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Hendrickx DM, Delva W, Hens N. Influence of sexual risk behaviour and STI co-infection dynamics on the evolution of HIV set point viral load in MSM. Epidemics 2021; 36:100474. [PMID: 34153622 DOI: 10.1016/j.epidem.2021.100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022] Open
Abstract
HIV viral load (VL) is an important predictor of HIV progression and transmission. Anti-retroviral therapy (ART) has been reported to reduce HIV transmission by lowering VL. However, apart from this beneficial effect, increased levels of population mean set-point viral load (SPVL), an estimator for HIV virulence, have been observed in men who have sex with men (MSM) in the decade following the introduction of ART in The Netherlands. Several studies have been devoted to explain these counter-intuitive trends in SPVL. However, to our knowledge, none of these studies has investigated an explanation in which it arises as the result of a sexually transmitted infection (STI) co-factor in detail. In this study, we adapted an event-based, individual-based model to investigate how STI co-infection and sexual risk behaviour affect the evolution of HIV SPVL in MSM before and after the introduction of ART. The results suggest that sexual risk behaviour has an effect on SPVL and indicate that more data are needed to test the effect of STI co-factors on SPVL. Furthermore, the observed trends in SPVL cannot be explained by sexual risk behaviour and STI co-factors only. We recommend to develop mathematical models including also factors related to viral evolution as reported earlier in the literature. However, this requires more complex models, and the collection of more data for parameter estimation than what is currently available.
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Affiliation(s)
- Diana M Hendrickx
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium.
| | - Wim Delva
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; The South African Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa; Department of Global Health, Faculty of Medicine and Health, Stellenbosch University, Stellenbosch, South Africa; International Centre for Reproductive Health, Ghent University, Ghent, Belgium; Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Niel Hens
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Relaño-Rodríguez I, Muñoz-Fernández MÁ. Emergence of Nanotechnology to Fight HIV Sexual Transmission: The Trip of G2-S16 Polyanionic Carbosilane Dendrimer to Possible Pre-Clinical Trials. Int J Mol Sci 2020; 21:ijms21249403. [PMID: 33321835 PMCID: PMC7764023 DOI: 10.3390/ijms21249403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Development of new, safe, and effective microbicides to prevent human immunodeficiency virus HIV sexual transmission is needed. Unfortunately, most microbicides proved ineffective to prevent the risk of HIV-infection in clinical trials. We are working with G2-S16 polyanionic carbosilane dendrimer (PCD) as a new possible vaginal topical microbicide, based on its short reaction times, wide availability, high reproducibility, and quantitative yields of reaction. G2-S16 PCD exerts anti-HIV activity at an early stage of viral replication, by blocking gp120/CD4/CCR5 interaction, and providing a barrier against infection for long periods of time. G2-S16 PCD was stable at different pH values, as well as in the presence of seminal fluids. It maintained the anti-HIV activity against R5/X4 HIV over time, did not generate any type of drug resistance, and retained the anti-HIV effect when exposed to semen-enhanced viral infection. Importantly, G2-S16 PCD did not modify vaginal microbiota neither in vitro or in vivo. Histopathological examination did not show vaginal irritation, inflammation, lesions, or damage in the vaginal mucosa, after administration of G2-S16 PCD at different concentrations and times in female mice and rabbit animal models. Based on these promising data, G2-S16 PCD could become a good, safe, and readily available candidate to use as a topical vaginal microbicide against HIV.
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Affiliation(s)
- Ignacio Relaño-Rodríguez
- Head Section of Immunology, Molecular Immunology Laboratory, General Universitary Hospital Gregorio Marañón, C/Dr. Esquerdo 46, 28007 Madrid, Spain;
| | - Maria Ángeles Muñoz-Fernández
- Head Section of Immunology, Molecular Immunology Laboratory, General Universitary Hospital Gregorio Marañón, C/Dr. Esquerdo 46, 28007 Madrid, Spain;
- Health Research Institute Gregorio Marañon (IiSGM), C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Spanish HIV HGM BioBank, C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Correspondence: or ; Tel.: +34-91-586-8565
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Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism. PLoS One 2017; 12:e0185790. [PMID: 29049306 PMCID: PMC5648111 DOI: 10.1371/journal.pone.0185790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope gp120 is partly an intrinsically disordered (unstructured/disordered) protein as it contains regions that do not fold into well-defined protein structures. These disordered regions play important roles in HIV’s life cycle, particularly, V3 loop-dependent cell entry, which determines how the virus uses two coreceptors on immune cells, the chemokine receptors CCR5 (R5), CXCR4 (X4) or both (R5X4 virus). Most infecting HIV-1 variants utilise CCR5, while a switch to CXCR4-use occurs in the majority of infections. Why does this ‘rewiring’ event occur in HIV-1 infected patients? As changes in the charge of the V3 loop are associated with this receptor switch and it has been suggested that charged residues promote structure disorder, we hypothesise that the intrinsic disorder of the V3 loop is permissive to sequence variation thus contributing to the switch in cell tropism. To test this we use three independent data sets of gp120 to analyse V3 loop disorder. We find that the V3 loop of X4 virus has significantly higher intrinsic disorder tendency than R5 and R5X4 virus, while R5X4 virus has the lowest. These results indicate that structural disorder plays an important role in HIV-1 cell tropism and CXCR4 binding. We discuss the potential evolutionary mechanisms leading to the fixation of disorder promoting mutations and the adaptive potential of protein structural disorder in viral host adaptation.
