High resistance to reverse transcriptase inhibitors among persons infected with human immunodeficiency virus type 1 subtype circulating recombinant form 02_AG in Ghana and on antiretroviral therapy

Abstract

This study sought to determine the dominant circulating human immunodeficiency virus type 1 (HIV-1) subtype and associated drug resistance mutations in Ghana.This cross-sectional study was conducted with archived samples collected from patients who received care at 2 hospitals in Ghana from 2014 to 2016. Blood samples were earlier processed into plasma and peripheral blood mononuclear cells and stored at -80 °C. Ribonucleic acid (RNA) was extracted from the archived plasma. Two HIV-1 genes; protease and reverse transcriptase, were amplified, sequenced using gene-specific primers and analyzed for subtype and drug resistance mutations using the Stanford HIV Database.Of 16 patient samples successfully sequenced, we identified the predominance of HIV-1 subtype CRF02_AG (11/16, 68%). Subtypes G (2/16, 13%), dual CRF02_AG/G (2/16, 13%), and CRF01_AE (1/16, 6%) were also observed. Major nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, M184I/V, D67N, T215F, and K70R/E were found. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, K103N, Y181C, V90I, F227L, and V106A were also prevalent. Additionally, and at a lower level, protease inhibitor (PI)-resistance mutations, M46I, I54 V, V82A, L90 M, and I471 V, were also present in the sequences from antiretroviral therapy (ART)-experienced individuals. Two NRTI-associated drug resistance mutations (DRMs) (D67N and T69N) were present in sequences from 1 ART-naive individual.HIV-1 subtype CRF02_AG was most frequently detected in this study thus confirming earlier reports of dominance of this subtype in the West-African sub-region and Ghana in particular. The detection of these drug resistance mutations in individuals on first-line regimen composed of NRTI and NNRTI is an indication of prolonged drug exposure without viral load monitoring. Routine viral load monitoring is necessary for early detection of virologic failure and drug resistance testing will inform appropriate choice of regimens for such patients.

Figure 1

Distribution of HIV-1 specific laboratory data. (A) Viral loads (copies/mL) and (B) CD4⁺ cell counts (cells/μL) from different groups of participants. FL = participants on First Line ART, FP = fast progressors, LTNP = long-term non-progressors, SL = participants on Second Line ART.

Figure 2

Neighbor joining phylogenetic tree showing the evolutionary relationship between the protease genes sequenced. ● HIV-1 Subtype B reference sequence. ▴ HIV-1 Subtype A reference sequence. ▾ HIV-1 Subtype G reference. ♦ HIV-1 Subtype CRF01_AE reference sequence. ▪ HIV-1 Subtype CRF02_AG reference sequence. □ HIV-1 Subtype CRF02_AG sample.

Figure 3

Neighbor joining phylogenetic tree showing the evolutionary relationship between the reverse transcriptase genes sequenced. ● HIV-1 Subtype B reference sequence. ▴ HIV-1 Subtype A reference sequence. ▾ HIV-1 Subtype G reference. ♦ HIV-1 Subtype CRF01_AE reference sequence. ▪ HIV-1 Subtype CRF02_AG reference sequence. □ HIV-1 Subtype CRF02_AG sample. ▿ HIV-1 Subtype G sample. ♦ HIV-1 Subtype CRF01_AE reference sequence. ■ HIV-1 Subtype CRF01_AE sample.