Evidence brief: HIV-1 genetic diversity and reverse transcriptase resistance mutations in Benin before dolutegravir era, West Africa

Abstract

Benin adopted the World Health Organization’s (WHO) “Test and Treat” recommendation in 2016 and, since 2019, has updated this protocol by including dolutegravir (DTG) as the preferred first-line treatment. Study aimed to assess the prevalence of virological failure (VL > 3log copies/mL) and review genetic diversity and antiretroviral resistance mutations in patients on antiretroviral treatment for at least 12 months before dolutegravir Era in Benin. Cross-sectional study included patient plasmas from antiretroviral treatment sites nationwide. Viral load was performed in National Reference Laboratory of Health Program Fighting Against AIDS using the Cobas® 5800 HIV-1 assay. For plasmas those VL above 1000 copies/mL, nested PCR were done along the entire protease and part of reverse transcriptase. The DNA obtained by the Sanger method was used to determine the subtypes of HIV-1 after editing with DNASTAR SeqMan Pro™ and alignment with ClustalW2 version 2.1. Phylogenetic trees were constructed by the Neighbor-Joining method and recombinants were investigated by bootscanning with Seaview software version 2.1. DNA was subjected to the Stanford University Antiretroviral Resistance Mutation Interpretation Algorithm (https://hivdb.stanford.edu/) to identify the positions of drug-associated resistance mutations. (178/253; 70.35%) of the samples were correctly amplified and sequenced. CRF02_AG (n = 104) was the predominant strain observed followed by CRF06_cpx (n = 21), G (n = 5), CRF43_02G (n = 2), CRF37_cpx (n = 2), A1 (n = 1) and unique recombinant forms (URFs) (n = 34) among the 169 samples sequenced on entire protease combined with part of the reverse transcriptase. (164/178; 92.1%), (141/178; 79.2%), (160/178; 89.9%) and (7/169; 4.1%) patients carried at least one drug resistance associated to NRTIs, NNRTIs and PIs respectively. M184I/V, TAMSI: (M41L, L210W, T215Y) and TAMSII: (D67N, K70R, K219Q/E, T215I/V) represented (71.3%), (21.9%), (35.4%) respectively. K103N/S was the most preponderant mutations encountered with a proportion of 64.6% followed by V179E (21.3%), P225H (20.2%), V108I (19.1%), Y181C (16.3%), A98G (15.2%), V106I/M/A (10.1%). I84V (1.8%) mutation was the major associated PIs encountered followed by L90M, V82A, M46I each encountered twice (1.2%) and I47A, V32I, I54V, G48A, each encountered once (0.6%). Study shows a high genetic diversity with the presence of new strains and underlines the need to regularly review data on genetic diversity and resistance among patients receiving antiretroviral therapy in the country.

Introduction

Benin is a West African country with a concentrated epidemic of HIV-1 infection. HIV-1 prevalence is low in the general population (0.8%) [1,2] and high in key populations such as female sex workers (FSW) and men who have sex with men (MSM), 7.2% and 7.7% % respectively [2]. Management of people living with HIV (PLHIV) began in 2002 with the adoption of « Test and Treat » in 2016. Systematic monitoring of patients on treatment was ensured by viral load quantification and CD4 + T- cell count. Following two consecutive viral loads exceeding 1000 copies/mL at three-month intervals, the patient was declared to have failed treatment [3,4] and resistance genotyping was requested. At the end of 2024, the number of PLHIV was estimated at 70000 and 60000 were actually on antiretroviral treatment, including 57480 adults and 2520 children [5]. For the triple objective 95-95-95 in HIV testing, treatment, and viral suppression, beyond the difficulties encountered, the country reached 89-98-82 in 2023 [6] and 89-99-91 in 2024 [5]. One of the areas on which we must act appears to be the first-line therapeutic line following the study on the primary resistance of HIV-1 in Benin that showed a prevalence of resistance associated with non-nucleoside reverse transcriptase inhibitors (NNRTIs) of around 10% [7]. Likewise, the study assessing resistance to pretreatment integrase inhibitors showed a prevalence of zero percent [8]. These data reinforce Benin’s strategy to adopt the 2019 WHO recommendations to close the gaps and achieve UNAIDS target 95. In children for whom antiretroviral therapy is known to be problematic, especially due to the need for a third party to administer antiretrovirals and monitor treatment adherence, a recent study in the country reported that (25/32; 78.12%), (28/32; 87.5%), (4/32; 12.90%), (22/32; 68.75%), (02/32; 6.25%) of children had at least one drug resistance mutation associated with NRTIs, NNRTIs, PIs, NNRTIs + NRTIs, and NNRTIs + NRTIs + PIs respectively. In addition, the majority of children were on an (efavirenz) EFV-based regimen (22/47; 46.8%). It then becomes clear that these mutations could be the cause of some cases of treatment failure, thus contributing to slowing down the indicators towards reaching the third UNAIDS 95 target. Although proportions of resistance mutations have been reported under therapeutic regimens without dolutegravir at one year [9] two years [10], five years [11], no study has presented the situation of drug resistance mutation in Benin after a twelve-month follow-up.