Drug susceptibility and replication capacity of a rare HIV-1 subtype C protease hinge region variant

2019 ◽  
Vol 24 (5) ◽  
pp. 333-342
Author(s):  
Jake Zondagh ◽  
Adriaan E Basson ◽  
Ikechukwu Achilonu ◽  
Lynn Morris ◽  
Heini W Dirr ◽  
...  
Keyword(s):  
Drug Susceptibility ◽  
Hinge Region ◽  
Replication Capacity ◽  
Subtype C ◽  
Hiv 1

Double trouble? Gag in conjunction with double insert in HIV protease contributes to reduced DRV susceptibility

2019 ◽  
Vol 476 (2) ◽  
pp. 375-384 ◽  
Author(s):  
Alison Williams ◽  
Adriaan Basson ◽  
Ikechukwu Achilonu ◽  
Heini W. Dirr ◽  
Lynn Morris ◽  
...  
Keyword(s):  
Specific Activity ◽  
Catalytic Efficiency ◽  
Drug Susceptibility ◽  
Hiv Protease ◽  
Titration Calorimetry ◽  
Replication Capacity ◽  
Subtype C ◽  
Viral Replication Capacity ◽  
Hiv 1

AbstractHIV protease is essential for processing the Gag polyprotein to produce infectious virions and is a major target in antiretroviral therapy. We have identified an unusual HIV-1 subtype C variant that contains insertions of leucine and asparagine (L38↑N↑L) in the hinge region of protease at position 38. This was isolated from a protease inhibitor naïve infant. Isothermal titration calorimetry showed that 10% less of L38↑N↑L protease was in the active conformation as compared with a reference strain. L38↑N↑L protease displayed a ±50% reduction in KM and kcat. The catalytic efficiency (kcat/KM) of L38↑N↑L protease was not significantly different from that of wild type although there was a 42% reduction in specific activity for the variant. An in vitro phenotypic assay showed the L38↑N↑L protease to be susceptible to lopinavir (LPV), atazanavir (ATV) and darunavir in the context of an unrelated Gag. However, in the presence of the related Gag, L38↑N↑L showed reduced susceptibility to darunavir while remaining susceptible to LPV and ATV. Furthermore, a reduction in viral replication capacity (RC) was observed in combination with the related Gag. The reduced susceptibility to darunavir and decrease in RC may be due to PTAPP duplication in the related Gag. The present study shows the importance of considering the Gag region when looking at drug susceptibility of HIV-1 protease variants.

scholarly journals The Envelope Cytoplasmic Tail of HIV-1 Subtype C Contributes to Poor Replication Capacity through Low Viral Infectivity and Cell-to-Cell Transmission

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0161596
Author(s):  
Eveline Santos da Silva ◽  
Martin Mulinge ◽  
Morgane Lemaire ◽  
Cécile Masquelier ◽  
Cyprien Beraud ◽  
...  
Keyword(s):  
Cytoplasmic Tail ◽  
Replication Capacity ◽  
Viral Infectivity ◽  
Subtype C ◽  
Cell Transmission ◽  
Hiv 1

scholarly journals Impact of Primary Elvitegravir Resistance-Associated Mutations in HIV-1 Integrase on Drug Susceptibility and Viral Replication Fitness

2013 ◽  
Vol 57 (6) ◽  
pp. 2654-2663 ◽  
Author(s):  
Michael E. Abram ◽  
Rebecca M. Hluhanich ◽  
Derrick D. Goodman ◽  
Kristen N. Andreatta ◽  
Nicolas A. Margot ◽  
...  
Keyword(s):  
Viral Replication ◽  
Drug Susceptibility ◽  
Viral Fitness ◽  
Cross Resistance ◽  
Replication Capacity ◽  
Strand Transfer ◽  
Recombinant Viruses ◽  
Transfer Inhibitor ◽  
Replication Fitness ◽  
Hiv 1

ABSTRACTElvitegravir (EVG) is an effective HIV-1 integrase (IN) strand transfer inhibitor (INSTI) in advanced clinical development. Primary INSTI resistance-associated mutations (RAMs) at six IN positions have been identified in HIV-1-infected patients failing EVG-containing regimens in clinical studies: T66I/A/K, E92Q/G, T97A, S147G, Q148R/H/K, and N155H. In this study, the effect of these primary IN mutations, alone and in combination, on susceptibility to the INSTIs EVG, raltegravir (RAL), and dolutegravir (DTG); IN enzyme activities; and viral replication fitness was characterized. Recombinant viruses containing the six most common mutations exhibited a range of reduced EVG susceptibility: 92-fold for Q148R, 30-fold for N155H, 26-fold for E92Q, 10-fold for T66I, 4-fold for S147G, and 2-fold for T97A. Less commonly observed primary IN mutations also showed a range of reduced EVG susceptibilities: 40- to 94-fold for T66K and Q148K and 5- to 10-fold for T66A, E92G, and Q148H. Some primary IN mutations exhibited broad cross-resistance between EVG and RAL (T66K, E92Q, Q148R/H/K, and N155H), while others retained susceptibility to RAL (T66I/A, E92G, T97A, and S147G). Dual combinations of primary IN mutations further reduced INSTI susceptibility, replication capacity, and viral fitness relative to either mutation alone. Susceptibility to DTG was retained by single primary IN mutations but reduced by dual mutation combinations with Q148R. Primary EVG RAMs also diminished IN enzymatic activities, concordant with their structural proximity to the active site. Greater reductions in viral fitness of dual mutation combinations may explain why some primary INSTI RAMs do not readily coexist on the same HIV-1 genome but rather establish independent pathways of resistance to EVG.

