22-EEID US-UK Collab: Integrating metaviromics with epidemiological dynamics: understanding rodent virus transmission in the Anthropocene
Lead Research Organisation:
Royal Veterinary College
Department Name: Pathobiology and Population Sciences
Abstract
Most emerging infectious diseases affecting humans, including AIDS, influenza, and COVID-19, are caused by RNA viruses originating from non-human animals. In recent years, such 'zoonotic' viral diseases have become more common and widespread, a pattern frequently attributed to increasing environmental change. Notably, escalating human activity has destroyed and disrupted wild animal habitats by converting natural landscapes into agricultural farmlands and urban environments. As a result, we have drastically altered wild animal communities and how viruses circulate within these communities while simultaneously increasing our exposure to new animal viruses by eliminating historical ecological barriers separating species. Temporal changes in the environment, such as seasonal variation or climate change, can also alter pathogen prevalence in wild animal populations and influence zoonotic risk.
Despite significant research on viral zoonoses, actionable, real-world predictions of virus spillover risk remain elusive. A critical barrier to preventing and controlling future viral zoonoses is a lack of basic knowledge about how physical and temporal differences in the environment impact virus transmission within wild animal populations and how changes in viral transmission and community composition translate to human risk.
Attaining a predictive understanding of the dynamics of zoonoses within their animal reservoirs is a precondition to anticipate emergence or devise interventions that prevent emergence. However, financial and logistical challenges in studying high-risk viruses in wild animals - from the need for regular monitoring of individuals to the costly biosafety precautions involved - currently impede such understanding in most wildlife disease systems.
We will address these challenges by focusing on wild rodents, which are important viral reservoirs globally, responsible for more zoonoses than any other mammalian order, and represent well-studied and tractable systems for understanding the environmental impact on zoonotic virus transmission. Many rodents live in close proximity to human populations and are highly responsive to environmental change, both in their population dynamics and via behavioural changes that increase contact with humans. However, despite this circumstantial evidence, the underlying ecological mechanisms driving virus transmission within wild rodent populations remain hypothetical and, importantly, are far from predictive. This project will investigate how viruses circulate in wild rodents using established field studies in England and Uganda, which monitor wild rodent communities over time and space:
1) To tackle the practical challenges of studying viral transmission, we will develop new tools to infer epidemiological dynamics and zoonotic risk from increasingly accessible and low-cost host virome data. This flexible approach will allow rapid discovery and monitoring of zoonotic viruses by enabling epidemiological inferences from cross-sectional samples and guidance for appropriate sampling strategies to interpret metaviromic data in new host systems.
2) Using a long-term capture-mark-recapture wild study in Oxfordshire, UK, we will determine how seasonal environmental change influences rodent viral communities.
3) We will use field sites along a gradient of land cover in Uganda to understand how physical environmental change influences the risk of zoonotics in rodent communities. Specifically, we will identify local and landscape drivers of zoonotic hazards and how humans change behaviour to affect zoonotic risk across this gradient.
Together, this research will substantially improve our understanding of viral pathogens within key reservoir hosts and identify important environmental drivers that increase zoonotic risk.
Despite significant research on viral zoonoses, actionable, real-world predictions of virus spillover risk remain elusive. A critical barrier to preventing and controlling future viral zoonoses is a lack of basic knowledge about how physical and temporal differences in the environment impact virus transmission within wild animal populations and how changes in viral transmission and community composition translate to human risk.
Attaining a predictive understanding of the dynamics of zoonoses within their animal reservoirs is a precondition to anticipate emergence or devise interventions that prevent emergence. However, financial and logistical challenges in studying high-risk viruses in wild animals - from the need for regular monitoring of individuals to the costly biosafety precautions involved - currently impede such understanding in most wildlife disease systems.
We will address these challenges by focusing on wild rodents, which are important viral reservoirs globally, responsible for more zoonoses than any other mammalian order, and represent well-studied and tractable systems for understanding the environmental impact on zoonotic virus transmission. Many rodents live in close proximity to human populations and are highly responsive to environmental change, both in their population dynamics and via behavioural changes that increase contact with humans. However, despite this circumstantial evidence, the underlying ecological mechanisms driving virus transmission within wild rodent populations remain hypothetical and, importantly, are far from predictive. This project will investigate how viruses circulate in wild rodents using established field studies in England and Uganda, which monitor wild rodent communities over time and space:
1) To tackle the practical challenges of studying viral transmission, we will develop new tools to infer epidemiological dynamics and zoonotic risk from increasingly accessible and low-cost host virome data. This flexible approach will allow rapid discovery and monitoring of zoonotic viruses by enabling epidemiological inferences from cross-sectional samples and guidance for appropriate sampling strategies to interpret metaviromic data in new host systems.
