Researchers in South Africa have developed a low-cost tool to test for HIV drug resistance, potentially opening the door to improved treatment for users of antiretroviral drugs (ARVs).
The researchers, based at the University of Western Cape’s South African National Bioinformatics Institute (SANBI), have developed a computer-based tool — Seq2Res — that vastly reduces the costs and time involved in analysing data about viral DNA compared to conventional methods.
Simon Travers, bioinformatics associate professor and project leader at SANBI, says the tool allows HIV drug resistance testing of samples from almost 50 patients pooled together, which makes it significantly cheaper. Conventional method can only assess one patient’s data at a time.
“Our tool makes this analysis easy,” Travers tells SciDev.Net.
It is also expected to be five times cheaper than the average conventional testing system.
Travers says that the tool offers a more sensitive HIV drug resistance test by identifying drug resistant viral variants circulating at low levels in individuals. Viral sequences are listed and compared to a reference virus to identify the presence of mutations that are known to cause drug resistance.
“The software will allow for more manageable processing and interpretation of sequence data obtained using next generation sequencing platforms for HIV resistance surveillance,” Gillian Hunt, a researcher from South Africa’s National Institute for Communicable Diseases, tells SciDev.Net.
Travers says the new tool will enable researchers and clinicians to easily process their drug resistance testing data without needing expert bioinformatics assistance.
The data will be collected and stored in a large database, which will be accessible to researchers at no charge as a service to the academic research community.
Travers explains that the researchers are three months into the development of the web application and that tests will start by end of June, with a final roll-out of the Seq2Res tool set for September this year.
The tool currently used in the research laboratory at SANBI is being developed into a web-based application with US$120,000 of funding from the South African government’s Department of Science and Technology (DST).
The tool is designed to be user-friendly, with no specialised training required: any clinician or research scientist who understands HIV drug resistance should be able to use it, Travers says.
The only tool required by the user is access to next-generation sequencing facilities to generate the input data, he adds. These systems are becoming increasingly available throughout Africa.
According to the 2012 UNAIDS report, the use of ARVs in Sub-Saharan Africa has substantially reduced death rates among HIV-positive people. Between 2005 and 2011, the number of people dying from AIDS-related causes in the region declined from 1.8 million to 1.2 million.
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