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Abisi HK, Otieno LE, Irungu E, Onyambu FG, Chepchirchir A, Anzala O, Wamalwa DC, Nduati RW, McKinnon L, Kimani J, Mulinge MM. Net charge and position 22 of the V3 loop are associated with HIV-1 tropism in recently infected female sex workers in Nairobi, Kenya. Medicine (Baltimore) 2022; 101:e32024. [PMID: 36626483 PMCID: PMC9750520 DOI: 10.1097/md.0000000000032024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection affects around 37 million people worldwide, and in Kenya, key populations especially female sex workers (FSW), are thought to play a substantial role in the wider, mostly heterosexual HIV-1 transmission structure. Notably, HIV tropism has been found to correlate with HIV-1 transmission and disease progression in HIV-infected patients. In this study, recently infected FSWs from Nairobi, Kenya, were assessed for HIV tropism and the factors related to it. We used a cross-sectional study design to analyze 76 HIV-1 positive plasma samples obtained from FSWs enrolled in sex worker outreach program clinics in Nairobi between November 2020 and April 2021. The effects of clinical, demographic, and viral genetic characteristics were determined using multivariable logistic regression. HIV-1 subtype A1 accounted for 89.5% of all cases, with a prevalence of CXCR4-tropic viruses of 26.3%. WebPSSMR5X4 and Geno2Pheno [G2P:10-15% false positive rate] showed high concordance of 88%. Subjects infected with CXCR4-tropic viruses had statistically significant lower baseline CD4+T-cell counts than those infected with CCR5-tropic viruses (P = .044). Using multivariable logistic regression and adjusting for potential confounders, we found that net charge, the amino acid at position 22 of the V3 loop, and the geographic location of the subject were associated with tropism. A unit increase in V3 loop's net-charge increased the odds of a virus being CXCR4-tropic by 2.4 times (OR = 2.40, 95%CI = 1.35-5.00, P = .007). Second, amino acid threonine at position 22 of V3 loop increased the odds of a strain being X4 by 55.7 times compared to the alanine which occurred in CCR5-tropic strains (OR = 55.7, 95%CI = 4.04-84.1, P < .003). The Kawangware sex worker outreach program clinic was associated with CXCR4-tropic strains (P = .034), but there was there was no evidence of a distinct CXCR4-tropic transmission cluster. In conclusion, this study revealed a high concordance of WebPSSMR5X4 and Geno2Pheno in predicting HIV tropism. The most striking finding was that amino acid position 22 of the V3 loop is linked to tropism in HIV-1 subtype A1. Additional studies with a large dataset are warranted to confirm our findings.
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Affiliation(s)
- Hellen K Abisi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Leon E Otieno
- Molecular Medicine and Infectious Diseases Laboratory, University of Nairobi, Nairobi, Kenya
| | - Erastus Irungu
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Frank G Onyambu
- School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
| | | | - Omu Anzala
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Dalton C Wamalwa
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Ruth W Nduati
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Lyle McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Manitoba, MB, Canada
| | - Joshua Kimani
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Martin M Mulinge
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- * Correspondence: Martin M Mulinge, University of Nairobi, Chiromo Campus - Nairobi 30197-00100, Kenya (e-mail: )
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Evolution of Multiple Domains of the HIV-1 Envelope Glycoprotein during Coreceptor Switch with CCR5 Antagonist Therapy. Microbiol Spectr 2022; 10:e0072522. [PMID: 35727047 PMCID: PMC9431240 DOI: 10.1128/spectrum.00725-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 uses CD4 as a receptor and chemokine receptors CCR5 and/or CXCR4 as coreceptors. CCR5 antagonists are a class of antiretrovirals used to inhibit viral entry. Phenotypic prediction algorithms such as Geno2Pheno are used to assess CCR5 antagonist eligibility, for which the V3 region is screened. However, there exist scenarios where the algorithm cannot give an accurate prediction of tropism. The current study examined coreceptor shift of HIV-1 from CCR5-tropic strains to CXCR4-tropic or dual-tropic strains among five subjects in a clinical trial of the CCR5 antagonist vicriviroc. Envelope gene amplicon libraries were constructed and subjected to next-generation sequencing, as well as single-clone sequencing and functional analyses. Approximately half of the amplified full-length single envelope-encoding clones had no significant activity for infection of cells expressing high levels of CD4 and CCR5 or CXCR4. Functional analysis of 9 to 21 individual infectious clones at baseline and at the time of VF were used to construct phylogenetic trees and sequence alignments. These studies confirmed that specific residues and the overall charge of the V3 loop were the major determinants of coreceptor use, in addition to specific residues in other domains of the envelope protein in V1/V2, V4, C3, and C4 domains that may be important for coreceptor shift. These results provide greater insight into the viral genetic determinants of coreceptor shift. IMPORTANCE This study is novel in combining single-genome sequence analysis and next-generation sequencing to characterize HIV-1 quasispecies. The work highlights the importance of mutants present at frequencies of 1% or less in development of drug resistance. This study highlights a critical role of specific amino acid substitutions outside V3 that contribute to coreceptor shift as well as important roles of the V1/V2, V4, C3, and C4 domain residues.
