Virological Failure, HIV-1 Drug Resistance and Early Mortality in Adults Admitted to Hospital in Malawi: A Nested Observational Cohort Study

Background: Antiretroviral therapy (ART) scale-up in sub-Saharan Africa (SSA) combined with weak routine virological monitoring has driven increasing HIV drug resistance. We investigated ART failure, drug resistance and early mortality among hospital inpatients in Malawi. Methods: An observational cohort study nested in a trial of urine-based TB screening in unselected HIV-positive adults followed up for 2 months. Patients taking ART for ≥6 months at hospital admission had frozen plasma samples tested for HIV-1 viral load. Those with HIV-1 RNA ≥1000 copies/ml had drug resistance testing by ultra-deep sequencing, with drug resistance defined as intermediate or high-level resistance using the Stanford HIVDR Algorithm Findings: Of 1316 patients recruited in the Malawi trial site between October 2015 and September 2017, 786 had taken ART for ≥6 months of whom 252/786 (32.1%) patients had viral load ≥1000 copies/ml (virological failure). Mean age was 38 years, 61.5% were female and median CD4 count was 60 cells/µL. Of 237 (94.0%) patients with HIV drug resistance results available, 195 (82.3%) had resistance to lamivudine, 128 (54.0%) to tenofovir and 219 (92.4%) to efavirenz. Resistance to at least 2 drugs was common (196/237, 82.7%) and this was associated with increased 2-month mortality (adjusted hazard ratio 1.7, 95% CI 1.2-2.4, p=0.004). Interpretation: HIV virological failure and HIV multidrug resistance were common in HIV-positive inpatients, and associated with increased early mortality. Targeted interventions including adherence support, rapid viral load testing and routine access to drug resistance testing are urgently needed. Enabling prompt diagnosis and switching to alternative ART could reduce early mortality among HIV-positive inpatients. Funding Statement: The Screening for TB to Reduce AIDS Related Mortality in Hospitalised Patients (STAMP) trial was funded by the Joint Global Health Trials Scheme of the UK Department of Health and Social Care, the Department for International Development, the Global Challenges Research Fund, the Medical Research Council and Wellcome Trust (MR/M007375/1). AGW has received a Royal College of Physicians London James Maxwell Grant Prophit Fellowship, and ELC has received a Wellcome Trust Fellowship (WT200901/Z/16/Z). Declaration of Interests: The authors declare no conflicts of interest exist. Ethics Approval Statement: All patients provided informed written consent for participation and sample storage. Retrospective HIV viral load and drug resistance testing was approved by the research ethics committee of the London School of Hygiene and Tropical Medicine, and the University of Malawi College of Medicine Research and Ethics Committee (COMREC).