Around 20% of people infected with HIV are infected with more than 1 genetically identifiable sub-strain of the virus, and this has been associated with worsening disease prognosis for the patient. The impact of this on the host immune response and viral evolution remains poorly understood.

We identified an African patient within the earliest stages of infection, and have been able to acquire blood samples from the earliest weeks to over a year post-infection. Using advanced virus sequencing and immunological techniques, we are exploring how the presence of multiple sub-strains impacts the battle between pathogen and host.

Individual virions were isolated and sequenced at numerous timepoints, allowing us to follow the changing genetics of the virus population. Using this information, we generated peptides representing all major variants of HIV in this patient, and tested how their T cells responded to each. This has revealed the sections of the HIV being targeted by the immune system, and following the virus sequences over time allows us to see how the virus evolves to escape from the immune system, improving survival of the virus.

Academic partners:

• Prof. Sir Andrew McMichael, NDM, University of Oxford
• Dr. Nilu Goonetilleke, NDM, University of Oxford
• Dr. Feng Gao, Duke University

Funded by:

NIAID - National Institute of Allergy and Infectious Diseases (CHAVI)