CROI 2020 Abstract eBook

Abstract eBook

Poster Abstracts

Background: The entry of HIV-1 into target cells is a critical event in the viral life cycle and an attractive target for drug development. The HIV-1 envelope protein (Env), comprised of three gp120 subunits and three gp41 subunits, binds to cell-surface receptors before triggering the fusion of viral and host cell membranes. Entry inhibitors targeting the gp41 (Enfuvirtide) or co-receptor CCR5 (Maraviroc) have been approved by FDA for HIV-1 treatment. To date, no entry inhibitors targeting the gp120 have been FDA-approved although a promising small-molecule lead, fostemsavir (the prodrug of active compound BMS-626529), is currently in phase III clinical trials. We previously reported the crystal structure of BMS-626529 in complex with HIV-1 Env trimer, revealing its molecular basis of entry inhibition. This drug binds to a conserved pocket beneath the ß20-ß21 hairpin between the inner and outer domains of gp120, suggesting that drug binding blocks the conformational changes required for viral fusion to occur. We also identified BMS-818251, a derivative of BMS- 626529, which is >10-fold more potent in pseudovirus neutralization assays. Crystal structure of BMS-818251 revealed interactions between a tail functional group and the Env that likely contributed to the higher neutralization potency. Methods: We characterized the viral suppression efficacy of BMS-818251 in ex vivo cell cultures that were derived from HIV-1 patients. In addition, we used a site-saturated mutational library of BG505 Env to map the potential resistance mutations of BMS-818251 and BMS-626529. Results: BMS-818251 exhibited superior viral suppression than BMS-616259 in HIV-1+ CD4 T-cell culture from two patients. The minimal inhibition concentration of BMS-818251 was >10-fold lower than BMS-626529, consistent with our previous observation in pseudovirus neutralization assays. In addition, we observed viral rebound in the cell culture of one patient treated with the highest concentration of BMS-626529 tested, suggesting selection of pre- existing resistance mutations. Viral rebound was not observed for BMS-818251 in the two samples tested. Mapping of resistance mutations by the BG505 mutation library revealed distinct resistance profiles by BMS-818251 and BMS-626529, suggesting different level of selection pressure between these two compounds. Conclusion: Our data support further development of BMS-818251, which represents a novel class of HIV-1 drugs targeting gp120, as a next-generation entry inhibitor. 528 META-ANALYSIS OF UNUSUAL AND APOBEC MUTATIONS IN HIV-1 POL NEXT-GENERATION SEQUENCES Philip L. Tzou 1 , Santiago Avila-Rios 2 , Susan Holmes 1 , Rami Kantor 3 , Sergei L. Kosakovsky Pond 4 , Robert Shafer 1 1 Stanford University, Stanford, CA, USA, 2 National Institute of Respiratory Diseases, Mexico City, Mexico, 3 Brown University, Providence, RI, USA, 4 Temple University, Philadelphia, PA, USA Background: Next generation sequencing (NGS) for HIV-1 genotypic resistance testing is subject to detection of artifactual mutations resulting from PCR error and APOBEC-mediated G-to-A hypermutation. We hypothesize that the presence of large numbers of unusual mutations at a mutation call frequency NGS threshold suggests the threshold is too low and that many of the detected mutations may be caused by PCR error or G-to-A hypermutation rather than HIV-1 replication. Methods: We systematically analyzed HIV-1 pol Illumina NGS data from published studies to characterize the distribution of usual and unusual amino acid mutations at 8 NGS thresholds: 20%, 10%, 5%, 2%, 1%, 0.5%, 0.2% and 0.1%. At each threshold we quantified the number of unusual mutations (defined as having prevalence of <0.01% in HIV-1 group M population Sanger sequences) or signature APOBEC mutations. Results: Eight studies containing 855 samples from 821 persons in the NCBI sequence read archive were analyzed. As the NGS threshold was lowered, there was a progressive increase in the proportion of positions with both usual and unusual mutations and a progressive increase in the proportion of mutations that were unusual (Figure). The median proportion of positions with an unusual mutation increased from 0% to 0.3% between the 20% and 1% thresholds and then increased to 1.3% at the 0.5% threshold, 6.9% at the 0.2% threshold, and 23.2% at the 0.1% threshold. In 2 of 3 studies reporting plasma HIV-1 RNA levels, the proportion of positions with unusual mutations was inversely associated with virus levels. Although the complete set of signature APOBEC mutations (n=296) was much smaller than the complete set of other unusual mutations (n=14,940), signature APOBEC mutations outnumbered non-APOBEC unusual mutations in one-sixth of samples at the 0.5%, 1% and 2% thresholds.

