As evidenced by the current Covid-19 pandemic, the human population remains highly susceptible to zoonotic viral threats. Novel respiratory-borne, viral pathogens are of particular concern, given their pathogenic potential, ease of transmission, and lack of effective “off-the-shelf” pharmaceutical interventions. Influenza A virus (IAV) exemplifies such a zoonotic pandemic threat, and over the last ~100 years there have been several IAV pandemics, the latest in 2009. While capable of infecting a wide range of mammals, the natural reservoir for most IAVs is wild birds like ducks and gulls. Widespread spill-over of highly-pathogenic “H5” strains into domestic avian species and wildlife increases the opportunities for zoonosis and facilitates mammalian adaptation, onward spread and pandemic potential. Furthermore, we are currently in an unprecedented situation globally with the emergence of novel H5 strains in wild birds, incursions into domestic animals, and humans with signs of mammalian adaptation. As such, there is a pressing need to develop “one health” environmentally focused solutions to this real-world challenge.

Environmental monitoring of IAV presents a great opportunity to track the virus, as well as identify ecological drivers of zoonosis facilitating understanding and risk assessment of threats. Of note, relying on direct human and animal clinical sampling is challenging given its resource intensity, health and safety risks, and its poor lead time relative to zoonosis. Typically, routine environmental sampling for IAV is not carried out. Monitoring of environmental wastewater samples can detect viruses circulating within the human population before clinical cases are detected and has potential for monitoring animal pathogens.

Since 2020, the QUB team have been using wastewater-based epidemiology (WBE) to track and understand the zoonotic SARS-CoV-2 spread in humans and have extended this out to novel viral disease threats (adenovirus; [Reyne et al., Sc Total Environ. 2023]) as well as endemic respiratory viruses like RSV and EVD68. Since early 2022, we have applied WBE to IAV and have developed tools to track IAV using PCR and nanopore-based whole genome sequencing in environmental samples, which has demonstrated the ability to track not just human IAV but also avian IAV from wildlife.

Aims and Objectives: The successful student will join the QUB labs of Dr Connor Bamford and the wastewater surveillance team led by Prof. John McGrath. The aim of this project is to further develop a WBE environmental surveillance platform for IAVs to track, understand, and assess their zoonotic risk working with partners in London and Cardiff. The expected outcome will help local stakeholder (AFBI) and be applied globally as this is a global problem.

The student will approach this project targeting 3 main objectives:

1. perform longitudinal one-health surveillance for IAV across NI using established PCR and WGS protocols and identify environmental/spatial correlates of IAV detection (QUB, AFBI). IAV will be monitored at sites across NI and Geographical Information System (GIS) mapping implemented to create a dashboard accessible to stakeholder (AFBI) and end-users (e.g. farmers). We have developed similar resources for SARS-CoV-2. [Y1-3.5];

2. Develop and optimise novel molecular and bioinformatic approaches (including cutting-edge phylodynamic methods to inform ecological studies of IAV transmission dynamics across space and time) for pan-IAV and variant-specific detection and tracking PCR and whole-genome sequencing (QUB, LSHTM) [Y1 & 2];

3. Integrate and understand environmental stability and host-cell interactions of detected IAVs to risk assess variants and prioritise geographical hotspots for future investigation (QUB, Cardiff, AFBI) [Y2 & 3].

The student and team (led by Bamford) will use the generated knowledge to actively engage with and advise interested parties to alert them to IAV threats and limit spillover.

Duration: 3.5 years full-time (or up to 7 years part-time)

Start Date: October 2023