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HIV-1 Glycan Density Drives the Persistence of the Mannose Patch within an Infected Individual. J Virol 2016; 90:11132-11144. [PMID: 27707925 PMCID: PMC5126371 DOI: 10.1128/jvi.01542-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/26/2016] [Indexed: 12/15/2022] Open
Abstract
The HIV envelope glycoprotein (Env) is extensively modified with host-derived N-linked glycans. The high density of glycosylation on the viral spike limits enzymatic processing, resulting in numerous underprocessed oligomannose-type glycans. This extensive glycosylation not only shields conserved regions of the protein from the immune system but also acts as a target for anti-HIV broadly neutralizing antibodies (bnAbs). In response to the host immune system, the HIV glycan shield is constantly evolving through mutations affecting both the positions and numbers of potential N-linked glycosylation sites (PNGSs). Here, using longitudinal Env sequences from a clade C-infected individual (CAP256), we measured the impact of the shifting glycan shield during HIV infection on the abundance of oligomannose-type glycans. By analyzing the intrinsic mannose patch from a panel of recombinant CAP256 gp120s displaying high protein sequence variability and changes in PNGS number and positioning, we show that the intrinsic mannose patch persists throughout the course of HIV infection and correlates with the number of PNGSs. This effect of the glycan density on the processing state was also supported by the analysis of a cross-clade panel of recombinant gp120 glycoproteins. Together, these observations underscore the importance of glycan clustering for the generation of carbohydrate epitopes for anti-HIV bnAbs. The persistence of the intrinsic mannose patch over the course of HIV infection further highlights this epitope as an important target for HIV vaccine strategies. IMPORTANCE Development of an HIV vaccine is critical for control of the HIV pandemic, and elicitation of broadly neutralizing antibodies (bnAbs) is likely to be a key component of a successful vaccine response. The HIV envelope glycoprotein (Env) is covered in an array of host-derived N-linked glycans often referred to as the glycan shield. This glycan shield is a target for many of the recently isolated anti-HIV bnAbs and is therefore under constant pressure from the host immune system, leading to changes in both glycan site frequency and location. This study aimed to determine whether these genetic changes impacted the eventual processing of glycans on the HIV Env and the susceptibility of the virus to neutralization. We show that despite this variation in glycan site positioning and frequency over the course of HIV infection, the mannose patch is a conserved feature throughout, making it a stable target for HIV vaccine design.
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Moncla LH, Zhong G, Nelson CW, Dinis JM, Mutschler J, Hughes AL, Watanabe T, Kawaoka Y, Friedrich TC. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus. Cell Host Microbe 2016; 19:169-80. [PMID: 26867176 PMCID: PMC4761429 DOI: 10.1016/j.chom.2016.01.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/26/2015] [Accepted: 01/25/2016] [Indexed: 01/14/2023]
Abstract
Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.
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Affiliation(s)
- Louise H Moncla
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Gongxun Zhong
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA
| | - Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Jorge M Dinis
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - James Mutschler
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Tokiko Watanabe
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA.
