SAMRC funds KRISP & Oxford to Sequence Children Genomes that are Protected from HIV in Africa

HIV genomics

This study plans to sequence and analyze large number of genomes on the African continent for the first time. In addition to identify genetics basis of protection to HIV, this project will set the benchmark for future genomic research in Africa by developing the whole genome sequence (WGS) protocols and bioinformatics workflows.

This is the first award from the SAMRC, who has committed US$ 500,000 to fund this project. The focus of the project is on the identification of human genetic variation that can protect children from developing HIV disease (i.e. AIDS).

HIV-host genetics is one area that offers the potential for new treatment strategies and is receiving significant attention. Substantial advancements in next generation sequencing (NGS) methods allow researchers to sequence the entire human genome in a few days. A recent collaboration with the SAMRC and the Beijing Genomics Institute (BGI) will bring this technology to Africa for the first time. This will enable researchers in South Africa and other parts of Africa to explore the role the human genome plays in local diseases.

Whole genome sequencing (WGS) as well as RNAseq, coupled with bioinformatics analysis, has identified numerous genes and polymorphisms which are associated with complex diseases. Using the WGS technology scientists at KRISP, collaborating with scientists from Oxford University, SAMRC and BGI, will examine 120 genomes from individuals of African descent in an attempt to decode the contribution of human genes to HIV disease progression. To achieve this goal, we will examine HIV-infected children aged >5yrs who have never received ART but have not developed AIDS. These children at termed paediatric ‘non-progressors’ (PNPs). Our key question to answer is what genetic factors are providing AIDS resistance within these children.