Evaluation of a broadly reactive nucleic acid sequence based amplification assay for the detection of noroviruses in faecal material

Human Norovirus Detection: How Much Are We Prepared?

Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.

Recent Developments in Isothermal Amplification Methods for the Detection of Foodborne Viruses

Foodborne and enteric viruses continue to impose a significant public health and economic burden globally. As many of these viruses are highly transmissible, the ability to detect them portably, sensitively, and rapidly is critical to reduce their spread. Although still considered a gold standard for detection of these viruses, real time polymerase chain reaction (PCR)-based technologies have limitations such as limited portability, need for extensive sample processing/extraction, and long time to result. In particular, the limitations related to the susceptibility of real time PCR methods to potential inhibitory substances present in food and environmental samples is a continuing challenge, as the need for extensive nucleic acid purification prior to their use compromises the portability and rapidity of such methods. Isothermal amplification methods have been the subject of much investigation for these viruses, as these techniques have been found to be comparable to or better than established PCR-based methods in portability, sensitivity, specificity, rapidity, and simplicity of sample processing. The purpose of this review is to survey and compare reports of these isothermal amplification methods developed for foodborne and enteric viruses, with a special focus on the performance of these methods in the presence of complex matrices.

Advances and Future Perspective on Detection Technology of Human Norovirus

Human norovirus (HuNoV) is a food-borne pathogen that causes acute gastroenteritis in people of all ages worldwide. However, no approved vaccines and antiviral drugs are available at present. Therefore, the development of accurate and rapid detection technologies is important in controlling the outbreak of HuNoVs. This paper reviewed the research progress on HuNoV detection, including immunological methods, molecular detection and biosensor technology. Immunological methods and molecular detection technologies are still widely used for HuNoV detection. Furthermore, biosensors will become an emerging developmental direction for the rapid detection of HuNoVs because of their high sensitivity, low cost, easy operation and suitability for onsite detection.

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.

Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment

Noroviruses are a primary cause of gastroenteritis and foodborne illness with cases that affect millions of people worldwide each year. Inexpensive tests for norovirus that do not require sophisticated laboratory equipment are important tools for ensuring that patients receive timely treatment and for containing outbreaks. Herein, we demonstrate a low-cost colorimetric assay that detects norovirus from clinical samples by combining paper-based cell-free transcription-translation systems, isothermal amplification and virus enrichment by synbodies. Using isothermal amplification and cell-free RNA sensing with toehold switches, we demonstrate that the assay enables detection of norovirus GII.4 Sydney from stool down to concentrations of 270 aM in reactions that can be directly read by eye. Furthermore, norovirus-binding synbodies and magnetic beads are used to concentrate the virus and provide a 1000-fold increase in assay sensitivity extending its detection limit to 270 zM. These results demonstrate the utility of paper-based cell-free diagnostic systems for identification of foodborne pathogens and provide a versatile diagnostic assay that can be applied to the concentration, amplification and detection of a broad range of infectious agents.

Norovirus: The Burden of the Unknown

Human noroviruses (HNoVs) are primarily transmitted by the fecal-oral route, either by person-to-person contact, or by ingestion of contaminated food or water as well as by aerosolization. Moreover, HNoVs significantly contribute to foodborne diseases being the causative agent of one-fifth of acute gastroenteritis worldwide. As a consequence of globalization, transnational outbreaks of foodborne infections are reported with increasing frequency. Therefore, in this review, state-of-the-art information regarding molecular procedures for human norovirus detection in food as well common food processing technologies have been summarized. Besides, the purpose of this chapter is to consolidate basic information on various aspects of HNoVs and to summarize food processing technologies that can potentially be applied in the food industry.

