Evaluation of a new real-time reverse transcription polymerase chain reaction assay for detection of norovirus in fecal specimens

Evaluation of a new fast in-house Real-Time PCR assay for detecting both Norovirus and toxigenic Clostridium difficile using fecal sample and rectal swab

BACKGROUND

Norovirus and toxigenic Clostridium difficile infections are the 2 most common causes of infectious gastroenteritis. Rapid and reliable detection of these to microorganisms is important to assess if contact precautions are indicated to prevent spreading and reduce cost of isolation.

METHODS

This study determines sensitivity and specificity of a new fast in-house PCR assay used on BD MAX platform to detect both norovirus and C difficile in 1 turn-over in clinical context. Furthermore, fecal samples as well as rectal swabs were used as analysis material to determine the accuracy of the new assay on a fecal samples and rectal swabs compared with standard methods.

RESULTS

From 227 included patients, 143 rectal swabs and 135 fecal samples obtained. The new in-house PCR showed a sensitivity of 73.3% and a specificity of 99.2% for norovirus on a fecal sample and a sensitivity of 57.1% and specificity 99.1% of for norovirus on a rectal swab. For C difficile a sensitivity of 100% and specificity of 100% on a fecal sample and a sensitivity of 90.9% and a specificity of 99.1% on a rectal swab was shown. The time consumption for detecting the 2 enteropathogens was reduced by half by using the new assay.

CONCLUSIONS

The new assay shows an acceptable sensitivity and specificity for C difficile and an acceptable specificity for norovirus when analysis was done on fecal samples and reduces half of the time consumption. Further research is needed to improve the accuracy of the new in-house PCR before clinical implication.

Evaluation of RIDA®GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis

BACKGROUND

Norovirus is the leading cause of epidemic and sporadic acute gastroenteritis (AGE) in the United States. Widespread prevalence necessitates implementation of accurate norovirus detection assays in clinical diagnostic laboratories.

OBJECTIVE

To evaluate RIDA^®GENE norovirus GI/GII real-time RT-PCR assay (RGN RT-PCR) using stool samples from patients with sporadic AGE.

STUDY DESIGN

Patients between 14 days to 101 years of age with symptoms of AGE were enrolled prospectively at four sites across the United States during 2014-2015. Stool specimens were screened for the presence of norovirus RNA by the RGN RT-PCR assay. Results were compared with a reference method that included conventional RT-PCR and sequencing of a partial region of the 5'end of the norovirus ORF2 gene.

RESULTS

A total of 259 (36.0%) of 719 specimens tested positive for norovirus by the reference method. The RGN RT-PCR assay detected norovirus in 244 (94%) of these 259 norovirus positive specimens. The sensitivity and specificity (95% confidence interval) of the RGN RT-PCR assay for detecting norovirus genogroup (G) I was 82.8% (63.5-93.5) and 99.1% (98.0-99.6) and for GII was 94.8% (90.8-97.2) and 98.6% (96.9-99.4), respectively. Seven specimens tested positive by the RGN-RT PCR that were negative by the reference method. The fifteen false negative samples were typed as GII.4 Sydney, GII.13, GI.3, GI.5, GI.2, GII.1, and GII.3 in the reference method.

CONCLUSIONS

The RGN RT-PCR assay had a high sensitivity and specificity for the detection of norovirus in stool specimens from patients with sporadic AGE.

Exploration of the metal coordination region of concanavalin A for its interaction with human norovirus

Rapid methods for the detection and clinical treatment of human norovirus (HuNoV) are needed to control foodborne disease outbreaks, but reliable techniques that are fast and sensitive enough to detect small amounts of HuNoV in food and aquatic environments are not yet available. We explore the interactions between HuNoV and concanavalin A (Con A), which could facilitate the development of a sensitive detection tool for HuNoV. Biophysical studies including hydrogen/deuterium exchange (HDX) mass spectrometry and surface plasmon resonance (SPR) revealed that when the metal coordinated region of Con A, which spans Asp16 to His24, is converted to nine alanine residues (mCon A^MCR), the affinity for HuNoV (GII.4) diminishes, demonstrating that this Ca²⁺ and Mn²⁺ coordinated region is responsible for the observed virus-protein interaction. The mutated carbohydrate binding region of Con A (mCon A^CBR) does not affect binding affinity significantly, indicating that MCR of Con A is a major region of interaction to HuNoV (GII.4). The results further contribute to the development of a HuNoV concentration tool, Con A-immobilized polyacrylate beads (Con A-PAB), for rapid detection of genotypes from genogroups I and II (GI and GII). This method offers many advantages over currently available methods, including a short concentration time. HuNov (GI and GII) can be detected in just 15 min with 90% recovery through Con A-PAB application. In addition, this method can be used over a wide range of pH values (pH 3.0 – 10.0). Overall, this rapid and sensitive detection of HuNoV (GI and GII) will aid in the prevention of virus transmission pathways, and the method developed here may have applicability for other foodborne viral infections.

