Fieldwork

Our environmental surveillance activities began in 2010 with research on viral dynamics in the Conwy River and estuary, driven by local water quality concerns. This work, supported by the UK Natural Environment Research Council (NERC), was expanded to include rivers and estuaries across Wales and England, funded by the water industry and the Food Standards Agency. 

In 2020, we received funding from DEFRA to establish a high-throughput laboratory, which became one of two national COVID-19 surveillance labs for wastewater-based epidemiology (WBE). In partnership with the Environment Agency, we delivered the English WBE programs for COVID-19 surveillance. Since 2021, we’ve led the Wales WBE programme, monitoring wastewater from treatment plants nationwide multiple times a week, analysing samples for antimicrobial resistance (AMR) genes, viruses, fungi, and chemicals. 

We also run the Wales component of the PathSafe project, which investigates the impact of hospital wastewater on the environment, and the EU Horizon BlueAdapt project, focusing on AMR and viral movement in coastal zones. To understand the fate and behaviour of enteric viruses and AMR, our fieldwork objectives include: 

1. Evaluating Methods for Virus and AMR Recovery 

We regularly collect representative wastewater, freshwater, marine water, and sediment samples from treatment plants, rivers, estuaries, and coastal areas. These samples are used in laboratory experiments where known concentrations of target viruses (e.g., SARS-CoV-2, Norovirus, AMR-carrying bacteria) are added. This allows us to evaluate different recovery techniques, leading to the development of standardized protocols. We also assess the persistence of antimicrobial resistance genes and mobile genetic elements. 

2. Assessing the Impact of Wastewater Treatment Plants on Viral and AMR Loads 

We study how viruses and bacteria decay as wastewater moves through the sewage network and undergoes treatment. Using RT-qPCR and infectivity assays, we estimate the viability of viruses and their discharge into the environment. This includes tracking the fate of pathogen surrogates and SARS-CoV-2, as well as using fluorescent dye and probes to measure wastewater transit times through the sewershed.

3. Exploring Viral and AMR Movement in the Environment 

We regularly sample surface water, wastewater, sediment, and shellfish at rivers, estuaries, and major treatment plants across England and Wales. Using RT-qPCR and dd-PCR, we measure viral and AMR concentrations, followed by metagenomic and infectivity analyses to assess human exposure risks. These samples help us understand the seasonal and spatial dynamics of these organisms, and their results inform our viral and AMR transport models, and aid risk assessments for recreational waters, beaches, and shellfish beds. 

4. Evaluating Viral and AMR Diversity Over Time 

We use high-throughput sequencing tools (Illumina NextSeq, Oxford Nanopore MinION and GridION) to sequence viruses and analyse the abundance and diversity of antimicrobial resistance genes in our samples. During the COVID-19 pandemic, these techniques helped detect new SARS-CoV-2 variants and are now being used to track the diversity of other viruses. Our findings have been integral in informing government policies, such as those presented to Health Minister Eluned Morgan at the Wales COVID-19 Inquiry.

5. Analysing the Usefulness of In-Situ Samplers for Temporal Dynamics 

At selected sites, we deploy a range of samplers to monitor viral and AMR dynamics over time. These include: 

• Automated refrigerated sample collection systems for nutrient and coliform bacteria analysis. 

• Passive samplers for chemical contamination studies. 

• Novel passive samplers using media designed to enrich viruses and bacteria, providing integrated data over several days. 

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.