2) Using a long-term capture-mark-recapture wild study in Oxfordshire, UK, we will determine how seasonal environmental change influences rodent viral communities.
3) We will use field sites along a gradient of land cover in Uganda to understand how physical environmental change influences the risk of zoonotics in rodent communities. Specifically, we will identify local and landscape drivers of zoonotic hazards and how humans change behaviour to affect zoonotic risk across this gradient.
Together, this research will substantially improve our understanding of viral pathogens within key reservoir hosts and identify important environmental drivers that increase zoonotic risk.
Technical Summary
Decreasing costs and increasing efficiency of metagenomic sequencing have rapidly expanded our knowledge of global virus diversity, particularly in well-known zoonotic reservoir species, such as rodents and bats. However, despite these advances, we cannot leverage this knowledge to shed light on virus transmission within reservoir populations -consequently, our ability to evaluate where, whence, and which viruses present the highest zoonotic risk. There are two outstanding challenges to this knowledge gap. First, longitudinal and spatially representative sampling in viral metagenomic studies is extremely rare, with most studies representing a single snapshot in time and space, limiting their use in studying transmission dynamics. Second, we lack a framework linking the composition of the virus community and the underlying transmission dynamics in the reservoir to the zoonotic risk.
We will address these obstacles by capitalising on established, tractable wild rodent field studies across changing environments and advancing epidemiological theory by integrating metaviromic data with mechanistic models of virus transmission. Specifically, we will (i) develop, implement and validate a methodological framework to infer epidemiological dynamics and zoonotic hazards from cross-sectional metaviromic data, (ii) identify environmental and ecological drivers of rodent virus transmission and zoonotic hazards in seasonally varying habitats using real-time microclimate, social network, and population data, and (iii) Using an existing gradient of land cover, quantify how anthropogenic land-use change shapes host demography, virus diversity, and transmission dynamics.
With this multidisciplinary approach, this research will provide new insights into the dynamics of virus transmission in wild animals across space and time and help advance our understanding of zoonotic risk in a rapidly changing world.
We will address these obstacles by capitalising on established, tractable wild rodent field studies across changing environments and advancing epidemiological theory by integrating metaviromic data with mechanistic models of virus transmission. Specifically, we will (i) develop, implement and validate a methodological framework to infer epidemiological dynamics and zoonotic hazards from cross-sectional metaviromic data, (ii) identify environmental and ecological drivers of rodent virus transmission and zoonotic hazards in seasonally varying habitats using real-time microclimate, social network, and population data, and (iii) Using an existing gradient of land cover, quantify how anthropogenic land-use change shapes host demography, virus diversity, and transmission dynamics.
With this multidisciplinary approach, this research will provide new insights into the dynamics of virus transmission in wild animals across space and time and help advance our understanding of zoonotic risk in a rapidly changing world.
