HIV-1 Subtype C Drug Resistance Mutations in Heavily Treated Patients Failing Integrase Strand Transfer Inhibitor-Based Regimens in Botswana

Abstract

There are limited real-world mutational and virological outcomes data of treatment-experienced persons diagnosed with HIV-1 subtype C (HIV-1 C) who are failing Integrase Strand Transfer Inhibitor-based regimens. Requisition forms sent for HIV-1 genotypic resistance testing (GRT) between May 2015 and September 2019 were reviewed and participants experiencing virologic failure while on dolutegravir (DTG) or raltegravir (RAL) cART at sampling recruited. Sanger sequencing of the HIV-1 Pol gene was performed from residual plasma samples and drug resistance mutational (DRM) analysis performed using the Stanford University HIV drug resistance database. 40 HIV-1C integrase sequences were generated from 34 individuals, 24 of whom were on DTG cART, three on RAL cART and seven on an unknown (DTG or RAL)-anchored cART at time of GRT. 11/34 (32%) individuals had DRMs to DTG and other integrase inhibitors. 7/11 (64%) patients had exposure to a RAL-based cART at the time of sampling. Out of the 11 individuals with DRMs, one (9%) had 2-class, 6 (55%) had 3-class, and 4 (36%) had 4-class multidrug-resistant HIV-1C. 7/11 individuals (64%) are currently virologically suppressed. Of the four individuals not virologically suppressed, three had extensive DRMs involving 4-classes of ARV drugs and one individual has demised. Resistance to DTG occurs more often in patients exposed to RAL cART. Individuals with 4-class DRMs plus integrase T97 and E157Q mutations appear to have worse outcomes. There is a need for frequent VL monitoring and GRT amongst treatment-experienced HIV-1C diagnosed individuals.

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

“…Participant samples were obtained from two studies conducted in Botswana. The first study consisted of sequences generated from residual plasma specimens obtained from therapy-experienced individuals experiencing VF while on DTG- or raltegravir (RAL)-based cART described elsewhere (BOSELE study; Figure 1 ) [ 7 ]. VF was defined as two or more consecutive plasma HIV-1 RNA levels (viral loads (VL)) > 400 copies/mL as per standard of care guidelines in Botswana.…”

“…VF was defined as two or more consecutive plasma HIV-1 RNA levels (viral loads (VL)) > 400 copies/mL as per standard of care guidelines in Botswana. The HIV-1 integrase region was amplified using nested reverse transcription-polymerase chain reactions (RT-PCRs) where necessary and sequenced using a BigDye™ Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Carlsbad, CA, USA) on a 3130xl Genetic Analyser (Life Technologies Corporation, Applied Biosystems, Carlsbad, CA, USA) as previously described [ 7 , 20 ]. Sequencing of the nef gene was attempted from the same HIV-1 extracts that integrase sequences were successfully generated from.…”

“…ND, not documented; VF, virologic failure; DTG, dolutegravir; cART, combination antiretroviral therapy; BCPP, Botswana Combination Prevention Project. Column 3 of this table is the same dataset represented in Column 3 of Table 1 of Seatla et al [ 7 ]. This table has been modified with permission from Seatla et al [ 7 ].…”

“…Column 3 of this table is the same dataset represented in Column 3 of Table 1 of Seatla et al [ 7 ]. This table has been modified with permission from Seatla et al [ 7 ].…”

“…However, resistance mutations within the integrase enzyme can cause reduced susceptibility to DTG [ 1 , 6 ]. Most major DTG resistance mutations amongst therapy-experienced individuals are usually located within the HIV-1 catalytic core domain of the integrase region [ 1 , 7 ]. However, a handful of studies have suggested associations between DTG failure and mutations outside the integrase region in the 3′-polypurine tract (3′PPT) of the HIV-1 nef gene [ 8 , 9 ].…”