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Ruhanya V, Jacobs GB, Paul RH, Joska JA, Seedat S, Nyandoro G, Glashoff RH, Engelbrecht S. HIV-1 Subtype C Vpr Amino Acid Residue 45Y and Specific Conserved Fragments Are Associated with Neurocognitive Impairment and Markers of Viral Load. AIDS Res Hum Retroviruses 2023; 39:166-175. [PMID: 36401355 DOI: 10.1089/aid.2022.0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There is increasing evidence that HIV-1 viral protein R (Vpr) plays an important role in the pathogenesis of cognitive impairment. We investigated the relationship between HIV-1 subtype C Vpr sequence variation and HIV-associated neurocognitive impairment as measured by global deficit score (GDS) in treatment-naive individuals. We used different bioinformatic tools and statistical models to correlate vpr variation and cognitive function. We identified a tyrosine at position 45 (45Y) as a signature for neurocognitive impairment and histidine (45H) as a signature in the non-impaired individuals. The presence of signature 45Y was associated by 3.66 times higher GDS, 525 times higher plasma viral load, 15.84 times higher proviral load, and 60% lower absolute CD4-T cell count compared with those without the signature. Additionally, we identified four conserved Vpr fragment sequences, PEDQGPQREPYNEWTLE (5-21), LGQYIY (42-47), TYGDTW (49-54), and PEDQGPQREPYNEW (5-18), that were associated with higher plasma viral load and proviral load. The implication of these findings is that variation of Vpr leads to neurocognitive impairment in HIV infection and worsens the progression of disease in general by promoting the production of provirus, promoting HIV replication and depletion of CD4+ T cells in the periphery.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Department of Medical Microbiology, University of Zimbabwe, Harare, Zimbabwe
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robert H Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, University Boulevard, St Louis, Missouri, USA
| | - John A Joska
- MRC Unit of Anxiety and Stress Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety and Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | - George Nyandoro
- Department of Medical Microbiology, University of Zimbabwe, Harare, Zimbabwe
| | - Richard Helmuth Glashoff
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unity, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Ruhanya V, Jacobs GB, Paul RH, Joska JA, Seedat S, Nyandoro G, Glashoff RH, Engelbrecht S. HIV-1 subtype C Tat exon-1 amino acid residue 24K is a signature for neurocognitive impairment. J Neurovirol 2022; 28:392-403. [PMID: 35394614 DOI: 10.1007/s13365-022-01073-4] [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: 09/27/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
Variation and differential selection pressures on Tat genes have been shown to alter the biological function of the protein, resulting in pathological consequences in a number of organs including the brain. We evaluated the impact of genetic variation and selection pressure on 147 HIV-1 subtype C Tat exon 1 sequences from monocyte-depleted peripheral lymphocytes on clinical diagnosis of neurocognitive impairment. Genetic analyses identified two signature amino acid residues, lysine at codon 24 (24K) with a frequency of 43.4% and arginine at codon 29 (29R) with a frequency of 34.0% in individuals with HIV-associated neurocognitive impairment. The analyses also revealed two signature residues, asparagine, 24 N (31.9%), and histidine, 29H (21.3%), in individuals without neurocognitive impairment. Both codons, 24 and 29, were associated with high entropy but only codon 29 was under positive selection. The presence of signature K24 increased by 2.08 times the risk of neurocognitive impairment, 3.15 times higher proviral load, and 69% lower absolute CD4 T-cell count compared to those without the signature. The results support a linkage between HIV-1 C Tat N24K polymorphism, proviral load, immunosuppression, and neurocognitive impairment. The signature may induce more neurotoxic effects, which contributes to establishment and severity of HIV-associated neurocognitive impairment.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa. .,Department of Medical Microbiology, Harare, Zimbabwe.
