Four-class drug-resistant HIV-1 subtype C in a treatment experienced individual on dolutegravir-based antiretroviral therapy in Botswana.

: There are limited data on the effectiveness of dolutegravir (DTG)-based combination antiretroviral therapy (ART) in real-life settings in southern Africa where HIV-1 subtype C predominates. We report a patient infected with HIV-1 subtype C on DTG-based ART previously exposed to raltegravir who developed multidrug resistance mutations to four antiretroviral classes. There is need for drug resistance monitoring and clinical vigilance to ensure effectiveness of HIV treatment programs even in the era of DTG-based ART

Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition : implications for active and passive immunization.

CAPRISA, 2016.Abstract available in PDF file

Comparison of an in-house 'home-brew' and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples.

BackgroundRoll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq™ Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals.MethodsWe used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time.ResultsAmong 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C.ConclusionsThe IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana

Geometric mean titer and tier 1A and 1B classification (n = 200).

<p>(A) Viruses are rank ordered according to neutralization sensitivity to 30 clade C chronic infection serum samples, from the least sensitive to the most sensitive along the x-axis by average log₁₀ GMTs. Two viruses were classified as highly sensitive tier 1A and an additional 17 as above-average sensitive tier 1B. A previously determined cut off ID₅₀ = 200, was used to distinguish between tier 1A and tier 1B is indicated on the graph, with tier 1B classified viruses above this cut off colored in red and those below in orange [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.ref016" target="_blank">16</a>]. Twelve pseudoviruses classified by both Seaman et al., (2010) and this study were found to be discrepant (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.s009" target="_blank">S1 Table</a>): Du156.12 consistently falls near the boundary of the tier 2 and tier 1B, was classified as tier 1B here however was previously classified as tier 2; and ZM197M and SM109F were classified as tier 2 here, however were previously classified as 1B. (B) Maximum likelihood phylogenetic analysis of southern African clade C acute/early envelope nucleotide sequences (n = 200) with branches colored according to tier. Bootstrap values > 80% of 100 resampled replicates are illustrated as filled circles on nodes.</p

Maximum likelihood phylogenetic analysis of southern African clade C acute/early envelope nucleotide sequences (n = 200) (Table 1).

<p>Branches are colored according to country/region. Bootstrap values > 80% of 100 resampled replicates are illustrated as filled circles on nodes. South African samples from Soweto/Johannesburg (Gauteng province), Cape Town (Western Cape Province), and KwaZulu-Natal are highlighted in light green, red, and blue respectively, sequences from other locations in South Africa are shown in grey. Clades that were from the same geographic region are highlighted. Only one of these regional grouping (>2 sequence clusters) had strong bootstrap support (4 sequences from Tanzania, highlighted in orange).</p

Relationship of clade C acute/early panel <i>env</i> genes/envelope proteins (n = 200) to clade C candidate vaccine strains compared to the relationship of CRF01_AE breakthrough viruses from RV144 (n = 66 placebo arm) to the RV144 vaccine.

<p><b>(A)</b> Gp120 amino acid distances (excluding signal peptide) for clade C viruses to clade-matched vaccine prime- and boost-strains (96ZM651, TV1 and Ce1086); and CRF01_AE viruses from breakthrough infections in the placebo arm of RV144 to clade-matched RV144 vaccine strains (92TH023 and CM244). Box plots for RV144 distances in light grey and clade C distances in dark grey, with means in red. Significance shown in p-values provided for a two-sided Mann-Whitney test. <b>(B)</b> Amino acid distances across V2 (HXB2 161–179) and V3 (HXB2 300–322) linear B cell epitopes for clade C viruses as well as for RV144 placebo CRF01_AE viruses to respective clade-matched vaccine protein boost strains, Ce1086 and TV1 and CM244. Significance shown in p-values provided for a two-sided Mann-Whitney test. <b>(C)</b> Logo conservation plots across V2 and V3 linear B cell epitope peptides which includes vaccine signature sites as identified in RV144 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.ref011" target="_blank">11</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.ref013" target="_blank">13</a>]. These illustrate clade C acute/early panel sequence amino acid frequency and corresponding vaccine strain residue conservation. Residues shared between clade C and either vaccine strain Ce1086 or TV1 are shown in black with the remaining residues in grey. Positions of RV144 identified signatures associated with reduced infection risk K169, I181X, I307 and F317X are shaded in blue. <b>(D)</b> Comparison of RV144 signature site frequencies in acute/early clade C panel (southern Africa) compared to Thai CRF01_AE sequences from the placebo arm (Thai). In RV144, a match to the vaccine at position 169 (with a K) and at 307 (with I) was associated with protection; while a mismatch to the vaccine at positions 181 (I181X) and 317 (F317X) was associated with protection [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.ref011" target="_blank">11</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005742#ppat.1005742.ref013" target="_blank">13</a>].</p