scholarly journals Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C

2011 ◽  
Vol 85 (8) ◽  
pp. 3996-4006 ◽  
Author(s):  
J. K. Wright ◽  
V. Novitsky ◽  
M. A. Brockman ◽  
Z. L. Brumme ◽  
C. J. Brumme ◽  
...  
Keyword(s):  
Disease Progression ◽  
Replication Capacity ◽  
Subtype C ◽  
Hiv 1

scholarly journals Gag-Protease-Mediated Replication Capacity in HIV-1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

2010 ◽  
Vol 84 (20) ◽  
pp. 10820-10831 ◽  
Author(s):  
Jaclyn K. Wright ◽  
Zabrina L. Brumme ◽  
Jonathan M. Carlson ◽  
David Heckerman ◽  
Carl M. Kadie ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Population Level ◽  
Hla Class I ◽  
Viral Fitness ◽  
Baseline Viral Load ◽  
Replication Capacity ◽  
Subtype C ◽  
Fitness Costs ◽  
The Impact ◽  
Hiv 1

ABSTRACT The mechanisms underlying HIV-1 control by protective HLA class I alleles are not fully understood and could involve selection of escape mutations in functionally important Gag epitopes resulting in fitness costs. This study was undertaken to investigate, at the population level, the impact of HLA-mediated immune pressure in Gag on viral fitness and its influence on HIV-1 pathogenesis. Replication capacities of 406 recombinant viruses encoding plasma-derived Gag-protease from patients chronically infected with HIV-1 subtype C were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. Viral replication capacities varied significantly with respect to the specific HLA-B alleles expressed by the patient, and protective HLA-B alleles, most notably HLA-B*81, were associated with lower replication capacities. HLA-associated mutations at low-entropy sites, especially the HLA-B*81-associated 186S mutation in the TL9 epitope, were associated with lower replication capacities. Most mutations linked to alterations in replication capacity in the conserved p24 region decreased replication capacity, while most in the highly variable p17 region increased replication capacity. Replication capacity also correlated positively with baseline viral load and negatively with baseline CD4 count but did not correlate with the subsequent rate of CD4 decline. In conclusion, there is evidence that protective HLA alleles, in particular HLA-B*81, significantly influence Gag-protease function by driving sequence changes in Gag and that conserved regions of Gag should be included in a vaccine aiming to drive HIV-1 toward a less fit state. However, the long-term clinical benefit of immune-driven fitness costs is uncertain given the lack of correlation with longitudinal markers of disease progression.

Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance

2013 ◽  
Vol 31 (12) ◽  
pp. 1370-1380 ◽  
Author(s):  
Previn Naicker ◽  
Ikechukwu Achilonu ◽  
Sylvia Fanucchi ◽  
Manuel Fernandes ◽  
Mahmoud A.A. Ibrahim ◽  
...  
Keyword(s):  
Drug Resistance ◽  
South African ◽  
Hinge Region ◽  
Subtype C ◽  
The South ◽  
Structural Insights ◽  
Hiv 1

scholarly journals Impact of the N348I Mutation in HIV-1 Reverse Transcriptase on Nonnucleoside Reverse Transcriptase Inhibitor Resistance in Non-Subtype B HIV-1

2011 ◽  
Vol 55 (4) ◽  
pp. 1806-1809 ◽  
Author(s):  
Adele L. McCormick ◽  
Chris M. Parry ◽  
Anne Crombe ◽  
Ruth L. Goodall ◽  
Ravindra K. Gupta ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Transcriptase Inhibitor ◽  
Drug Susceptibility ◽  
Replication Capacity ◽  
Replicative Capacity ◽  
Double Mutation ◽  
Nonnucleoside Reverse Transcriptase Inhibitor ◽  
Subtype B ◽  
Reverse Transcriptase Inhibitor ◽  
Hiv 1

ABSTRACTWe investigated the effect of N348I alone and with M184V on nonnucleoside reverse transcriptase inhibitor (NNRTI) drug susceptibility and replicative capacity in B and non-B HIV-1 isolates. N348I reduced the susceptibility to all NNRTI drugs across subtypes. The replication capacity of all viruses in a variety of cell lines was impaired by N348I. Interestingly, the N348I and M184V double mutation compensated for the reduced NNRTI drug susceptibility observed in the N348I single mutant and marginally improved viral replicative capacity.

scholarly journals HIV-1 Protease Codon 36 Polymorphisms and Differential Development of Resistance to Nelfinavir, Lopinavir, and Atazanavir in Different HIV-1 Subtypes