Development of a Recombinase Polymerase Amplification Assay for Detection of Epidemic Human Noroviruses

Human norovirus is a leading cause of viral gastroenteritis worldwide. Rapid detection could facilitate control, however widespread point-of-care testing is infrequently done due to the lack of robust and portable methods. Recombinase polymerase amplification (RPA) is a novel isothermal method which rapidly amplifies and detects nucleic acids using a simple device in near real-time. An RT-RPA assay targeting a recent epidemic human norovirus strain (GII.4 New Orleans) was developed and evaluated in this study. The assay successfully detected purified norovirus RNA from multiple patient outbreak isolates and had a limit of detection of 3.40 ± 0.20 log₁₀ genomic copies (LGC), which is comparable to most other reported isothermal norovirus amplification methods. The assay also detected norovirus in directly boiled stool, and displayed better resistance to inhibitors than a commonly used RT-qPCR assay. The assay was specific, as it did not amplify genomes from 9 non-related enteric viruses and bacteria. The assay detected norovirus in some samples in as little as 6 min, and the entire detection process can be performed in less than 30 min. The reported RT-RPA method shows promise for sensitive point-of-care detection of epidemic human norovirus, and is the fastest human norovirus amplification method to date.

Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses

Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.

Bovine noroviruses: A missing component of calf diarrhoea diagnosis

Noroviruses are RNA viruses that belong to the Genus Norovirus, Family Caliciviridae, and infect human beings and several animal species, including cattle. Bovine norovirus infections have been detected in cattle of a range of different ages throughout the world. Currently there is no suitable cell culture system for these viruses and information on their pathogenesis is limited. Molecular and serological tests have been developed, but are complicated by the high genetic and antigenic diversity of bovine noroviruses. Bovine noroviruses can be detected frequently in faecal samples of diarrhoeic calves, either alone or in association with other common enteric pathogens, suggesting a role for these viruses in the aetiology of calf enteritis.

Inactivation of murine norovirus-1 and hepatitis A virus on fresh meats by atmospheric pressure plasma jets

In the current study, inactivation effect of atmospheric pressure plasma (APP) jets (10s-20min) was investigated against murine norovirus (MNV-1), as a norovirus (NoV) surrogate and hepatitis A virus (HAV) associated with three types of fresh meats (beef loin, pork shoulder and chicken breast). The quality characteristics of fresh meats, such as surface color, moisture content and thiobarbituric acid reactive substance (TBARS) were also examined. After 5-20min of treatment with APP jets, the reduction in MNV-1 titers (initial inoculums of 10⁷ plaque-forming units (PFU)) were >2log₁₀PFU/mL in the three types of meat. After 5-20min treatment with APP jets, the reduction in HAV titers (initial inoculums of 10⁶PFU) were >1log₁₀PFU/mL in the three types of meat. There was no significant difference (p>0.05) in the L*, a*, and b* values for APP jet treatment times below 5min. Furthermore, there was no significant difference (p>0.05) in the water content (%) value for treatment times under 5min. Although the TBARS values gradually increased with increase in APP jet treatment times, these TBA values were below 1.0mgMA/kg (an indicator of meat rancidity). The results of the current study indicate that 5min of APP jet treatment showed >99% reduction (2log₁₀PFU/mL) of MNV-1 titer and >90% reduction (1log₁₀PFU/mL) of HAV titer without concomitant changes in meat quality; thus, this procedure can be considered in fresh meat production, processing and distribution processes to enhance fresh meat safety.

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.

Norovirus

Norovirus, an RNA virus of the family Caliciviridae, is a human enteric pathogen that causes substantial morbidity across both health care and community settings. Several factors enhance the transmissibility of norovirus, including the small inoculum required to produce infection (<100 viral particles), prolonged viral shedding, and its ability to survive in the environment. In this review, we describe the basic virology and immunology of noroviruses, the clinical disease resulting from infection and its diagnosis and management, as well as host and pathogen factors that complicate vaccine development. Additionally, we discuss overall epidemiology, infection control strategies, and global reporting efforts aimed at controlling this worldwide cause of acute gastroenteritis. Prompt implementation of infection control measures remains the mainstay of norovirus outbreak management.