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa
| | - Robert H Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, University Boulevard, St Louis, USA
| | - John A Joska
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | | | - Richard H Glashoff
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
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Subtype Differences in the Interaction of HIV-1 Matrix with Calmodulin: Implications for Biological Functions. Biomolecules 2021; 11:biom11091294. [PMID: 34572507 PMCID: PMC8464830 DOI: 10.3390/biom11091294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/28/2021] [Indexed: 01/10/2023] Open
Abstract
The HIV-1 Gag polyprotein plays essential roles during the late stage of the HIV-1 replication cycle, and has recently been identified as a promising therapeutic target. The N-terminal portion of the HIV-1 Gag polyprotein encodes the myristoylated matrix (MA) protein, which functions in the trafficking of the structural proteins to the plasma membrane (PM) and facilitation of envelope incorporation into budding virus. Numerous host cell proteins interact with the MA portion of the Gag polyprotein during this process. One such factor is the ubiquitous calcium-binding protein calmodulin (CaM), which interacts preferentially with myristoylated proteins, thereby regulating cell physiology. The exact role of this interaction is poorly understood to date. Atomic resolution structures revealed the nature of the CaM-MA interaction for clade B isolates. In this study, we expanded our knowledge and characterized biophysically and computationally the CaM interaction with MA from other HIV-1 clades and discovered differences in the CaM recognition as compared to the prototypical clade B MA, with significant alterations in the interaction with the MA protein from clade C. Structural investigation and in silico mutational analysis revealed that HIV-1 MA protein from clade C, which is responsible for the majority of global HIV-1 infections, interacts with lower affinity and altered kinetics as compared to the canonical clade B. This finding may have implications for additional altered interaction networks as compared to the well-studied clade B. Our analysis highlights the importance of expanding investigations of virus-host cell factor interaction networks to other HIV-1 clades.
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Mhandire K, Zijenah LS, Tshabalala M, Yindom LM, Mlambo T, Mhandire DZ, Musarurwa C, Duri K, Rowland-Jones S, Dandara C, Stray-Pedersen B. KIR and HLA-C Genetic Polymorphisms Influence Plasma IP-10 Concentration in Antiretroviral Therapy-Naive HIV-Infected Adult Zimbabweans. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:111-118. [PMID: 30614763 DOI: 10.1089/omi.2018.0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Past studies on the relationship between Killer cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genetic variation and chronic immune activation (CIA) in HIV infection are not uniformly consistent. Moreover, interferon-γ-induced protein 10 (IP-10) is a soluble biomarker of immune activation, with high plasma concentrations predicting accelerated disease progression in HIV infection. Thus, we investigated the association of KIR and HLA-C genetic polymorphisms with plasma IP-10 concentration in 183 treatment-naive chronically HIV-infected adults of Bantu origin from Zimbabwe. KIR genetic variation was determined using allele-specific primer PCR while HLA-C typing was characterized by sequencing. Plasma IP-10 was quantified using enzyme-linked immunosorbent assay. The KIR2DL3 gene was significantly associated with CIA as observed from IP-10 concentrations among KIR2DL3 carriers (265.20 pg/mL, IQR: 179.99-385.19) compared with KIR2DL3 noncarriers (183.56 pg/mL; IQR: 110.98-230.81; p = 0.001) and among KIR2DL3+HLA-C2 carriers (226.23 pg/mL, IQR: 187.96-394.73) compared with KIR2DL3+HLA-C2 noncarriers (212.86 pg/mL, IQR: 160.15-344.99; p = 0.017), respectively. Similarly, IP-10 concentrations were significantly higher (p = 0.030) in the KIR3DS1 carriers (313.86 pg/mL, IQR: 230.05-469.20) compared with KIR3DS1 noncarriers (246.01 pg/mL, IQR: 169.58-373.32). Thus, KIR and HLA-C could be playing important roles in HIV-associated immune activation. The elevation of IP-10 in KIR2DL3 and KIR2DL3+C2 could potentially be explained by increased IFN-γ secretion from activated NK cell activation due to the absence of KIR2DL3's cognate C1 ligand. To the best of our knowledge, this is the first study on a potential link between KIR and HLA-C genetic determinants and plasma IP-10 concentration in this population sample. Future studies are called for in other world populations for biomarkers of disease progression and mechanisms of IP-10 variability in HIV infection.