Organisations
- Royal Veterinary College (Lead Research Organisation)
- Medical Research Council (Co-funder)
- Duke-NUS Graduate Medical School (Collaboration)
- Uganda National Health Research Organisation (Collaboration)
- University College London (Collaboration)
- University of Antwerp (Collaboration)
- Natural History Museum (Collaboration)
Publications

Catalano S
(2024)
Pathogen genomics and One Health: A scoping review of current practices in zoonotic disease research
in IJID One Health

Pei S
(2024)
Anthropogenic land consolidation intensifies zoonotic host diversity loss and disease transmission in human habitats
in Nature Ecology & Evolution
Description | Developing and deploying methods to measure rodent movement to inform zoonotic hazard |
Amount | £87,713 (GBP) |
Funding ID | BB/Y514251/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 06/2024 |
Description | Glasgow Early Career Mobility Scheme 2024-2025 |
Amount | £4,932 (GBP) |
Organisation | University of Glasgow |
Sector | Academic/University |
Country | United Kingdom |
Start | 11/2024 |
End | 07/2025 |
Description | Collaborative One Health Research Initiative on Epidemics (COHRIE) |
Organisation | Uganda National Health Research Organisation |
Country | Uganda |
Sector | Public |
PI Contribution | We hosted COHRIE members in the field and trained them in capture-mark recapture in January 2025 |
Collaborator Contribution | COHRIE members met with Glasgow and Vector Control Division in August 2024 in Entebbe for knowledge exchange. |
Impact | Currently seeking funding to support more field activities and personnel |
Start Year | 2024 |
Description | Rodent Metaviromics Consoritium |
Organisation | Duke-NUS Graduate Medical School |
Department | Microbiology Duke-NUS |
Country | United States |
Sector | Academic/University |
PI Contribution | We set up the network in September 2024 between multiple groups using similar genomic approaches to characterise small mammal viromes and understand environmental and ecological drivers of rodent virus spillover. The aim of this network is to foster knowledge exchange between research groups working in complementary areas, for example to discussing and getting feedback on preliminary findings. Our research team presented their research on understanding relationship between metaviromic and viral load data. |
Collaborator Contribution | The other partners provided feedback on the first meeting, and Sophie Gryseels (University of Antwerp) will present her team's work on using metaviromics for virus surveillance and understanding virus ecology. |
Impact | Knowledge exchange and intellectual input on research related to metaviromics and rodent virus ecology |
Start Year | 2024 |
Description | Rodent Metaviromics Consoritium |
Organisation | Natural History Museum |
Department | Parasites and Vectors |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | We set up the network in September 2024 between multiple groups using similar genomic approaches to characterise small mammal viromes and understand environmental and ecological drivers of rodent virus spillover. The aim of this network is to foster knowledge exchange between research groups working in complementary areas, for example to discussing and getting feedback on preliminary findings. Our research team presented their research on understanding relationship between metaviromic and viral load data. |
Collaborator Contribution | The other partners provided feedback on the first meeting, and Sophie Gryseels (University of Antwerp) will present her team's work on using metaviromics for virus surveillance and understanding virus ecology. |
Impact | Knowledge exchange and intellectual input on research related to metaviromics and rodent virus ecology |
Start Year | 2024 |
Description | Rodent Metaviromics Consoritium |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We set up the network in September 2024 between multiple groups using similar genomic approaches to characterise small mammal viromes and understand environmental and ecological drivers of rodent virus spillover. The aim of this network is to foster knowledge exchange between research groups working in complementary areas, for example to discussing and getting feedback on preliminary findings. Our research team presented their research on understanding relationship between metaviromic and viral load data. |
Collaborator Contribution | The other partners provided feedback on the first meeting, and Sophie Gryseels (University of Antwerp) will present her team's work on using metaviromics for virus surveillance and understanding virus ecology. |
Impact | Knowledge exchange and intellectual input on research related to metaviromics and rodent virus ecology |
Start Year | 2024 |
Description | Rodent Metaviromics Consoritium |
Organisation | University of Antwerp |
Country | Belgium |
Sector | Academic/University |
PI Contribution | We set up the network in September 2024 between multiple groups using similar genomic approaches to characterise small mammal viromes and understand environmental and ecological drivers of rodent virus spillover. The aim of this network is to foster knowledge exchange between research groups working in complementary areas, for example to discussing and getting feedback on preliminary findings. Our research team presented their research on understanding relationship between metaviromic and viral load data. |
Collaborator Contribution | The other partners provided feedback on the first meeting, and Sophie Gryseels (University of Antwerp) will present her team's work on using metaviromics for virus surveillance and understanding virus ecology. |
Impact | Knowledge exchange and intellectual input on research related to metaviromics and rodent virus ecology |
Start Year | 2024 |
Description | University of Antwerp |
Organisation | University of Antwerp |
Country | Belgium |
Sector | Academic/University |
PI Contribution | We extracted, preparred libraries and sequenced DNA from Mastomys samples from Uganda and Tanzania |
Collaborator Contribution | Provided samples and datasets for Tanzanian Mastomys |
Impact | Currently analyzing sequence data |
Start Year | 2024 |
Description | Talk (Abingdon) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Gave a talk on the Wytham rodent project to the Abingdon Naturalists Society |
Year(s) Of Engagement Activity | 2024 |