Evaluation of Immunomagnetic Separation Method for the Recovery of Hepatitis A Virus and GI.1 and GII.4 Norovirus Strains Seeded on Oyster and Mussel

Outbreaks of viral diseases are frequently associated with the consumption of minimally processed shellfish. Among the viruses in these outbreaks, hepatitis A virus (HAV) and human norovirus (NoV) have been increasingly reported as the most common food-borne pathogens. These viruses must be concentrated in tested samples in order to be detected. In this study, a method for the detection of NoV and HAV in shellfish using an immuno-magnetic separation (IMS) procedure combined with reverse transcriptase (RT)-PCR was developed. The IMS/RT-PCR method was applied to investigate the recovery rates of HAV, NoV GI.1, and GII.4 from oyster and mussel. Based on IMS/RT-PCR results, recovery rates for HAV from oyster and mussel test samples were 2.4 and 1.1%, respectively. The NoV GI.1 recovery rates from oyster and mussel samples were 4.9-9.2% (mean 6.9%) and 4.3-8.6% (mean 6.2%), respectively, and the NoV GII.4 recovery rates were 8.8 and 8.5%, respectively. These results verified that HAV, NoV GI.1, and GII.4 can be detected in all the test samples using the IMS/RT-PCR method, although the three inoculated viruses were recovered with low efficiency. In conclusion, the IMS/RT-PCR method can be used to efficiently and rapidly detect viruses such as HAV and NoV in shellfish such as oyster and mussel.

Virus-like Particle Vaccines for Norovirus Gastroenteritis

Gastroenteritis (GE) and its associated diarrheal diseases remain as one of the top causes of death in the world. Noroviruses (NoVs) are a group of genetically diverse RNA viruses that cause the great majority of nonbacterial gastroenteritis in humans. However, there is still no vaccine licensed for human use to prevent NoV GE. The lack of a tissue culture system and a small animal model further hinders the development of NoV vaccines.

Virus-like particles (VLPs) that mimic the antigenic architecture of authentic virions, however, can be produced in insect, mammalian, and plant cells by the expression of the capsid protein. The particulate nature and high-density presentation of viral structure proteins on their surface render VLPs as a premier vaccine platform with superior safety, immunogenicity, and manufacturability. Therefore, this chapter focuses on the development of effective NoV vaccines based on VLPs of capsid proteins. The expression and structure of NoV VLPs, especially VLPs of Norwalk virus, the prototype NoV, are extensively discussed. The ability of NoV VLPs in stimulating a potent systemic and mucosal anti-NoV immunity through oral and intranasal delivery in mice is presented.

The advantages of plant expression systems as a novel production platform for VLP-based NoV vaccines are discussed in light of their cost-effectiveness, production speed, and scalability. Recent achievements from the first successful demonstration of NoV VLP production in plant expression system under the current Good Manufacture Practice (cGMP) regulation by the US Food and Drug Administration (FDA) are detailed.

Moreover, results of human clinical trials demonstrating the safety and efficacy of insect and plant-derived NoV VLPs are also presented. Due to the diversity of capsid protein among different NoV strains and its rapid antigenic drift, we speculate that vaccine development should focus on multivalent VLP vaccines derived from capsid proteins of the most prevalent strains. With the very recent approval of the first plant-made biologics by the FDA, we also speculate that plant-based production systems will play an important role in manufacturing such multivalent VLP-based NoV vaccines.

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.

Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection

Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.

Application of a modified loop-mediated isothermal amplification kit for detecting Norovirus genogroups I and II

Norovirus is a major etiologic agent in worldwide outbreaks of gastroenteritis associated with food as well as person‐to‐person transmission. The ubiquitous nature of Norovirus necessitates simple and rapid detection methods with high accuracy and sensitivity. To this end, several investigators have evaluated the usefulness of commercial reverse‐transcription loop‐mediated isothermal amplification (RT‐LAMP) kits for detecting Norovirus genogroups I (GI) and II (GII). In previous studies, the conventional Loopamp kit for Norovirus GII showed a relatively high detection rate, while that for Norovirus GI showed a relatively low detection rate. In the present study, clinical Norovirus specimens were used to compare the detection rate of a modified Loopamp kit for Norovirus GI with the rates of the conventional Loopamp kit for Norovirus GI and an “in‐house” RT‐LAMP GI primer set, methods which had a high detection rate. Results from the present study showed that the modified Loopamp kit for Norovirus GI had a higher detection rate for two viral genotypes (GI.3, GI.11). On comparison with an “in‐house” GII primer set using genotype GII.4 viruses circulating recently, the detection rate by the Loopamp kit for Norovirus GII was found to be higher, with a 98% detection rate. These results indicate the applicability of the modified LAMP kit for GI and the conventional LAMP kit for GII for detection of Noroviruses in clinical samples. J. Med. Virol. 81:2072–2078, 2009. © 2009 Wiley‐Liss, Inc.