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Affiliation(s)
- Kudakwashe Mhandire
- 1 Department of Chemical Pathology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- 2 Letten Foundation Research House, Harare, Zimbabwe
| | - Lynn Sodai Zijenah
- 3 Department of Immunology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Mqondisi Tshabalala
- 3 Department of Immunology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Louis-Marie Yindom
- 4 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tommy Mlambo
- 3 Department of Immunology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Doreen Zvipo Mhandire
- 1 Department of Chemical Pathology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- 2 Letten Foundation Research House, Harare, Zimbabwe
- 5 Division of Human Genetics, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Cuthbert Musarurwa
- 1 Department of Chemical Pathology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Kerina Duri
- 3 Department of Immunology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Sarah Rowland-Jones
- 4 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Collet Dandara
- 5 Division of Human Genetics, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Babill Stray-Pedersen
- 2 Letten Foundation Research House, Harare, Zimbabwe
- 6 Institute of Clinical Medicine, University of Oslo and Women's Clinic, Rikshospitalet, University Hospital, Oslo, Norway
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DeLeon O, Hodis H, O’Malley Y, Johnson J, Salimi H, Zhai Y, Winter E, Remec C, Eichelberger N, Van Cleave B, Puliadi R, Harrington RD, Stapleton JT, Haim H. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model. PLoS Biol 2017; 15:e2001549. [PMID: 28384158 PMCID: PMC5383018 DOI: 10.1371/journal.pbio.2001549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 01/08/2023] Open
Abstract
The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties of variants expected to appear in the future. HIV-1 is the causative agent of the global AIDS pandemic. The envelope glycoproteins (Envs) of HIV-1 constitute a primary target for antibody-based vaccines. However, the diversity of Envs in the population limits the potential efficacy of this approach. Accurate estimates of the range of variants that currently infect patients and those expected to appear in the future will likely contribute to the design of population-targeted immunogens. We found that different properties (features) of Env have different propensities for small “fluctuations” in their values among viruses that infect patients at any given time point. This propensity of each feature for in-host variance, which we designate “volatility”, is conserved among patients. We apply this parameter to model the evolution of features (in patients and population) as a diffusion process driven by their “diffusion coefficients” (volatilities). Using volatilities measured from a few patient samples from the 1980s, we accurately predict properties of viruses that evolved in the population over the course of 30 years. The diffusion-based model described here efficiently captures evolution of phenotypes in biological systems controlled by a dominant random component.
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Affiliation(s)
- Orlando DeLeon
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hagit Hodis
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yunxia O’Malley
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jacklyn Johnson
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hamid Salimi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yinjie Zhai
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Elizabeth Winter
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Claire Remec
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Noah Eichelberger
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Brandon Van Cleave
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramya Puliadi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert D. Harrington
- Center for AIDS Research (CFAR) at the University of Washington, Seattle, Washington, United States of America
| | - Jack T. Stapleton
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Veterans Affairs Medical Center, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Huang A, Hogan JW, Luo X, DeLong A, Saravanan S, Wu Y, Sirivichayakul S, Kumarasamy N, Zhang F, Phanuphak P, Diero L, Buziba N, Istrail S, Katzenstein DA, Kantor R. Global Comparison of Drug Resistance Mutations After First-Line Antiretroviral Therapy Across Human Immunodeficiency Virus-1 Subtypes. Open Forum Infect Dis 2016; 3:ofv158. [PMID: 27419147 PMCID: PMC4943563 DOI: 10.1093/ofid/ofv158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/19/2015] [Indexed: 12/02/2022] Open
