Identifying mechanisms driving spatiotemporal disease dynamics in converted landscapes
Lead Research Organisation:
University of Glasgow
Department Name: College of Medical, Veterinary, Life Sci
Abstract
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.
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.
Organisations
- University of Glasgow (Lead Research Organisation)
- Uganda National Health Research Organisation (Collaboration)
- University of Antwerp (Collaboration)
- University of Stirling (Collaboration)
- Ministry of Health, Uganda (Collaboration)
- Smithsonian Institution (Collaboration)
- Cary Institute of Ecosystem Studies (Collaboration)
Publications
Catalano S
(2024)
Pathogen genomics and One Health: A scoping review of current practices in zoonotic disease research
in IJID One Health
Plowright R
(2024)
Ecological countermeasures to prevent pathogen spillover and subsequent pandemics
in Nature Communications
Raghwani J
(2023)
Seasonal dynamics of the wild rodent faecal virome.
in Molecular ecology
| Description | District level dissemination |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Description | Policy Synthesis |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Contribution to new or improved professional practice |
| URL | https://pdf.usaid.gov/pdf_docs/PA00Z5GN.pdf |
| Description | IAPETUS2: Delivering excellence in PhD training across the spectrum of environmental science |
| Amount | £11,185,566 (GBP) |
| Funding ID | NE/S007431/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 09/2028 |
| Description | International Institutional Awards Tranche 1 Glasgow |
| Amount | £270,830 (GBP) |
| Funding ID | BB/Y514251/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 06/2024 |
| 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 | The Blodwen Lloyd Binns Bequest |
| Amount | £1,960 (GBP) |
| Organisation | Glasgow Natural History Society |
| Sector | Learned Society |
| Country | United Kingdom |
| Start | 11/2024 |
| End | 11/2025 |
| 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 | Component model iterations for inputs into a multi-scale model describing the effect of host conditions on Hendra virus shedding, eastern Australia, 2008-2019 |
| Description | The data provided here are model iteration objects and rasters needed to run the multi-scale modelling process and predict how the host condition affects probability of Hendra virus shedding. The dataset contains predictions of three proxies for host conditions (including food shortage, rehabilitation admissions and formation of a new roost) across eastern Australia in 2008-2019. The Roost Species Distribution Model (SDM) has predictions of roost suitability. These are monthly, spatially explicit predictions of particular conditions or probability of roost occupations. The model objects are iterations of models that were initially trained on data held in figshare (https://figshare.com/s/ddb5a1584609b20f6596). These data objects are linked with code provided at https://github.com/hanlab-ecol/BatOneHealth to be able to run the models and analyses. This includes comparisons of virus predictions of seven different multiscale model structures to observed Hendra virus shedding in field surveys. The purpose of this study was to determine if quantifying and incorporating host condition into epidemiological models improves predictions of virus shedding in space and time. The data objects relate to the 1,000 iterations run of this process to better able to account for uncertainty. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | The modelling process is applicable to other disease systems and can be used by other researchers to evaluate the multi-scale impacts on disease outcomes. |
| 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: https://github.com/jnarag/Wytham-rodent-virome |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.612jm645s |
| Description | COHRIE, https://www.uvri.go.ug/projects/cohrie-ug |
| Organisation | Uganda National Health Research Organisation |
| Country | Uganda |
| Sector | Public |
| PI Contribution | We provided training for capture-mark recapture for PhD and Masters students in February 2025 |
| Collaborator Contribution | Provide expert opinion and knowledge exchange in August 2024. Ongoing contact to apply for new grants |
| Impact | Ongoing training |
| Start Year | 2024 |
| 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 | Smithsonian-ILRI |
| Organisation | Smithsonian Institution |
| Country | United States |
| Sector | Public |
| PI Contribution | Sharing SOPs and study designs. Supported application for knowledge exchange visit |
| Collaborator Contribution | Hosting a PhD student for field activities |
| Impact | £5000 Travel grant to PhD student for knowledge exchange |
| Start Year | 2023 |
| 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 |