Members of the Travers group involved in the development of Seq2Res

The introduction of HIV antiretroviral (ARV) therapy programmes in Southern Africa has substantially reduced the burden of infection in HIV-positive individuals. In fact, the 2012 UNAIDS report estimates that as many as 14 million lives have been saved as a result of the rollout of such programmes throughout the world. There is, however, a problem facing the continued success of ARV therapy programmes: the emergence of viral resistance to ARVs. To date, no cost-effective HIV drug resistance test has been available for routine use in South Africa and other countries suffering from a high burden of HIV infections.

Recent advances in DNA sequencing have made it possible to offer a more sensitive HIV drug resistance test at a fraction of the cost (as much as a fivefold decrease). The downside of this approach, however, is that these technologies generate a vast amount of data that needs to be analysed and interpreted in a specialised and expensive manner, and are thus not easy to incorporate into routine testing procedures within South African hospitals and clinics, especially in remote and resource-limited settings.

The South African National Bioinformatics Institute (SANBI) at the University of the Western Cape has a solution. A team led by Prof Simon Travers has developed an easy-to-use computational tool called Seq2ResTM that can effectively process this data, meaning that the realisation of a cost-effective HIV drug resistance test is now a reality.

While Seq2ResTM is being used routinely within SANBI by bioinformatics specialists, the team has recently received significant funding from the South African Department of Science and Technology to deliver Seq2ResTM as a web-based application. This application will enable researchers and clinicians to routinely and easily process their drug resistance testing data without needing expert bioinformatics assistance. This development is being undertaken in collaboration with partners at the National Health Laboratory Service (NHLS) genotyping units in Tygerberg (Cape Town), the NHLS/University of the Witwatersrand Medical School (Johannesburg) and the National Institute for Communicable Diseases (NICD) in Johannesburg.

According to Prof Travers: “The real value of this approach is that it has been developed in a research environment in conjunction with all of the prospective end users in the South African public sector.”

When completed, SANBI will present Seq2ResTM for clinical, research and surveillance use, enabling the establishment of routine HIV drug resistance testing in Southern Africa.

For more information about SANBI’s involvement in the projects mentioned above, please visit the Travers’ Group site.