Abstract
Background. Human immunodeficiency virus (HIV)-1 drug resistance mutations (DRMs) often accompany treatment failure. Although subtype differences are widely studied, DRM comparisons between subtypes either focus on specific geographic regions or include populations with heterogeneous treatments. Methods. We characterized DRM patterns following first-line failure and their impact on future treatment in a global, multi-subtype reverse-transcriptase sequence dataset. We developed a hierarchical modeling approach to address the high-dimensional challenge of modeling and comparing frequencies of multiple DRMs in varying first-line regimens, durations, and subtypes. Drug resistance mutation co-occurrence was characterized using a novel application of a statistical network model. Results. In 1425 sequences, 202 subtype B, 696 C, 44 G, 351 circulating recombinant forms (CRF)01_AE, 58 CRF02_AG, and 74 from other subtypes mutation frequencies were higher in subtypes C and CRF01_AE compared with B overall. Mutation frequency increased by 9%-20% at reverse transcriptase positions 41, 67, 70, 184, 215, and 219 in subtype C and CRF01_AE vs B. Subtype C and CRF01_AE exhibited higher predicted cross-resistance (+12%-18%) to future therapy options compared with subtype B. Topologies of subtype mutation networks were mostly similar. Conclusions. We find clear differences in DRM outcomes following first-line failure, suggesting subtype-specific ecological or biological factors that determine DRM patterns.
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Affiliation(s)
| | | | - Xi Luo
- Brown University , Providence, Rhode Island
| | | | | | - Yasong Wu
- National Centre for AIDS/STD Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing Ditan Hospital, Capital Medical University , China
| | | | | | - Fujie Zhang
- National Centre for AIDS/STD Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing Ditan Hospital, Capital Medical University , China
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Gallerano D, Ndlovu P, Makupe I, Focke-Tejkl M, Fauland K, Wollmann E, Puchhammer-Stöckl E, Keller W, Sibanda E, Valenta R. Comparison of the specificities of IgG, IgG-subclass, IgA and IgM reactivities in African and European HIV-infected individuals with an HIV-1 clade C proteome-based array. PLoS One 2015; 10:e0117204. [PMID: 25658330 PMCID: PMC4319756 DOI: 10.1371/journal.pone.0117204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/20/2014] [Indexed: 02/05/2023] Open
Abstract
A comprehensive set of recombinant proteins and peptides of the proteome of HIV-1 clade C was prepared and purified and used to measure IgG, IgG-subclass, IgA and IgM responses in HIV-infected patients from Sub-Saharan Africa, where clade C is predominant. As a comparison group, HIV-infected patients from Europe were tested. African and European patients showed an almost identical antibody reactivity profile in terms of epitope specificity and involvement of IgG, IgG subclass, IgA and IgM responses. A V3-peptide of gp120 was identified as major epitope recognized by IgG1>IgG2 = IgG4>IgG3, IgA>IgM antibodies and a C-terminal peptide represented another major peptide epitope for the four IgG subclasses. By contrast, gp41-derived-peptides were mainly recognized by IgG1 but not by the other IgG subclasses, IgA or IgM. Among the non-surface proteins, protease, reverse transcriptase+RNAseH, integrase, as well as the capsid and matrix proteins were the most frequently and strongly recognized antigens which showed broad IgG subclass and IgA reactivity. Specificities and magnitudes of antibody responses in African patients were stable during disease and antiretroviral treatment, and persisted despite severe T cell loss. Using a comprehensive panel of gp120, gp41 peptides and recombinant non-surface proteins of HIV-1 clade C we found an almost identical antibody recognition profile in African and European patients regarding epitopes and involved IgG-sublass, IgA- and IgM-responses. Immune recognition of gp120 peptides and non-surface proteins involved all four IgG subclasses and was indicative of a mixed Th1/Th2 immune response. The HIV-1 clade C proteome-based test allowed diagnosis and monitoring of antibody responses in the course of HIV-infections and assessment of isotype and subclass responses.
