Application of next generation sequencing in HIV drug resistance studies in Africa, 2005–2019: A systematic review

The control of HIV transmission is a high priority for Africa, in line with Agenda 2063 of the African Union. The development of HIV drug resistance poses a significant challenge in maintaining suppressed viral load in the management of patients. Next generation sequencing (NGS) is a more sensitive approach to determine the burden of HIV drug resistance. We aimed to describe the uptake of NGS in HIV drug resistance studies in Africa. An electronic search was conducted for studies published between 2005 and 2019, from three databases: PubMed, Web of Science and Google scholar. The search approach was carried out according to PRISMA guidelines. Studies included in the analysis were those that reported the use of NGS on HIV drug resistance using samples from Africa or in which the studies were done in Africa. A total of 4180 articles were identified according to the search criteria. Out of these, 237 studies (5.7%), all of which were in English, met the inclusion criteria and were included in the analysis. Of the total number of studies, 29 (12.2%) used NGS only, 194 (81.9%) used Sanger sequencing, and 14 (5.9%) used both techniques. Evidence of in-country application of NGS was observed in six studies (14.0%), all from South Africa. In other studies, NGS was either done outside of Africa using samples obtained from Africa, or the country in which NGS was done was not indicated. From 2005 to 2012, only one study was reported on HIV drug resistance using NGS; however, 43 studies were published by 2019. Out of the 54 African countries, investigators from 13 countries (24.1%) published data on HIV drug resistance using NGS, as at the end of 2019. Illumina platform was the most preferred NGS platform (p