FULLY FUNDED - The epidemiological underpinnings of viral spillover risk from bats

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Emerging infectious diseases are one of the greatest threats to global human health, and most come from wildlife. Bats are a key source of viruses that cause severe disease in humans, including SARS-CoV-2 (the causative agent of COVID-19), ebolaviruses, and the almost invariably lethal lyssaviruses. While much recent research has catalogued virus diversity in bats, we understand very little about how viruses are maintained within bat populations or how human actions, which change bat behaviour, alter viral emergence risk. This PhD is part of a NIH-funded project which focuses on three important and tractable host-virus systems: coronaviruses, rabies virus, and Bombali ebolavirus in their wild bat hosts in Taita Hills, Kenya and Orange Walk, Belize. The project will use a combination of longitudinal monitoring, bat behaviour studies, and field experiments to examine how virus diversity, shedding dynamics and bat use of anthropogenic structures shape virus exposure risk for humans and domestic animals. To assess whether human disturbance of bats triggers the shedding of latent viruses, we will further use proteomic and metagenomic approaches to characterize stress, immunological responses and shifts in viral diversity following experimental displacement of bats from their roosts. These studies comprise an unusually comprehensive investigation into the dynamics of viruses in wild bat populations, representing a critical advance towards evidence-based risk evaluation and prevention.

The PhD student will be responsible for the components of the project related to metagenomic sequencing, machine learning and data-driven epidemiological modelling. They should be eager to learn laboratory and computational skills within the field of infectious disease ecology and evolution.

The specific aims of this PhD are to:

1.    Characterize the diversity and zoonotic potential of viruses circulating in wild caught bats from Belize and Kenya using shotgun metagenomic sequencing

2.    Develop competing epidemiological models of the within and between host dynamics of three key viruses: Bombali ebolavirus, coronavirus, and rabies virus

3.    Evaluate the impacts of experimental bat displacement on viral community composition

This PhD project will be primarily based at the School of Biodiversity, One Health and Veterinary Medicine at the University of Glasgow under the guidance of Prof. Daniel Streicker and Dr Mafalda Viana. The larger project involves a team of experts including Dr Dan Becker (University of Oklahoma, USA), Dr Tamika Lunn (University of Georgia, USA) and Dr Kris Forbes (University of Arkansas, USA) and their associated teams, with whom the successful applicant would regularly interact

The applicant will ideally have some quantitative experience (i.e., working with R and basic statistics) and should be familiar with core concepts in the ecology and evolution of infectious diseases, including wildlife-associated zoonoses. The applicant should be very comfortable with basic molecular techniques (DNA/RNA extraction, PCR) and ideally would have some experience with high throughput sequencing. Experience carrying out field work in remote conditions or with wildlife is desirable, but not required.

Student training objectives

Develop expertise in the design, laboratory processing and analysis of metagenomic sequencing experiments.

Fit Bayesian state space models to field-collected molecular and serological data.

Apply pre-trained machine learning algorithms to predict zoonotic potential from viral genome sequences

Opportunities to participate in capture and sampling of wild bats in Belize and/or Kenya

Gain experience in international collaborative research

More information about the supervisory team can be found at the following websites:

• https://streickerlab.com/
• https://mafaldaviana.wordpress.com/
• https://www.gla.ac.uk/schools/bohvm/staff/laurabergner/

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