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.
I head a multi-pathogen sequencing laboratory 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, I 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.
Twohig KA. et al, (2022), The Lancet Infectious Diseases, 22, 35 - 42
Lin G-L. et al, (2021), Nature Communications, 12
Abueg M. et al, (2021), npj Digital Medicine, 4
Vieira VA. et al, (2021), Journal of virology
Ratcliff J. et al, (2021)