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David Bonsall

Group Leader and PI

  • Sequencing and Sequencing Methods
  • BDI - Pathogen Dynamics - Wellcome Centre for Human Genetics


I am a Clinical Lecturer in Infectious Diseases and Microbiology (Oxford University Hospital NHS Foundation Trust) and Associate Group Leader based primarily at the Wellcome Centre for Human Genetics.

Research interests:

We are a multi-pathogen sequencing lab that has delivered bespoke sequencing methods and large NGS datasets to a  range of studies and consortia including PANGEA, BEEHIVE, HIV Prevention and Trials Network (HPTN), COG-UK, (UK) Office of National Statistics COVID-19 Prevalence Survey and the Oxford Vaccine Group (Oxford, AstraZeneca vaccine).

We develop pathogen-genotyping and sequencing solutions for a range of technology platforms, and have a track-record of developing methods around the question. 

  • Long-read protocols (transmission and long-range haplotyping)
  • Bait enrichment (diverse pathogens)
  • Multi-pathogen bait enrichment (viromes, microbiomes) 
  • Rapid genotyping protocols (diagnostics).
  • High-thoughput, low-cost surveillance (COVID surveillance)
  • Portable, scalable sequencing (AMPHEUS)  

Additionally, we collaborate on a variety of projects to develop, test-simulate and evaluate digital health interventions for infectious diseases

  • Exposure Notification Apps (Contact Tracing Apps)
  • Community Access Diagnostics
  • Public engagement (@OxfordViromics) 


AMPHEUS: Analytical Microbiology for Precision Health and Epidemiology – A Unified Solution. AMPHEUS will establish scalable and portable, high-throughput sequencing laboratories in Sub-Saharan Africa. The project is funded by the Bill and Melinda Gates foundation and is a collaboration with Zambart (LSHTM and University of Zambia's School of Medicine). 

PopART Phylogenetics (HPTN 071-2): A Zambian phylogenetic study of HIV transmission and prevention. 

Oxford Viromics: An Oxford University pipeline for sequencing and studying clinically relevant viral pathogens.