Detection of waterborne norovirus genogroup I strains using an improved real time RT-PCR assay

Cho, Han-Gil; Lee, Sung-Geun; Mun, Su-Kyoung; Lee, Myung-Jin; Park, Po-Hyun; Jheong, Weon-Hwa; Yoon, Mi‐Hye; Paik, Soon-Yong

doi:10.1007/s00705-017-3505-z

Cited by 5 publications

(2 citation statements)

References 30 publications

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“…The inability to identify NoV GI with qRT-PCR might be related to the mismatched base present in the forward primer sequence used for detection, but even without mismatches, primer-probe pairs can be improved to provide better detection. In a recent study, researchers designed an improved probe for NoV GI.2 strains, lowering the limit of detection for these strains from waterborne samples ( 47 ). It is, therefore, possible that the NoV GI.2 detected here with viromics methods was present below the limit of detection of the ISO standard primer/probe combination ( 48 ) used in our study.…”

Section: Discussionmentioning

confidence: 99%

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

et al. 2018

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Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.

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Section: Discussionmentioning

confidence: 99%

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

et al. 2018

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“…While the known NoV GI.2 genotypes do not have a mismatch in the qRT-PCR probe sequence, it is possible that the genome recovered in this study fell below the limit of detection using the ISO standard primer/probe combination (ISO/TS 15216-2:2013). In a recent study, researchers designed an improved probe and observed lower Ct values and a lower limit of detection for GI.2 strains from waterborne samples (47). Viromics as a means of investigating water samples for the presence of norovirus, does have the advantage of demonstrating the presence of an undegraded genome, provided the sample processing requirements do not lead to excessive loss of virus particles resulting in false negatives.…”

Section: Discussionmentioning

confidence: 99%

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Adriaenssens

Farkas

Harrison

et al. 2018

Preprint

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13Detection of viruses in the environment is heavily dependent on PCR-based 14 approaches that require reference sequences for primer design. While this strategy 15 can accurately detect known viruses, it will not find novel genotypes, nor emerging 16 and invasive viral species. In this study, we investigated the use of viromics, i.e. 17 high-throughput sequencing of the biosphere viral fraction, to detect human/animal 18 pathogenic RNA viruses in the Conwy river catchment area in Wales, UK. Using a 19 combination of filtering and nuclease treatment, we extracted the viral fraction from 20 wastewater, estuarine river water and sediment, followed by RNASeq analysis on 21 the Illumina HiSeq platform for the discovery of RNA virus genomes. We found a 22 the range of potentially pathogenic viruses that are present in the environment and 37 identify prevalent genotypes. The ultimate goal is to trace the fate of these 38 pathogenic viruses from origin to the point where they are a threat to human health, 39 informing reference-based detection methods and water quality management. 40Recent reviews have proposed the use of viral metagenomics or viromic approaches 58 as an alternative method to test for the presence of pathogenic viruses in the 59 environment (2, 9, 10). Provided the entire viral community is sampled and 60 4 sequenced, novel genotypes or even entirely novel viruses can be detected. 61Potential new viral markers for faecal contamination have already been revealed, 62 such as pepper mild mottle virus and crAssphage (11, 12), among the huge diversity 63 of human viruses found in sludge samples (13). 64In this pilot study, we have used viromics to investigate the presence of human 65 pathogenic RNA viruses in wastewater, estuarine surface water and sediment in a 66 single catchment. The water and sediment samples were collected at, and 67 downstream of, the wastewater treatment plant (Lanrwst, Wales, UK), at the estuary 68 of the river Conwy (Wales, UK) near Morfa beach (Figure 1). To our knowledge, this 69 is the first study to use unamplified environmental viral RNA for sequencing library 70 construction, sequence dataset production and subsequent analysis. Because we 71 used a directional library sequencing protocol on RNA, rather than amplifying to 72 cDNA, we were able to distinguish single-stranded from double-stranded RNA 73 genome fragments. 74

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Noroviruses, Sapoviruses, and Aichi Viruses Emergence in Wastewater Associated With Viral Pandemic Gastroenteritis

Ibrahim

Hammami

Hassen

2020

Emerging and Reemerging Viral Pathogens

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Detection of waterborne norovirus genogroup I strains using an improved real time RT-PCR assay

Cited by 5 publications

References 30 publications

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Noroviruses, Sapoviruses, and Aichi Viruses Emergence in Wastewater Associated With Viral Pandemic Gastroenteritis

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