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Pacheco-Martínez E, Figueroa-Medina E, Villarreal C, Cocho G, Medina-Franco JL, Méndez-Lucio O, Huerta L. Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype. Virol J 2016; 13:28. [PMID: 26879054 PMCID: PMC4754869 DOI: 10.1186/s12985-016-0486-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in coreceptor tropism, although there is no consensus about the positions involved. Here we analyze the association of physicochemical properties of gp41 amino acid residues with viral tropism (X4, R5, and R5X4) using a large set of HIV-1 sequences. Under the assumption that conserved regions define the complex structural features essential for protein function, we focused our search only on amino acids in the gp41 variable regions. METHODS Gp41 amino acid sequences of 2823 HIV-1 strains from all clades with known coreceptor tropism were retrieved from Los Alamos HIV Database. Consensus sequences were constructed for homologous sequences (those obtained from the same patient and having the same tropism) in order to avoid bias due to sequence overrepresentation, and the variability (entropy) per site was determined. Comparisons of hydropathy index (HI) and charge (Q) of amino acid residues at highly variable positions between coreceptor groups were performed using two non-parametrical tests and Benjamini-Hochberg correction. Pearson's correlation analysis was performed to determine covariance of HI and Q values. RESULTS Calculation of variability per site rendered 58 highly variable amino acid positions. Of these, statistical analysis rendered significantly different HI or Q only for the R5 vs. R5X4 comparison at twelve positions: 535, 602, 619, 636, 640, 641, 658, 662, 667, 723, 756 and 841. The largest differences in particular amino acid frequencies between coreceptor groups were found at 619, 636, 640, 641, 662, 723 and 756. A hydrophobic tendency of residues 619, 640, 641, 723 and 756, along with a hydrophilic/charged tendency at residues 636 and 662 was observed in R5X4 with respect to R5 sequences. HI of position 640 covariated with that of 602, 619, 636, 662, and 756. CONCLUSIONS Variability and significant correlations of physicochemical properties with viral phenotype suggest that substitutions at residues in the loop (602 and 619), the HR2 (636, 640, 641, 662), and the C-terminal tail (723, 756) of gp41 may contribute to phenotype of R5X4 strains.
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Affiliation(s)
- Elena Pacheco-Martínez
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Distrito Federal, 04510, México
| | - Evangelina Figueroa-Medina
- Unidad de Radio Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Avenida Vasco de Quiroga No.15, ᅟDistrito Federal, 14080, México
| | - Carlos Villarreal
- Departmento de Física Teórica, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - Germinal Cocho
- Departmento de Sistemas Complejos, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - José L Medina-Franco
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Oscar Méndez-Lucio
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Leonor Huerta
- Departmento de Immunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Distrito Federal, México.
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Briz V, Sepúlveda-Crespo D, Diniz AR, Borrego P, Rodes B, de la Mata FJ, Gómez R, Taveira N, Muñoz-Fernández MÁ. Development of water-soluble polyanionic carbosilane dendrimers as novel and highly potent topical anti-HIV-2 microbicides. NANOSCALE 2015; 7:14669-14683. [PMID: 26274532 DOI: 10.1039/c5nr03644e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The development of topical microbicide formulations for vaginal delivery to prevent HIV-2 sexual transmission is urgently needed. Second- and third-generation polyanionic carbosilane dendrimers with a silicon atom core and 16 sulfonate (G2-S16), napthylsulfonate (G2-NS16) and sulphate (G3-Sh16) end-groups have shown potent and broad-spectrum anti-HIV-1 activity. However, their antiviral activity against HIV-2 and mode of action have not been probed. Cytotoxicity, anti-HIV-2, anti-sperm and antimicrobial activities of dendrimers were determined. Analysis of combined effects of triple combinations with tenofovir and raltegravir was performed by using CalcuSyn software. We also assessed the mode of antiviral action on the inhibition of HIV-2 infection through a panel of different in vitro antiviral assays: attachment, internalization in PBMCs, inactivation and cell-based fusion. Vaginal irritation and histological analysis in female BALB/c mice were evaluated. Our results suggest that G2-S16, G2-NS16 and G3-Sh16 exert anti-HIV-2 activity at an early stage of viral replication inactivating the virus, inhibiting cell-to-cell HIV-2 transmission, and blocking the binding of gp120 to CD4, and the HIV-2 entry. Triple combinations with tenofovir and raltegravir increased the anti-HIV-2 activity, consistent with synergistic interactions (CIwt: 0.33-0.66). No vaginal irritation was detected in BALB/c mice after two consecutive applications for 2 days with 3% G2-S16. Our results have clearly shown that G2-S16, G2-NS16 and G3-Sh16 have high potency against HIV-2 infection. The modes of action confirm their multifactorial and non-specific ability, suggesting that these dendrimers deserve further studies as potential candidate microbicides to prevent vaginal/rectal HIV-1/HIV-2 transmission in humans.
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Affiliation(s)
- Verónica Briz
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R. Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS One 2015; 10:e0125502. [PMID: 25970632 PMCID: PMC4430318 DOI: 10.1371/journal.pone.0125502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/18/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES We analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment. METHODS 87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in triplicate, 43 samples with the ESTA assay and 45 with next-generation sequencing. The influence of the genotypic susceptibility score (GSS) and 16 MVC-resistance mutations on clinical outcome was also studied. RESULTS Concordance between single-amplification testing compared to ESTA and to NGS was in the order of 80%. Concordance with NGS was higher at lower FPR cut-offs. Detection of baseline R5 viruses in RNA and DNA samples by all methods significantly correlated with treatment success, even with FPR cut-offs of 3.75%-7.5%. Triple amplification did not improve the prediction value but reduced the number of patients eligible for MVC. No influence of the GSS or MVC-resistance mutations but adherence to treatment, on the clinical outcome was detected. CONCLUSIONS Proviral DNA is valid to select candidates for MVC treatment. FPR cut-offs of 5%-7.5% and single amplification from RNA or DNA would assure a safe administration of MVC without excluding many patients who could benefit from this drug. In addition, the new prediction system T-CUP produced reliable results.