2010 ◽  
Vol 54 (7) ◽  
pp. 2878-2885 ◽  
Author(s):  
Irene Lisovsky ◽  
Susan M. Schader ◽  
Jorge-Luis Martinez-Cajas ◽  
Maureen Oliveira ◽  
Daniela Moisi ◽  
...  
Keyword(s):  
Viral Replication ◽  
Resistance Mutation ◽  
Fold Increase ◽  
Replication Capacity ◽  
Protease Gene ◽  
Subtype C ◽  
Phenotypic Analysis ◽  
Subtype B ◽  
Viral Replication Capacity ◽  
Hiv 1

ABSTRACT The amino acid at position 36 of the HIV-1 protease differs among various viral subtypes, in that methionine is usually found in subtype B viruses but isoleucine is common in other subtypes. This polymorphism is associated with higher rates of treatment failure involving protease inhibitors (PIs) in non-subtype B-infected patients. To investigate this, we generated genetically homogeneous wild-type viruses from subtype B, subtype C, and CRF02_AG full-length molecular clones and showed that subtype C and CRF02_AG I36 viruses exhibited higher levels of resistance to various PIs than their respective M36 counterparts, while the opposite was observed for subtype B viruses. Selections for resistance with each variant were performed with nelfinavir (NFV), lopinavir (LPV), and atazanavir (ATV). Sequence analysis of the protease gene at week 35 revealed that the major NFV resistance mutation D30N emerged in NFV-selected subtype B viruses and in I36 subtype C viruses, despite polymorphic variation. A unique mutational pattern developed in subtype C M36 viruses selected with NFV or ATV. The presence of I47A in LPV-selected I36 CRF02_AG virus conferred higher-level resistance than L76V in LPV-selected M36 CRF02_AG virus. Phenotypic analysis revealed a >1,000-fold increase in NFV resistance in I36 subtype C NFV-selected virus with no apparent impact on viral replication capacity. Thus, the position 36 polymorphism in the HIV-1 protease appears to have a differential effect on both drug susceptibility and the viral replication capacity, depending on both the viral subtype and the drug being evaluated.

scholarly journals Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression

2017 ◽  
Vol 91 (13) ◽  
Author(s):  
Marion W. Kiguoya ◽  
Jaclyn K. Mann ◽  
Denis Chopera ◽  
Kamini Gounder ◽  
Guinevere Q. Lee ◽  
...  
Keyword(s):  
Disease Progression ◽  
Sub Saharan Africa ◽  
Replication Capacity ◽  
Binding Motif ◽  
Replicative Capacity ◽  
Subtype C ◽  
East African ◽  
Recombinant Viruses ◽  
Subtype B ◽  
Hiv 1

ABSTRACT There are marked differences in the spread and prevalence of HIV-1 subtypes worldwide, and differences in clinical progression have been reported. However, the biological reasons underlying these differences are unknown. Gag-protease is essential for HIV-1 replication, and Gag-protease-driven replication capacity has previously been correlated with disease progression. We show that Gag-protease replication capacity correlates significantly with that of whole isolates (r = 0.51; P = 0.04), indicating that Gag-protease is a significant contributor to viral replication capacity. Furthermore, we investigated subtype-specific differences in Gag-protease-driven replication capacity using large well-characterized cohorts in Africa and the Americas. Patient-derived Gag-protease sequences were inserted into an HIV-1 NL4-3 backbone, and the replication capacities of the resulting recombinant viruses were measured in an HIV-1-inducible reporter T cell line by flow cytometry. Recombinant viruses expressing subtype C Gag-proteases exhibited substantially lower replication capacities than those expressing subtype B Gag-proteases (P < 0.0001); this observation remained consistent when representative Gag-protease sequences were engineered into an HIV-1 subtype C backbone. We identified Gag residues 483 and 484, located within the Alix-binding motif involved in virus budding, as major contributors to subtype-specific replicative differences. In East African cohorts, we observed a hierarchy of Gag-protease-driven replication capacities, i.e., subtypes A/C < D < intersubtype recombinants (P < 0.0029), which is consistent with reported intersubtype differences in disease progression. We thus hypothesize that the lower Gag-protease-driven replication capacity of subtypes A and C slows disease progression in individuals infected with these subtypes, which in turn leads to greater opportunity for transmission and thus increased prevalence of these subtypes. IMPORTANCE HIV-1 subtypes are unevenly distributed globally, and there are reported differences in their rates of disease progression and epidemic spread. The biological determinants underlying these differences have not been fully elucidated. Here, we show that HIV-1 Gag-protease-driven replication capacity correlates with the replication capacity of whole virus isolates. We further show that subtype B displays a significantly higher Gag-protease-mediated replication capacity than does subtype C, and we identify a major genetic determinant of these differences. Moreover, in two independent East African cohorts we demonstrate a reproducible hierarchy of Gag-protease-driven replicative capacity, whereby recombinants exhibit the greatest replication, followed by subtype D, followed by subtypes A and C. Our data identify Gag-protease as a major determinant of subtype differences in disease progression among HIV-1 subtypes; furthermore, we propose that the poorer viral replicative capacity of subtypes A and C may paradoxically contribute to their more efficient spread in sub-Saharan Africa.

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