Rapid and sensitive detection of norovirus genomes in oysters by a two-step isothermal amplification assay system combining nucleic acid sequence-based amplification and reverse transcription-loop-mediated isothermal amplification assays

We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h.

A nucleic acid sequence-based amplification assay for real-time detection of norovirus genogroup II

AIMS

To use molecular beacon based nucleic acid sequence-based amplification (NASBA) to develop a rapid, sensitive, specific detection method for norovirus (NV) genogroupII (GII).

METHODS AND RESULTS

A method to detect NV GII from environmental samples using real-time NASBA was developed. This method was routinely sensitive to 100 copies of target RNA and intermittent amplification occurred with as few as 10 copies. Quantitative estimates of viral load were possible over at least four orders of magnitude.

CONCLUSIONS

The NASBA method described here is a reliable and sensitive assay for the detection of NV. This method has the potential to be linked to a handheld NASBA device that would make this real-time assay a portable and inexpensive alternative to bench-top, lab-based assays.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development of the real-time NASBA assay described here has resulted in a simple, rapid (<1 h), convenient testing format for NV. To our knowledge, this is the first example of a molecular beacon based NASBA assay for NV.

Use of TaqMan real-time reverse transcription-PCR for rapid detection, quantification, and typing of norovirus

Noroviruses (NoVs) are the most commonly identified cause of outbreaks and sporadic cases of acute gastroenteritis. We evaluated and optimized NoV-specific TaqMan real-time reverse transcription (RT)-PCR assays for the rapid detection and typing of NoV strains belonging to genogroups GI and GII and adapted them to the LightCycler platform. We expanded the detection ability of the assays by developing an assay that detects the GIV NoV strain. The assays were validated with 92 clinical samples and 33 water samples from confirmed NoV outbreaks and suspected NoV contamination cases. The assays detected NoV RNA in all of the clinical specimens previously confirmed positive by conventional RT-PCR and sequencing. Additionally, the TaqMan assays successfully detected NoV RNA in water samples containing low viral concentrations and inhibitors of RT and/or PCR, whereas the conventional method with region B primers required dilution of the inhibitors. By means of serially diluted NoV T7 RNA transcripts, a potential detection limit of <10 transcript copies per reaction mixture was observed with the GII assay and a potential detection limit of <100 transcript copies per reaction mixture was observed with the GI assay. These results and the ability to detect virus in water that was negative by RT-PCR demonstrate the higher sensitivity of the TaqMan assay compared with that of a conventional RT-PCR assay. The TaqMan methods dramatically decrease the turnaround time by eliminating post-PCR processing. These assays have proven useful in assisting scientists in public health and diagnostic laboratories report findings quickly to outbreak management teams.

Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay

In this study, we developed a one-step, single-tube genogroup-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of norovirus (NoV) genomes targeting from the C terminus of the RNA-dependent RNA polymerase gene to the capsid N-terminal/shell domain region. This is the first report on the development of an RT-LAMP assay for the detection of NoV genomes. Because of the diversity of NoV genotypes, we used 9 and 13 specially designed primers containing mixed bases for genogroup I (GI) and II (GII), respectively. The RT-LAMP assay had the advantages of rapidity, simplicity, specificity, and selectively and could obtain results within 90 min, generally even within 60 min, under isothermal conditions at 62 degrees C. The detection limits for NoV genomes were between 10(2) and 10(3) copies/tube for GI and GII with differentiation by genotype, and no cross-reactions among NoV GI and GII and other gastroenteritis viruses, such as sapovirus, human astrovirus, adenovirus type 40 and 41, and group A and C rotavirus, were found. In the evaluation tests with fecal specimens obtained from gastroenteritis outbreaks, the sensitivity and specificity of the RT-LAMP assay with regard to RT-PCR were 100 and 94% for GI and 100 and 100% for GII, respectively. These findings establish that the RT-LAMP assay is potentially useful for the rapid detection of NoV genomes from fecal specimens in outbreaks of food-borne and person-to-person-transmitted gastroenteritis.

