Our group focuses on developing a quantitative understanding of the tempo and mode of pathogen evolution, particularly in viruses with pandemic potential. As George Simpson put it in 1944, “tempo” refers to the pace of evolution—how it speeds up or slows down over time—while “mode” relates to the patterns and processes behind evolution, of which tempo is only one part. Understanding both is essential for tracing the evolutionary dynamics of pathogens and piecing together their natural history.
We bring together pathogen evolution and ecology, phylogenetics, population genetics theory, and AI-assisted protein structure prediction to create new tools and insights for reconstructing pathogen outbreaks, tracing their origins in non-human reservoirs, and evaluating their potential to cause new epidemics or pandemics. Our research advances our understanding of pathogen evolutionary history, with direct public health implications—enabling us to assess the risk of pathogen spillovers into humans, accurately determine the timing of outbreaks, identify key factors influencing pathogen evolutionary dynamics, such as emergence of drug-resistant and immune escape mutations, and connect genetic change to protein structure, function, and immune recognition.
Learn more about our team, see our publications, and explore our ongoing research projects. Explore current opportunities and ways to join us!
Postdoctoral Research Associate
My main research interests lie in characterising and quantifying the factors influencing evolutionary rates, transmission dynamics of pathogens, and host-dependent variation in molecular evolutionary dynamics.
Recognised Student
I investigate the early evolutionary dynamics of SARS-CoV-2. My research focuses on how molecular evolutionary rates vary over time and across lineages to improve the robustness of evolutionary timeline inference.
DPhil Student
My project focuses on host-pathogen interactions using bioinformatics, statistics, and genomics to elucidate new trends, clinical associations, and genomic footprints.
DPhil Student
I develop and benchmark molecular evolutionary models of substitution and clock rates to quantify how evolutionary rates vary over time and across hosts.
DPhil Student
I study how SARS-CoV-2 evolves and interacts with the human host using statistical and evolutionary approaches. By integrating host and viral genomic data, my work explores why disease outcomes vary between individuals and how combinations of mutations drive major evolutionary shifts.
DPhil Student
I integrate viral genomic data, molecular phylogenetics, molecular-clock models, and protein structural analysis to investigate how pathogens evolve, emerge, and adapt across different timescales.
Our goal is to develop a quantitative framework to understand how both methodological factors (such as the choice of sequence evolution model, sampling frequency, and duration) and biological factors (like population size, host characteristics, strength of selection, and mutation and recombination rates) impact inferences of molecular clock rates. These factors are critical in shaping our estimates of pathogen evolutionary histories. We analyse genomic sequence data from pandemic and epidemic viruses, including SARS-CoV-2, influenza A virus, and HIV, alongside other animal and plant pathogens. In parallel, we simulate populations under various evolutionary forces and sampling strategies to investigate how these forces impact molecular dating estimations over time.
The emergence of SARS-CoV-2 has underscored the urgent need to understand how zoonotic viruses evolve across different hosts and over time. These viruses typically originate in animal reservoirs, cross species barriers, and then adapt to new hosts, such as humans. Accurately estimating viral evolutionary rates is crucial for understanding these processes and reconstructing their natural history. A key observation during the early stages of the COVID-19 pandemic was the elevated evolutionary rate of SARS-CoV-2 compared to related coronaviruses in bats, along with the rapid evolution of highly divergent variants like Alpha and Omicron lineages, including BA.1/BA.2 and JN.1. Persistent infections may provide opportunities for accelerated evolution, raising important questions about the pace and mechanisms of viral evolution, particularly in viruses with pandemic potential, over time and across hosts.
Our research aims to tackle these questions by investigating the sources of viral evolutionary rate variation in both humans and animal hosts. We seek to evaluate whether the emergence of novel viral variants in humans is driven by periods of accelerated evolution. By analysing evolutionary signatures of rapid mutation accumulation in newly emergent pandemic viruses, we are developing a quantitative framework for inferring evolutionary rates from a mechanistic evolutionary perspective. Ultimately, this work will provide valuable insights into the dynamics that drive zoonotic viruses, the emergence of variants capable of crossing species barriers, and the factors contributing to the generation of novel variants with higher fitness advantages in humans.