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Affiliation(s)
- Daniela Gallerano
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | | | | | - Margarete Focke-Tejkl
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Kerstin Fauland
- Institute of Molecular Biosciences—Structural Biology, Karl Franzens University, Graz, Austria
| | - Eva Wollmann
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | | | - Walter Keller
- Institute of Molecular Biosciences—Structural Biology, Karl Franzens University, Graz, Austria
| | - Elopy Sibanda
- Asthma, Allergy and Immune Dysfunction Clinic, Parirenyatwa University Teaching Hospital, Harare, Zimbabwe
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Huruy K, Maier M, Mulu A, Liebert UG. Limited increase in primary HIV-1C drug resistance mutations in treatment naïve individuals in Ethiopia. J Med Virol 2015; 87:978-84. [PMID: 25649964 DOI: 10.1002/jmv.24110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2014] [Indexed: 11/06/2022]
Abstract
Antiretroviral drug resistance is a major challenge for management and control of HIV-1 infection worldwide and particularly in resource limited countries. The frequency of primary drug resistance mutations (DRMs) and of naturally occurring polymorphisms was determined in 83 antiretroviral treatment (ART) naïve Ethiopian individuals infected with HIV-1, consecutively enrolled in 2010. In all individuals HIV-1C was found. The median (interquartile range) of CD4(+) T-cell count and viral load were 100 (49-201) cells/μl and 44,640 (12,553-134,664) copies/ml, respectively. Protease (PR) and reverse transcriptase (RT) genes of HIV-1 RNA were amplified and sequenced. The proportion of primary DRM to any drug class, using the World Health Organization mutation lists, was 7.2% (6/83), thus exceeding the WHO threshold limit of 5%. Three individuals (3.6%) had non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations, two individuals (2.4%) had protease inhibitor mutations, and one (1.2%) had mutations associated with two drug classes (nucleoside reverse transcriptase inhibitor and NNRTI). In addition, the frequency of polymorphisms in the PR and RT genes was higher compared with previous studies in Ethiopian as well as worldwide isolates. Hence, genotypic drug resistance testing as part of routine management of individuals seems reasonable even in resource limited countries prior to treatment in order to allow proper choice of ART.
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Affiliation(s)
- Kahsay Huruy
- Institute of Virology, Leipzig University, Leipzig, Germany; Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
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Hosseinzadeh MR, Shams-Bakhsh M, Osaloo SK, Brown JK. Phylogenetic relationships, recombination analysis, and genetic variability among diverse variants of tomato yellow leaf curl virus in Iran and the Arabian Peninsula: further support for a TYLCV center of diversity. Arch Virol 2013; 159:485-97. [PMID: 24068582 DOI: 10.1007/s00705-013-1851-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022]
Abstract
The discovery of five strains of TYLCV in Iran, including the most well-known and widespread, TYLCV-IL, spurred a detailed study of the full-length genomes of additional TYLCV field isolates and an in-depth analysis of phylogenetic relationships, extent of recombination, and genetic variability of TYLCV isolates within Iran and throughout the Arabian Peninsula. Phylogenetic analysis of complete genome sequences of TYLCV isolates from Iran and other countries revealed four monophyletic clusters could be differentiated based on geographical origin, indicating that recent dispersal of these populations (by the vector or by humans) from these four regions has occurred minimally, or not at all. Genetic analysis revealed that TYLCV-IL isolates from southern Iran possessed greater genetic variability than the northeastern isolates, a pattern that may be reflective of evolution driven by geographically dependent isolation. Similarly, isolates of TYLCV-OM originating from Oman showed greater genetic variability than TYLCV-OM variants from Iran. Major recombination events, which were detected in all strains of TYLCV had breakpoints initiating in the C1, C1/C4, C2/C3 and V1 open reading frames (ORFs) and ending at the non-coding region and the C1, C1/C2 and C3 ORFs. Hence, these regions have consistently served as hot spots for recombination worldwide during the evolution of all currently recognized isolates and strains of TYLCV.
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