We originally started our environmental suveillance activities back in 2010 exploring viral dynamics in the Conwy River and estuary due to the known water quality issues in the region. This work was supported by the UK Natural Environmental Research Council under the Environmental Microbiology and Human Health Programme. This was then expanded to other rivers and estuaries in Wales and England usng funding from the water industry and the Food Standards Agency. Funding was then provided by DEFRA to establish a high throughput laboratory that became one of two national COVID-19 surveillance labs for wastewater-based epidemiology (WBE). We worked with the Environment Agency to deliver the English WBE programmes for COVID-19 suveillance. Since 2021 we have run the Wales WBE programme which samples wastewater from a national network of wastewater treatment plants, multiple times a week and analyses the samples for antimicrobial resistance genes, viruses, fungi and a range of chemicals. We also run the Wales component of the PathSafe project on the impact of hospital wastewater on the environment and the Welsh partner in the EU Horizon BlueAdapt project looking at AMR and virus flow in the coastal zone. In order to investigate the fate and behaviour of enteric viruses and AMR, the goals of the fieldwork are:
1. To evaluate techniques for virus recovery from environmental samples.
Representative wastewater, freshwater, marine water and sediment samples are regularly collected at wastewater treatment plants, river sites, estuaries, and coastal locations. These samples are being used in laboratory spiking experiments, where known concentrations of target viruses (e.g. SARS-CoV-2, Phi 6, Norovirus, Adenovirus, CrAssphage) are added. Using the spiked water and sediment samples the efficacy of different methods for the recovery of viruses from environmental matrixes can be evaluated. This has led to the development of standard protocols. We also using the same samples to look at the persistence of antimicrobial resistance genes and mobile genetic elements.
2. To estimate the impact of wastewater treatment plants on viral loads and their movements.
We have been studying the rate of decay of viruses and pathogenic bacteria as wastewater passes through the sewage network to the treatment plant and then its decay during wastewater treatments. This uses both RT-qPCR and infectivity assays to estimate the viability of viruses and their rate of discharge to the wider environment. This work has involved tracing the fate of pathogen surrogates (e.g. Phi6, PMMoV) as well as SARS-CoV-2 and different variants.
3. To explore viral movements, focusing on their potential to reach shellfish beds, recreational waters and beaches.
Regular sampling of surface water, wastewater, sediment and shellfish is being undertaken in rivers, estuaries and the major wastewater treatment plants in England and Wales. Viral concentrations in the collected samples are then determined by RT-qPCR and dd-PCR. These samples are also subjected to viral metagenomics and infectivity studies. Regular sampling allows us to discover the seasonal and spatial viral dynamics and results will be used for modelling viral transport and creating risk maps for improved risk assessment. It will also allow us to measure disease incidence at the community level.
4. Evaluation of the viral diversity and how this evolves over time.
We use an Illumina NextSeq and Oxford Nanopore MinION and GridION platform to sequence the viruses in our samples. This has been used to detect the emergence of new variants of SARS-CoV-2 and is now being used to explore the diversity of other viruses.
5. Evaluation of the usefulness of in situ samplers to explore temporal viral dynamics.
At sampling sites where the target viruses are present the following samplers are being deployed:
- Conventional automated sample collection system usually used for the nutrients and coliform bacteria investigations.
- Passive samplers traditionally used to evaluate chemical contamination.
- Novel passive samplers using media suitable for the enrichment of viruses.
These tools are being used to study temporal changes in the sewer network (e.g. near-source monitoring) and to estimate diurnal discharge patterns from wastewater treatment plants and during tidal cycles.