FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

Arredondo-Hernandez, Luis Jose Rene; Díaz-Ávalos, Carlos; López‐Vidal, Yolanda; Castillo-Rojas, Gonzalo; Mazarí-Hiriart, Marisa

doi:10.1371/journal.pone.0170399

Cited by 11 publications

(9 citation statements)

References 49 publications

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“…While there have been recent breakthroughs in growing human NoV ( 49 , 50 ), its culture remains very difficult and not yet suitable for routine testing for NoV in the environment. Hence, studies using male-specific coliphages, such as MS2 and GA, which are ssRNA phages belonging to the family Leviviridae , are still worthwhile as alternative model systems ( 51 , 52 ). Interestingly, while some levivirus signatures were present in all wastewater samples (<500 reads), we observed a striking cooccurrence of these viruses with norovirus signatures in both libraries of sample LE_11-10 (>2,500 reads).…”

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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“…Due to the virtual impossibility of culturing noroviruses in the lab, many studies have used male-specific coliphages such as MS2 and GA, which are ssRNA phages belonging to the family Leviviridae, as alternative model systems (48, 49). Interestingly, while some levivirus signatures were present in all wastewater samples (< 500 reads), we observed a striking co-occurrence of these viruses with norovirus signatures in both libraries of sample LE_11-10 (> 2500 reads).…”

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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“…Other markers have also been developed to estimate fecal contamination. FRNA bacteriophages have been employed as enteric viral indicator for fecal contamination in tropical aquatic systems ( Arredondo-Hernandez et al, 2017 ) and host-specific bacteroidale markers have been employed as indicators for fecal contamination ( Wilkes et al, 2013 ). With the improved purification and RT-qPCR methods, it might be more convenient to measure HuNoV directly from environmental water samples rather than using indirect indicators.…”

Section: Discussionmentioning

confidence: 99%

Concurrent Detection of Human Norovirus and Bacterial Pathogens in Water Samples from an Agricultural Region in Central California Coast

et al. 2017

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Bacterial pathogens and human norovirus (HuNoV) are major cause for acute gastroenteritis caused by contaminated food and water. Public waterways can become contaminated from a variety of sources and flood after heavy rain events, leading to pathogen contamination of produce fields. We initiated a survey of several public watersheds in a major leafy green produce production region of the Central California Coast to determine the prevalence of HuNoV as well as bacterial pathogens. Moore swabs were used to collect environmental samples bi-monthly at over 30 sampling sites in the region. High prevalence of HuNoV and bacterial pathogens were detected in environmental water samples in the region. The overall detection rates of HuNoV, O157 Shiga toxin-producing Escherichia coli (STEC), non-O157 STEC, Salmonella, and Listeria were 25.58, 7.91, 9.42, 59.65, and 44.30%, respectively. The detection rates of Salmonella and L. monocytogenes were significantly higher in the spring. Fall and spring had elevated detection rates of O157 STEC. The overall detection rates of non-O157 STEC in the fall were lower than the other seasons but not significant. The overall detection rates of HuNoV were highest in fall, followed by spring and winter, with summer being lowest and significantly lower than other seasons. This study presented the first study of evaluating the correlation between the detection rate of HuNoV and the detection rates of four bacterial pathogens from environmental water. Overall, there was no significant difference in HuNoV detection rates between samples testing positive or negative for the four bacterial pathogens tested. Pathogens in animal-impacted and human-impacted areas were investigated. There were significant higher detection rates in animal-impacted areas than that of human-impacted areas for bacterial pathogens. However, there was no difference in HuNoV detection rates between these two areas. The overall detection levels of generic E. coli and detection rate of HuNoV showed no correlation.

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FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

Cited by 11 publications

References 49 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

Concurrent Detection of Human Norovirus and Bacterial Pathogens in Water Samples from an Agricultural Region in Central California Coast

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