We are extending this work by connecting viral sequence evolution with protein structure and antigenic data. AI-assisted structure prediction and structural phylogenetics can help reveal distant viral relationships when sequence similarity has eroded, while structure-aware models help us investigate how mutations affect protein stability, receptor binding, and immune escape. We assess these predictions alongside phylogenetic and experimental evidence. Read our reviews on AI and deep viral evolution and linking sites, structure, and serology.
We want to put together our understanding of pathogen evolutionary dynamics and the factors that influence evolutionary rate estimates to address critical questions in public health. This includes accurately estimating epidemic onset dates over short evolutionary timescales (a few years to decades) and determining the origin of pathogens in animal reservoirs over much longer periods (thousands to millions of years). For shorter timescales, our insights help improve estimates of pathogen origin dates, viral growth rates, and reproduction numbers, as well as the emergence of new viral lineages—especially in regions where limited sequencing data increases uncertainties around the spread and evolution of viruses. On longer timescales, our estimates provide a clearer picture of how long humans have been exposed to specific pathogens, how frequently these pathogens have caused disease outbreaks, and their potential to trigger future epidemics and pandemics.
Our preparedness research also examines vaccine equity: how financing, procurement, allocation, and delivery can be planned before an emergency so that vaccines reach populations at greatest risk. Our UNU-INWEH policy brief and vaccine-readiness paper set out an equity-by-design approach, supported by genomic surveillance, transparent data sharing, and stronger delivery systems.
You can find an up-to-date and complete list of publications on Google Scholar. A selection of papers in each of our research areas are listed below:
We’re delighted to welcome Shixuan (Rocky) Peng to the group as we begin Michaelmas term.
Javier joined our group for a six-month Master’s project as part of the European Master Programme in Evolutionary Biology (MEME).
A few highlights from Freya and Javier presenting their works.
We are always keen to hear from dedicated and motivated researchers. If you are interested in joining us as an MBiol or DPhil student, or as a postdoctoral researcher, please get in touch with Mahan at mahan.ghafari@biology.ox.ac.uk for further information and upcoming positions.
Our group welcomes people of all ethnicities, religions, nationalities, socio-economic backgrounds, gender identities, sexual orientations, ages, and abilities. We are committed to promoting equity and inclusion both within our group and in the broader community.
PhD with Spyros Lytras — Institut Pasteur PPU: Viral ANTigen evolution Across Genomic and Evolutionary scales (VANTAGE; project 467), co-supervised by Spyros Lytras and Mahan Ghafari. The project explores deep evolutionary relationships and structural conservation in viral antigen proteins. Please apply by 14 November 2026, as requested in the project announcement; applications are reviewed on a rolling basis. See the programme information and project announcement.
DPhil with Miles Carroll — PSI, University of Oxford: Unravelling the true incidence of Lassa fever virus in West Africa (project 1738), with Miles Carroll and Mahan Ghafari. Combining serology, virology, phylogenetics, and evolutionary analysis, the project investigates cross-reactivity with related arenaviruses to help clarify Lassa fever burden, focusing on Guinea and Liberia.
MBiol students: We offer several Year 4 projects in the Microbiology and Infectious Disease section, focused on molecular evolution and epidemiology of viral pathogens.
These previous announcements are retained for reference. For current availability, please contact Mahan.
Postdoctoral researchers: We advertised a postdoc position in our group to study how pathogens evolve—across hosts, over time, and through molecular and structural change. Learn more about the role here .
DPhil students: We advertised a DPhil project through the NDM DPhil in Clinical Medicine, on "Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness and targeted interventions".
DPhil students: We advertised a DPhil project through the DPhil in Biology programme, on "Investigating sources of evolutionary rate variation in viruses with pandemic potential over time and across different hosts".
We offered a UNIQ+ project as part of the University's flagship graduate access programme.
Address: Life & Mind Building, Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3EL