Conclusion: The marked increase in the proportion of unusual mutations at thresholds below 1% and in samples with lower virus loads suggest that many detected unusual mutations may derive from PCR error. However, in some samples, APOBEC-mediated G-to-A hypermutation may be a greater contributor to sequence artifacts than PCR error. Post hoc analyses of NGS data that quantify the numbers of unusual and signature APOBEC mutations at different NGS thresholds may be useful to avoid selecting a threshold that is too low and that poses an unacceptable risk of identifying artifactual mutations.

Poster Abstracts

529 ABSENCE OF GS-6207 PHENOTYPIC RESISTANCE IN HIV Gag CLEAVAGE SITE AND OTHER MUTANTS Nicolas A. Margot 1 , Renee R. Ram 1 , Martin Rhee 1 , Christian Callebaut 1 1 Gilead Sciences, Inc, Foster City, CA, USA Background: GS-6207 is a potent, first in class, multistage inhibitor of HIV-1 capsid function with the potential to be used as a subcutaneous (SC) long-acting agent with dosing every 3 months or longer. In the clinic, a single SC injection of GS-6207 (50 mg to 450 mg) in people living with HIV (PLWH) showed a rapid and strong antiviral effect, with a >1.8 mean log 10 decrease in HIV-1 RNA at day 10. Mutations in HIV-1 gag near protease (PR) cleavage sites have emerged with the use of protease inhibitors (PIs), resulting in increased fitness and/or PI-resistance. Here we have characterized the activity of GS-6207 in mutants with HIV-1 gag cleavage site mutations, as well as mutants with resistance to other drug classes. Methods: HIV mutations were inserted into the pXXLAI infectious clone either by site-directed mutagenesis or by cloning of plasma samples. Infectious clones with HIV gag cleavage site mutations, or HIV gag-PR fragments from treatment- naïve or experienced PLWH were evaluated using a standard 5-day antiviral assay (MT-2-cells). Isolates with resistance mutations against the 4 major drug classes (NRTI, NNRTI, PI, INSTI) were tested phenotypically using a single-cycle assay (Monogram Biosciences). Results: In all, 19 HIV gag cleavage site mutants (single and double mutants with L363F/M, A364V, Q430R, A431V, K436E, I437T/V, L449H/V/F, P453L, and/ or PR mutations V82A and I84V) as well as 55 patient derived clones were analyzed phenotypically. GS-6207 EC 50 fold-change compared to wild-type (WT) ranged from 0.3 to 2.1 in these mutants, similar to the control drug. In contrast, high levels of reduced susceptibility to PIs (>500 fold) and maturation inhibitors (MIs) (>70 fold) were noted in some mutants. Testing of isolates with resistance mutations against the 4 main classes of drugs (n=40) indicated WT susceptibility to GS-6207 (fold-change ranging from 0.3 to 1.1), while highly reduced susceptibility was observed for control drugs of each class. Conclusion: HIV gag cleavage site mutations did not impact the activity of GS-6207, while some conferred resistance to MIs and PIs. Similarly, GS-6207 activity was not affected by naturally occurring variations in HIV gag, in contrast to the loss of activity observed for MIs in nearly half of the mutants. Finally, the activity of GS-6207 was not affected by the presence of resistance mutations to the 4 main ARV classes. These data support the evaluation of GS-6207 in PLWH with multi-class resistance. 530 SUSCEPTIBILITY OF NRTI-RESISTANT HIV-2 ISOLATES TO A NEW NRTI, GS-9131 Quentin Le Hingrat 1 , Gilles Collin 1 , Samuel Lebourgeois 2 , Benoit Visseaux 1 , Florence Damond 1 , Jade Ghosn 1 , Antoine Bachelard 1 , Valentine Ferré 1 , Sophie Matheron 1 , Charlotte Charpentier 1 , Diane Descamps 1 , for the ANRS CO5 HIV-2 cohort

CROI 2020 189