value was 6.466 (2.735, 15.283) and 7.561 (3.560, 16.057), p < 0.001, respectively. Co-detection of EV71 with rotavirus or norovirus is probably associated with severe HFMD.

Development of a strand specific real-time RT-qPCR assay for the detection and quantitation of murine norovirus RNA

Murine norovirus (MNV), currently the only norovirus that efficiently replicates in cell culture, is often used as a model system to understand the molecular mechanisms of norovirus replication. MNV is a single stranded positive sense RNA virus of the Caliciviridae family. Replication of MNV involves the synthesis of both full length genomic and sub-genomic RNAs. The replication of these RNAs involves the synthesis of negative strand intermediates. To understand the molecular mechanism of RNA replication and the role of viral and host factors in virus replication, it is necessary to quantify accurately both positive and negative sense RNA molecules of the viral RNA during replication. Increasingly, strand specific reverse transcription-quantitative PCR (RT-qPCR) is becoming the method of choice for this kind of quantitation. Many strategies have been developed to avoid the false priming property of reverse transcriptase and to amplify specifically one strand in the presence of excess opposite strand. In this report, a SYBR based, real time RT-qPCR assay was developed to detect and quantify specifically the negative and the positive sense RNAs of MNV genomic RNA. This assay is based on using a tagged RT primer containing a non-viral sequence at the 5' end of the viral strand specific sequence. This non-viral sequence is then used to amplify selectively the strand specific cDNA at the PCR stage. This assay can be used for a range of MNV strains including MNV-1 and 3, as these are now widely accepted for use in molecular studies. The specificity of this assay was determined by its ability to quantify one strand in the presence of up to 10(6) copies of competitor opposite sense RNA. Using this assay, the production of both strands of MNV-1 RNA was monitored during viral single step growth curve.

Discrimination between infectious and non-infectious human norovirus using porcine gastric mucin

Human noroviruses (NoVs) are known to bind to human histo-blood group antigens, as well as to chemically-similar porcine gastric mucins. Here, the binding ability of NoV to porcine mucin is shown to be substantially deficient after UV, thermal, and high pressure treatments. Using qRT-PCR, ≥ 68% of GI.1 NoV (Norwalk strain) bound to porcine gastric mucin-conjugated magnetic beads (PGM-MBs). Application of 600-MPa high pressure treatments reduced binding of the virus to PGM-MBs by 4.7-log₁₀, as determined by qRT-PCR, while a 300-MPa pressure treatment, reduced binding to PGM-MBs by only 0.45-log₁₀. This is consistent with a previously reported clinical trial (Leon et al., 2011. Appl. Environ Microbiol. 77:5476-5482.) which demonstrated inactivation of 4-log₁₀ of GI.1 NoV at 600-MPa. After thermal treatment, binding to PGM-MBs decreased when samples were heated from 0 to 80 °C. Ultraviolet treatments of 0.5 and 2 J/cm² reduced observed PGM-MB binding of norovirus to 33% and negligible levels, respectively, from an initially observed 84% binding for untreated NoV. Although thermal and UV treatments are generally recognized to inactivate viruses, verification of NoV inactivation by these treatments may require volunteer studies. In total, these results suggest the loss of NoV binding to porcine mucin as a potential means to preferentially exclude non-infectious virus particles from subsequent RT-PCR detection.