Identifying mechanisms driving spatiotemporal disease dynamics in converted landscapes

Lead Research Organisation: University of Glasgow
Department Name: College of Medical, Veterinary, Life Sci


Around the globe, landscapes are being converted from natural habitats into a mosaic of agriculture and other human-dominated landscapes. These shifts in land use impact plant and animal species and usually lead to declines in biodiversity compared to undisturbed landscapes. Concomitant to this decline in biodiversity is a change in abundance and diversity of the pathogens that infect the animals and plants present. Transmission of a pathogen can decline or increase due to changes in availability of suitable hosts, changes in the abiotic environment, altered movement of hosts or some other impact of changing landscapes. It is timely and critical to quantify changes in pathogen burden, as there is an ongoing increase in frequency and scale of landscape conversion globally. We currently lack the ability to accurately predict the response of a particular pathogen in a landscape undergoing conversion.

In this project I will use a combination of approaches to disentangle factors affecting pathogens in changing landscapes: 1) I will establish a longitudinal survey of small mammals at sites that have been converted from natural forests to smallholder agricultural fields from 1 to 15 years prior. I will then examine how the small mammal abundance and diversity changes across time and determine how that impacts prevalence of a parasitic nematode. 2) I will investigate how the types of environments and distribution of different habitats across the regional landscape affect movement of hosts and pathogens between populations. 3) I will develop models and analyze a global database to investigate which underlying host, parasite, and environmental traits are important for predicting short-term responses to land conversion. This approach is expected to lead to an improved understanding of how pathogen transmission is altered in dynamic landscapes and provide a better ability to predict how transmission may change in the future, particularly with different anthropogenic induced land use change.


10 25 50
Description Policy Synthesis
Geographic Reach Multiple continents/international 
Policy Influence Type Contribution to new or improved professional practice
Description LOreal-Unesco For Women in Science
Amount £15,000 (GBP)
Organisation United Nations Educational, Scientific and Cultural Organization 
Sector Academic/University
Country France
Start 06/2022 
End 07/2023
Description NEOF Pilot Genomics Competition
Amount £7,906 (GBP)
Funding ID NEOF No: 1486 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 08/2022 
End 01/2023
Description RESTOREID: Restoring Ecosystems to Stop the Threat of Re-emerging Infectious Diseases
Amount £132,259 (GBP)
Funding ID Horizon Europe Grant - covered by UKRI Guarantee 
Organisation United Kingdom Research and Innovation 
Sector Public
Country United Kingdom
Start 01/2024 
End 12/2027
Description US-UK Collab: Integrating metaviromics with epidemiological dynamics: understanding virus transmission in the Anthropocene
Amount £1,570,854 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2023 
End 04/2028
Title Seasonal dynamics of the wild rodent faecal virome 
Description Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact The raw sequencing data generated in this study have been deposited in the Sequence Read Archive (BioProject ID: PRJNA803204) under accession nos.: SRX14033113-SRX14033125. Assembled picornavirus genomes have been deposited in GenBank under accession nos.: ON136174-ON136181. Data from the bioinformatics pipeline and metadata associated with this research are available on Dryad at doi:10.5061/dryad.612jm645s, while associated code is available via Github: 
Description Cary Institute 
Organisation Cary Institute of Ecosystem Studies
Country United States 
Sector Charity/Non Profit 
PI Contribution I provide expertise in genomic datasets, in particular those relevant to rodent-borne diseases.
Collaborator Contribution Partners provide expertise in machine learning.
Impact We have submitted an NSF-BBSRC UK-US Ecology and Evolution of Infectious Disease Grant- the outcome is still pending.
Start Year 2021
Description Universiteit Antwerpen 
Organisation University of Antwerp
Country Belgium 
Sector Academic/University 
PI Contribution Our group provides UK data collection and analysis in restored landscapes to explore how woodland creation impacts disease
Collaborator Contribution University of Antwerp has led organization of project meetings
Impact We collaborated on a joint research proposal for Horizon Europe to examine how spatiotemporal changes in restoration affect disease dynamics
Start Year 2023
Description University of Stirling 
Organisation University of Stirling
Department Biological and Environmental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution I provide pathogen diagnostic services and sample study design for extending the conservation research into disease ecology research
Collaborator Contribution The University of Stirling has established a landscape-level experiment (WReN) by identifying and gaining access to over 80 woodlands in Scotland that vary in age and connectivity to other woodlands. We are using these sites and metadata to understand how woodland creation impacts rodent populations and the diseases they carry
Impact We applied for and successfully recruited an IAPETUS2 Phd student who will continue research on rodents and their pathogens at WrEN sites.
Start Year 2022
Description Vector Control Division, Ministry of Health, Uganda 
Organisation Ministry of Health, Uganda
Department Vector Control Division
Country Uganda 
Sector Public 
PI Contribution Trained technicians in field and laboratory techniques. Provide advice and expertise on epidemiological modelling and zoonoses.
Collaborator Contribution Collaborators provide field support and translate research findings to local, regional and national stakeholders.
Impact Prior to my fellowship, we had several joint publications. New outputs are forthcoming.
Start Year 2016