An audit of the HIV drug resistance testing program in Malawi

For persons failing on dolutegravir- and protease inhibitor-based antiretroviral therapy (ART) regimens, Malawi's HIV program requires confirmation of HIV drug resistance (HIVDR) before switching to next-line regimens. Approval of applications for HIVDR testing is determined by a national HIVDR committee that also provides management recommendations based on HIVDR test results. We audited HIVDR test applications for all ages in Malawi's national ART program to evaluate the HIVDR testing process and explore short-term outcomes, including viral suppression.

We conducted a retrospective review of routinely collected data from applications for HIVDR testing registered between July 2020 and December 2021. We determined drop-offs at steps of the HIVDR testing cascade: approval for genotyping, sample collection, receiving results, completion of genotypic sequencing, provision of management recommendations and implementation of recommendations. We assessed ART outcomes, including the first viral load (VL) result ≥6 months after recommendations from the HIVDR committee.

228 HIVDR applications were received, of which 75% (172/228) were approved. Of these, 72% (124/172) had samples sent to laboratory and 122 genotyping results were obtained. 75% (92/122) of samples were successfully sequenced and 68% (65/92) sequences had ≥1 major drug resistance-associated mutation, including 17% with moderate or high-level dolutegravir resistance of individuals on dolutegravir-based regimens. Treatment outcomes were available for 90 clients: 65 were alive on ART, 3 had defaulted, 12 died, 9 transferred out and 1 stopped ART. Of 68 available follow-up VL results, 34 (51%) were <1,000 copies/mL.

This audit demonstrates gaps in Malawi's HIVDR testing cascade and concerning clinical outcomes among those with follow up results: considerable attrition from care and low VL suppression. These results suggest that improvements in HIVDR testing in the Malawi HIV program need to be considered, including in-country sequencing and more efficient procedures for applications, approvals, clinical recommendations and clinical follow up.