Limited HIV-1 Subtype C nef 3'PPT Variation in Combination Antiretroviral Therapy Naïve and Experienced People Living with HIV in Botswana

Kaelo K Seatla, Dorcas Maruapula, Wonderful T Choga, Olorato Morerinyane, Shahin Lockman, Vladimir Novitsky, Ishmael Kasvosve, Sikhulile Moyo, Simani Gaseitsiwe, Kaelo K Seatla, Dorcas Maruapula, Wonderful T Choga, Olorato Morerinyane, Shahin Lockman, Vladimir Novitsky, Ishmael Kasvosve, Sikhulile Moyo, Simani Gaseitsiwe

Abstract

Dolutegravir (DTG) is a potent anti-HIV drug that is used to treat HIV globally. There have been reports of mutations in the HIV-1 3'-polypurine tract (3'PPT) of the nef gene, contributing to DTG failure; however, there are limited 'real-world' data on this. In addition, there is a knowledge gap on the variability of 3'PPT residues in patients receiving combination antiretroviral therapy (cART) with and without viral load (VL) suppression. HIV-1 subtype C (HIV-1C) whole-genome sequences from cART naïve and experienced individuals were generated using next-generation sequencing. The nef gene sequences were trimmed from the generated whole-genome sequences using standard bioinformatics tools. In addition, we generated separate integrase and nef gene sequences by Sanger sequencing of plasma samples from individuals with virologic failure (VF) while on a DTG/raltegravir (RAL)-based cART. Analysis of 3'PPT residues was performed, and comparison of proportions computed using Pearson's chi-square test with p-values < 0.05 was considered statistically significant. A total of 6009 HIV-1C full genome sequences were generated and had a median log10 HIV-1 VL (Q1, Q3) copies/mL of 1.60 (1.60, 2.60). A total of 12 matching integrase and nef gene sequences from therapy-experienced participants failing DTG/ RAL-based cART were generated. HIV-1C 3'PPT nef gene sequences from therapy-experienced patients failing DTG cART (n = 12), cART naïve individuals (n = 1263), and individuals on cART with and without virological suppression (n = 4696) all had a highly conserved 3'PPT motif with no statistically significant differences identified. Our study confirms the high conservation of the HIV-1 nef gene 3'PPT motif in 'real-world' patients and showed no differences in the motif according to VL suppression or INSTI-based cART failure. Future studies should explore other HIV-1 regions outside of the pol gene for associations with DTG failure.

Keywords: 3′-polypurine tract; Botswana; HIV-1; dolutegravir; drug resistance mutations; nef.

Conflict of interest statement

All authors have no conflict of interest to declare.

Figures

Figure 1
Figure 1
Study schema depicting the selection of study sequences. (A), selection and analysis of 3′PPT nef gene sequences according to participant cART status and HIV-1 RNA levels; (B), selection and analysis of 3′PPT of nef gene amongst individuals with VF while on DTG/RAL-based cART. Seqs, sequences; PID, participant identification number; VL, viral load; VF, virologic failure; RAL, raltegravir; DTG, dolutegravir; cART, combination antiretroviral therapy; 3′PPT, 3′-polypurine tract; RT, reverse transcriptase HIV-1 gene; PR, protease HIV-1 gene; DRMs, drug resistance mutations; HIV-1C, HIV-1 subtype C.
Figure 2
Figure 2
HIV-1C nef gene 3′PPT variability amongst 6009 sequences from individuals on cART and not on cART. 3′PPT, 3′polypurine tract; cART, combination antiretroviral therapy; HIV-1C, HIV-1 subtype C.

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