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Affiliation(s)
- Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | - J Nikolai Dybowski
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Alejandro Pironti
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Dominik Heider
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Lisa Güney
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Alex Thielen
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Stefan Reuter
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology, University of Duisburg-Essen, Essen, Germany
| | - Gerd Fätkenheuer
- First Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Daniel Hoffmann
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Herbert Pfister
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
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Joshi A, Lee RTC, Mohl J, Sedano M, Khong WX, Ng OT, Maurer-Stroh S, Garg H. Genetic signatures of HIV-1 envelope-mediated bystander apoptosis. J Biol Chem 2013; 289:2497-514. [PMID: 24265318 DOI: 10.1074/jbc.m113.514018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The envelope (Env) glycoprotein of HIV is an important determinant of viral pathogenesis. Several lines of evidence support the role of HIV-1 Env in inducing bystander apoptosis that may be a contributing factor in CD4(+) T cell loss. However, most of the studies testing this phenomenon have been conducted with laboratory-adapted HIV-1 isolates. This raises the question of whether primary Envs derived from HIV-infected patients are capable of inducing bystander apoptosis and whether specific Env signatures are associated with this phenomenon. We developed a high throughput assay to determine the bystander apoptosis inducing activity of a panel of primary Envs. We tested 38 different Envs for bystander apoptosis, virion infectivity, neutralizing antibody sensitivity, and putative N-linked glycosylation sites along with a comprehensive sequence analysis to determine if specific sequence signatures within the viral Env are associated with bystander apoptosis. Our studies show that primary Envs vary considerably in their bystander apoptosis-inducing potential, a phenomenon that correlates inversely with putative N-linked glycosylation sites and positively with virion infectivity. By use of a novel phylogenetic analysis that avoids subtype bias coupled with structural considerations, we found specific residues like Arg-476 and Asn-425 that were associated with differences in bystander apoptosis induction. A specific role of these residues was also confirmed experimentally. These data demonstrate for the first time the potential of primary R5 Envs to mediate bystander apoptosis in CD4(+) T cells. Furthermore, we identify specific genetic signatures within the Env that may be associated with the bystander apoptosis-inducing phenotype.
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Affiliation(s)
- Anjali Joshi
- From the Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, Texas 79905
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Mild M, Gray RR, Kvist A, Lemey P, Goodenow MM, Fenyö EM, Albert J, Salemi M, Esbjörnsson J, Medstrand P. High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch. INFECTION GENETICS AND EVOLUTION 2013; 19:369-77. [PMID: 23672855 DOI: 10.1016/j.meegid.2013.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 04/29/2013] [Accepted: 05/04/2013] [Indexed: 12/20/2022]
Abstract
In approximately 70% of individuals infected with HIV-1 subtype B, the virus switches coreceptor use from exclusively CCR5 use (R5 virus) to either inclusion of or exclusively CXCR4 use (X4 virus) during infection. This switch is associated with an accelerated loss of CD4(+) T-cells and a faster progression to AIDS. Despite intensive research, the mechanisms responsible for coreceptor switch remains elusive. In the present study, we investigated associations between viral evolutionary rate and selection pressure versus viral coreceptor use and rate of disease progression in eight patients with longitudinally sampled HIV-1 env V1-V3 sequences. By employing a Bayesian hierarchical phylogenetic model, we found that the HIV-1 evolutionary rate was more strongly associated with coreceptor switch than with rate of disease progression in terms of CD4(+)T-cell decline. Phylogenetic analyses showed that X4 variants evolved from R5 populations. In addition, coreceptor switch was associated with higher evolutionary rates on both the synonymous and non-synonymous substitution level, but not with dN/dS ratio rates. Our findings suggest that X4 viruses evolved from pre-existing R5 viral populations and that the evolution of coreceptor switch is governed by high replication rates rather than by selective pressure. Furthermore, the association of viral evolutionary rate was more strongly associated with coreceptor switch than disease progression. This adds to the understanding of the complex virus-host interplay that influences the evolutionary dynamics of HIV-1 coreceptor use.
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Affiliation(s)
- Mattias Mild
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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