Over the past decade, the world has witnessed an unprecedented increase in the use of antiretroviral therapy (ART) which has saved the lives of millions of people living with HIV/AIDS. Concurrent with the increased use of treatment has been the emergence of HIV drug resistance. This global rise in resistance to crucial HIV drugs has a significant clinical impact and threatens the significant progress that has been made in suppressing HIV. In Africa, this threat is particularly acute where several countries have reported levels of HIV resistance exceeding 10% to the standard first-line therapy.

The advent of portable sequencing technology means viral genomic sequencing is now positioned to exert a greater public health impact to the upsurge in resistance. This project aims to develop a nanopore sequencing-based pipeline for HIV resistance genotyping. The student will optimize, evaluate, and validate the sequencing method using spiked plasma samples followed by a clinical evaluation from HIV-infected patients with known levels of drug-resistance. Lastly, it is proposed that the student will develop an open-source data processing and analysis pipeline for reporting HIV drug resistance. It is envisaged that this pipeline will support public health decisions and aid clinicians and laboratories in interpreting genotypic resistance. Taken together, this project will serve as the underlying basis for exploring how rapid viral sequencing can be best used in the future towards integration into local public health surveillance to decrease the incidence of drug resistance and onwards transmission.

The student will benefit from a highly multidisciplinary supervisory team and will spend time at the MRC Uganda unit. This work is innovative, implements genome sequencing technologies and big data bioinformatics. This project is expected to yield scientific publications and deliver novel tools to support public health surveillance of drug resistance.