Real-time detection of noroviruses in surface water by use of a broadly reactive nucleic acid sequence-based amplification assay

Noroviruses are the most common agents causing outbreaks of viral gastroenteritis. Outbreaks originating from contaminated drinking water and from recreational waters have been described. Due to a lack of cell culture systems, noroviruses are detected mostly by molecular methods. Molecular detection assays for viruses in water are often repressed by inhibitory factors present in the environment, like humic acids and heavy metals. To study the effect of environmental inhibitors on the performance of nucleic acid sequence-based amplification (NASBA), we developed a real-time norovirus NASBA targeting part of the RNA-dependent RNA polymerase (RdRp) gene. Specificity of the assay was studied with 33 divergent clones that contained part of the targeted RdRp gene of noroviruses from 15 different genogroups. Viral RNA originated from commercial oysters, surface waters, and sewage treatment plants in The Netherlands. Ninety-seven percent of the clones derived from human noroviruses were detected by real-time NASBA. Two clones containing animal noroviruses were not detected by NASBA. We compared the norovirus detection by real-time NASBA with that by conventional reverse transcriptase PCR (RT-PCR) with large-volume river water samples and found that inhibitory factors of RT-PCR had little or no effect on the performance of the norovirus NASBA. This consequently resulted in a higher sensitivity of the NASBA assay than of the RT-PCR. We show that by combining an efficient RNA extraction method with real-time NASBA the sensitivity of norovirus detection in water samples increased at least 100 times, which consequently has implications for the outcome of the infectious risk assessment.

Comparative evaluation of RT-PCR, nucleic acid sequence-based amplification (NASBA) and real-time RT-PCR for detection of noroviruses in faecal material

Using different primer and probe sets, RT-PCR, NASBA and TaqMan RT-PCR molecular methods were compared to detect NoV GII in 13 clinical stool samples. The RT-PCR results observed by gel electrophoresis (Ando, Kageyama and Anderson amplification and probe systems), dot blot hybridization (Ando and Kageyama) and real-time TaqMan assay (Ando and Kageyama) were shown to be consistent and reproducible for the detection of NoV GII. Whereas, the NASBA assay using Ando primers showed some reproducibility discrepancies. Detection limits of the NoV GII/Kageyama system were found to be equal or significantly higher than the Ando system. Real-time TaqMan RT-PCR assay showed similar detection limits to that of NASBA with the Kageyama amplification and detection system, while it was 1log less sensitive than the Ando system. In a clinical context, RT-PCR, NASBA and real-time TaqMan RT-PCR methods using undiluted samples were all suitable for the detection of NoV GII, however the NASBA assay provided less consistent signals. The NoV GII Kageyama real-time TaqMan RT-PCR assay was reliable with a high analytical sensitivity and has shown the capability of detecting one genomic equivalent copy.

Real-time nucleic acid sequence-based amplification using molecular beacons for detection of enterovirus RNA in clinical specimens

Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays were significantly more sensitive than culture. Real-time NASBA-beacon reagents and equipment rental were more expensive than those for NASBA-ECL; however, time to result was shortened by 1.5 h, hands-on time was reduced by 25 min, and the assay was much simpler for technologists to learn and perform.

Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A

The development and introduction of effective treatment for influenza A in the form of neuraminidase inhibitors have made the rapid diagnosis of infection important especially in high-risk populations. The aim of this study was to develop a real-time nucleic acid sequenced based amplification (NASBA) using a molecular beacon that could detect a wide range of influenza A subtypes and strains in a single reaction by targeting a conserved region of the influenza genome, and to evaluate its sensitivity and specificity against traditional laboratory techniques on a range of clinical samples usefulness during the 2003/2004 influenza season. The results demonstrated the assay to be highly sensitive and specific, detecting <0.1 TCID50 of virus stock. Three hundred eighty-nine clinical samples were tested in total from two patient groups. Overall, the real-time NASBA assay detected 64% (66/103) more influenza positive samples than cell culture and direct immunofluorescence (IF) and, therefore, was shown to be more sensitive in detecting influenza A in a wide range of respiratory samples than traditional methods. In conclusion, the real-time influenza A assay demonstrated clinical usefulness in both hospital and community populations.