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.
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.
Kläser K. et al, (2022), Scientific Reports, 12
Aggarwal D. et al, (2022), Nature Communications, 13
Nickbakhsh S. et al, (2022), Scientific Reports, 12
Christensen KT. et al, (2022), J Clin Virol, 155
Eales O. et al, (2022), BMC Infect Dis, 22