Pathogen Genomic Epidemiology

Phylodynamic and evolutionary modelling are a core focus of the Centre, where we focus on developing and optimising methods to enable the inference of epidemiological parameters from genomic data. We translate these insights into epidemiological models to maximise the public health impact of genomic data and forecast the response to new interventions, such as next generation vaccines, or to estimate evolutionary parameters linked with the emergence of viral disease outbreaks or antimicrobial resistance.

To better understand the broader impact of ecological changes on epidemic risk, we develop species-agnostic ecological -omics tool kits to improve multi-level surveillance across viral zoonoses, bacterial and fungal pathogens using metabarcoding and metagenomic pipelines.

The Centre conducts extensive research in the laboratory and the field using cutting-edge genomic technologies that address a wide range of globally policy-relevant questions. Our teams actively support knowledge exchange and capacity-strengthening initiatives across Latin America, Africa, Asia, and Europe, frequently engaging with national and international stakeholders. We also provide support to national agencies and laboratories across all implementation stages of genomic surveillance programmes.

Publication highlights

NR Faria, TA Mellan, C Whittaker et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 14-04-2021. DOI: https://doi.org/10.1126/science.abh2644

J Rhodes, A Abdolrasouli, K Dunne et al. Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment. Nature Microbiology, 25-04-2022. DOI: https://doi.org/10.1038/s41564-022-01091-2