Evaluation of real-time RT-PCR assays for detection and quantification of norovirus genogroups I and II

Noroviruses are the leading cause of acute gastroenteritis in humans. Real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) is a promising molecular method for the detection of noroviruses. In this study, the performance of three TaqMan real-time RT-PCR assays was assessed, which were one commercially available real-time RT-PCR kit (assay A: Norovirus Real Time RT-PCR kit) and two in-house real-time RT-PCR assays (assay B: LightCycler RNA Master Hybprobe and assay C: RealTime ready RNA Virus Master). Assays A and B showed higher sensitivity than assay C for norovirus GI, while they all had the same sensitivity (10³ DNA copies/mL) for GII DNA standard controls. Assay B had the highest efficiency for both genogroups. No cross-reactivity was observed among GI and GII noroviruses, rotavirus, hepatitis A virus, and poliovirus. The detection rates of these assays in GI and GII norovirus-positive fecal samples were not significantly different. However, the mean quantification cycle (Cq) value of assay B for GII was lower than assays A and C with statistical significance (P-value, 0.000). All three real-time RT-PCR assays could detect a variety of noroviruses including GI.2, GII.2, GII.3, GII.4, GII.6, GII.12, GII.17, and GII.21. This study suggests assay B as a suitable assay for the detection and quantification of noroviruses GI and GII due to good analytical sensitivity and higher performance to amplify norovirus on DNA standard controls and clinical samples.

Molecular epidemiology of norovirus in asymptomatic food handlers in Busan, Korea, and emergence of genotype GII.17

The molecular epidemiology of norovirus infections was studied in food handlers without any symptoms from January to December 2015 in Busan city, Korea. A total of 2,174 fecal specimens from asymptomatic food handlers were analyzed, and 2.3% (49/2,174) were norovirus-positive. Fourteen of 335 samples (4.2%) were positive in January; fifteen of 299 samples (5.0%) in February, and seven of 189 samples (3.7%) in December. However, norovirus was rarely detected in other months. From sequencing analysis, 11 genotypes (five GI and six GII genotypes) were detected. Among the 42 capid gene sequences identified, 14 were from the GI genogroup, while 28 were from the GII genogroup. The most commonly detected genotype was GII.17, comprising 15 (35.7%) of positive samples. From January 2012 to December 2015, 5,138 samples were collected from gastroenteritis patients and outbreaks in Busan. The most detected genotype in 2012, 2013, and 2014 was GII.4 (121, 24, and 12 cases, respectively), but in 2015, GII.17 (25 cases) was the most common. The GII.4 genotype was the major cause of acute gastroenteritis from 2012 to 2014, but the GII.17 genotype became the most prevalent cause in 2015. Continued epidemiological surveillance of GII.17 is needed, together with assessment of the risk of norovirus infection.

Advanced PCR-based molecular diagnosis of gastrointestinal infections: challenges and opportunities

Acute infections of the gastrointestinal tract are among the most common infectious diseases. The etiological agents of gastroenteritis may be bacteria, viruses or protozoa. Identification of the etiological agents of acute diarrhea is important for the treatment and management of diarrheal diseases. Conventional stool culture for bacteria shows a low sensitivity and requires more than 24 hours. In addition, other approaches to detect viruses and protozoa mainly involve antigen detection, but this is not available for all enteropathogens, and microscopic observation requires training and is of low sensitivity. In this review, the authors describe currently available molecular methods to detect different enteropathogens and analyze the main advantages and disadvantages of these methods for laboratory diagnosis of gastroenteritis.

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.