[From abstract] In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere’s viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included.
Full references to the paper can be seen on our publications page http://www.viraqua.uk/publications/.
This paper analyses the distribution of enteric viruses in the Conwy River and estuary. We have validated a novel two-step concentration method suitable for low and high turbidity (e.g. wastewater), freshwater and seawater samples. We used this and previously established methods for the 1-year surveillance of enteric viruses in wastewater, the receiving river and estuarine water, sediment and shellfish samples. For the first time, we found sapovirus (enteric virus causing gastroenteritis with symptoms similar to norovirus infection) in UK wastewater samples. We also found norovirus in high concentrations during local gastroenteritis outbreaks in all sample types. We also found that due to their high concentrations and lack of seasonal distribution, adenoviruses can be suitable indicators for wastewater contamination tracking in the water environment. Full references to the paper can be seen on our publications page http://www.viraqua.uk/publications/.
The second paper to be publish from the VIRAQUA project has been published and is now available to download (http://link.springer.com/article/10.1007/s12560-017-9293-5). In this study, the authors developed and validated two multiplex qRT-PCR assays for aquatic sediment and shellfish samples targeting viruses that are a common cause of gastroenteritis, along with mengovirus (MgV), which is often used as a sample process control for the assessment of RNA extraction efficiency. It was concluded that ‘these assays allow the thorough assessment of the target viruses in sediment and shellfish samples and are useful for quantitative risk assessment of wastewater-contaminated environments’. A full reference for this paper can be found on our publications page.
A collaborative paper, co-authored by Davey Jones, Shelagh Malham and others from Bangor University, Liverpool University, Natural Resources Wales and Bangor Mussel Producers Ltd. reviewing the risk of norovirus infection from the consumption of shellfish had been published in Food and Environmental Virology. Conclusions are drawn as to the likely impact of climate change and shellfish role in the transmission of norovirus to the human population. A full reference for this paper can be found on our publications page.
The new year kicked off with the first Viraqua project publication with Kata Farkas, Francis Hassard, James McDonald, Shelagh Malham and Davey Jones all co-authors on a paper in Frontiers in Microbiology evaluating molecular methods for the detection and quantification of pathogen-derived nucleic acids in sediment.” Full references can be found on our publications
The last week has seen two new project publications; David Lees is co-author of a paper modelling risk factors for norovirus contamination of shellfish water http://dx.doi.org/10.1016/j.ijfoodmicro.2016.10.028 whilst Kata Farkas, Davey Jones, Shelagh Malham and James McDonald are all co-authors of a review paper addressing the abundance and distribution of enteric bacteria and viruses in coastal and estuarine sediments http://dx.doi.org/10.3389/fmicb.2016.01692 Full references to both papers can be seen on our publications page http://www.viraqua.uk/publications/.