Project Reference: TRG27-GEN-ND1

Project title: Global genomic viral surveillance with pandemic-scale phylodynamics

Project outline

Viral genomics is a transformative tool for epidemiology and public health. By comparing viral genomes from different hosts we can reconstruct patterns of transmission and evolution with remarkable precision. During the COVID-19 pandemic, this enabled the identification of variants of concern and the reconstruction of viral spread within and between countries. Current computational methods are however not sufficiently scalable or robust to analyse the thousands to millions of viral genomes now available, leaving much of their potential unrealised.

Building on phylogenetic algorithms and models developed by the De Maio Lab, this project will address current methodological limitations, enabling the real-time, large-scale reconstruction and prediction of virus evolution and transmission, using adenovirus as an initial case study.

Methodology

  • Enable scalable reconstruction of pathogen recombination. We will extend pandemic-scale phylogenetic techniques (De Maio et al. 2023, 2025, 2026)  to infer mosaic ancestry arising from recombination within massive ancestral recombination graphs of up to millions of genomes.
  • Investigate the evolution and immune escape of adenoviruses. These viruses have high divergence and recombination rates, challenging existing phylogenetic approaches. We will analyse thousands of human and primate adenovirus genomes from outbreaks, community, and wildlife samples using the developed computational methods.
  • Maximise impact and community adoption. The PhD student will collaborate with leaders in the field to integrate methodological advances into widely used phylogenetic software packages (e.g. IQ-TREE), ensuring rapid dissemination and adoption by the wider community. 

This project will enable the study of pathogen recombination at unprecedented scale and accuracy.

Principal Supervisor

Dr Nicola De Maio

Email address: nd597@cam.ac.uk

Department / Partner Institute: Genetics

Website: https://bioinfotraining.bio.cam.ac.uk/staff/nicola-de-maio

BBSRC strategic theme

Transformative technologies