Detection of circulating norovirus genotypes: hitting a moving target

Abstract

BackgroundAlthough national surveillance programs are in place to monitor norovirus epidemiology, the emergence of new strains and the genetic diversity among genotypes can be challenging for clinical laboratories. This study evaluated the analytical and clinical performance characteristics of one real-time RT-PCR and two end-point RT-PCRs commonly used in microbiology laboratories.MethodsLower limit of detection (LoD) was determined using 10-fold dilutions of noroviruses belonging to different genotypes. The clinical performance of the real-time and end-point RT-PCRs was assessed in parallel using nucleic acids extracted from 186 stool specimens.ResultsThe real-time RT-PCR was highly sensitive and specific for the detection of norovirus genotypes that are currently circulating in Canada. In contrast, the two end-point RT-PCRs displayed poor analytical sensitivity or complete failure to detect certain norovirus genotypes, which was correlated to sequence mismatches in the primer-binding sites. In an attempt to improve norovirus detection with the end-point RT-PCRs, both assays were processed concurrently and detection from either assay was considered a positive result. Concurrent testing resulted in only a modest increase in clinical sensitivity (75.0%) compared to each assay alone (62.5% and 71.9%). However, the false positivity rate increased from 1.98% and 3.36% for the assays alone to 5.47% with concurrent testing.ConclusionsThis study emphasizes the benefits of a real-time method and provides support for routine surveillance to monitor norovirus epidemiology and ongoing proficiency testing to ensure detection of circulating norovirus genotypes.

Evaluation of a laboratory-developed test for simultaneous detection of norovirus and rotavirus by real-time RT-PCR on the Panther Fusion® system

“…The primer and probe sequences (Table 1) for norovirus genogroup II (G2) detection (CoG2f, CoG2r, Ring2), targeting the ORF1-ORF2 junction, were previously published [12]. We confirmed the specificity of these norovirus G2 primer and probe sequences with an alignment of 500 randomly selected norovirus G2 sequences from the National Center for Biotechnology Information (NCBI) nonredundant nucleotide collection (dataset S1).…”

“…Primer and probe sequences for norovirus genogroup I (G1) detection were based on previously published sequences (CoG1f, CoG1r, Ring1a/b), targeting the ORF1-ORF2 junction [12]. Changes to the published sequences were made according to an alignment of 165 randomly selected norovirus G1 sequences from NCBI's non-redundant nucleotide collection and four sequences from clinical samples.…”

Viral Agent That Causing Diarrhoea Among Children in Al-Najaf Province, Iraq

“…This study like with a study by Hussan (2012) in Baghdad who detected 36.4% of Rotavirus isolates from diarrhoea sources. After introduction of the Rotarix vaccine, which was correlated with an increase in the incidence of other viruses in many countries Rooney et al,(2014 Kirby et al,(2011).…”

An ultrasensitive SiO2-encapsulated alloyed CdZnSeS quantum dot-molecular beacon nanobiosensor for norovirus

“…Noroviruses (NVs) are the leading etiological viral agent of acute gastroenteritis and are the predominant causative agents of outbreaks of foodborne disease (Ando et al, 1995;Rooney et al, 2014). Conventional diagnostic techniques for NV have certain limitations.…”