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Tang R, Yu Z, Ma Y, Wu Y, Phoebe Chen YP, Wong L, Li J. Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning. Bioinformatics 2021; 37:750-758. [PMID: 33063094 DOI: 10.1093/bioinformatics/btaa887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/12/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION Infection with strains of different subtypes and the subsequent crossover reading between the two strands of genomic RNAs by host cells' reverse transcriptase are the main causes of the vast HIV-1 sequence diversity. Such inter-subtype genomic recombinants can become circulating recombinant forms (CRFs) after widespread transmissions in a population. Complete prediction of all the subtype sources of a CRF strain is a complicated machine learning problem. It is also difficult to understand whether a strain is an emerging new subtype and if so, how to accurately identify the new components of the genetic source. RESULTS We introduce a multi-label learning algorithm for the complete prediction of multiple sources of a CRF sequence as well as the prediction of its chronological number. The prediction is strengthened by a voting of various multi-label learning methods to avoid biased decisions. In our steps, frequency and position features of the sequences are both extracted to capture signature patterns of pure subtypes and CRFs. The method was applied to 7185 HIV-1 sequences, comprising 5530 pure subtype sequences and 1655 CRF sequences. Results have demonstrated that the method can achieve very high accuracy (reaching 99%) in the prediction of the complete set of labels of HIV-1 recombinant forms. A few wrong predictions are actually incomplete predictions, very close to the complete set of genuine labels. AVAILABILITY AND IMPLEMENTATION https://github.com/Runbin-tang/The-source-of-HIV-CRFs-prediction. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Runbin Tang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China.,Advanced Analytics Institute, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Zuguo Yu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China.,School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Yuanlin Ma
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China
| | - Yaoqun Wu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Limsoon Wong
- School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Jinyan Li
- Advanced Analytics Institute, University of Technology Sydney, Sydney, NSW 2007, Australia
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Knyazev S, Hughes L, Skums P, Zelikovsky A. Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. Brief Bioinform 2021; 22:96-108. [PMID: 32568371 PMCID: PMC8485218 DOI: 10.1093/bib/bbaa101] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 01/04/2023] Open
Abstract
The unprecedented coverage offered by next-generation sequencing (NGS) technology has facilitated the assessment of the population complexity of intra-host RNA viral populations at an unprecedented level of detail. Consequently, analysis of NGS datasets could be used to extract and infer crucial epidemiological and biomedical information on the levels of both infected individuals and susceptible populations, thus enabling the development of more effective prevention strategies and antiviral therapeutics. Such information includes drug resistance, infection stage, transmission clusters and structures of transmission networks. However, NGS data require sophisticated analysis dealing with millions of error-prone short reads per patient. Prior to the NGS era, epidemiological and phylogenetic analyses were geared toward Sanger sequencing technology; now, they must be redesigned to handle the large-scale NGS datasets and properly model the evolution of heterogeneous rapidly mutating viral populations. Additionally, dedicated epidemiological surveillance systems require big data analytics to handle millions of reads obtained from thousands of patients for rapid outbreak investigation and management. We survey bioinformatics tools analyzing NGS data for (i) characterization of intra-host viral population complexity including single nucleotide variant and haplotype calling; (ii) downstream epidemiological analysis and inference of drug-resistant mutations, age of infection and linkage between patients; and (iii) data collection and analytics in surveillance systems for fast response and control of outbreaks.
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Dimeglio C, Raymond S, Jeanne N, Reynes C, Carcenac R, Lefebvre C, Cazabat M, Nicot F, Delobel P, Izopet J. THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage. Bioinformatics 2020; 36:416-421. [PMID: 31350559 DOI: 10.1093/bioinformatics/btz585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/28/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION The circulating recombinant form of HIV-1 CRF02-AG is the most frequent non-B subtype in Europe. Anti-HIV therapy and pathophysiological studies on the impact of HIV-1 tropism require genotypic determination of HIV-1 tropism for non-B subtypes. But genotypic approaches based on analysis of the V3 envelope region perform poorly when used to determine the tropism of CRF02-AG. We, therefore, designed an algorithm based on information from the gp120 and gp41 ectodomain that better predicts the tropism of HIV-1 subtype CRF02-AG. RESULTS We used a bio-statistical method to identify the genotypic determinants of CRF02-AG coreceptor use. Toulouse HIV Extended Tropism Algorithm (THETA), based on a Least Absolute Shrinkage and Selection Operator method, uses HIV envelope sequence from phenotypically characterized clones. Prediction of R5X4/X4 viruses was 86% sensitive and that of R5 viruses was 89% specific with our model. The overall accuracy of THETA was 88%, making it sufficiently reliable for predicting the tropism of subtype CRF02-AG sequences. AVAILABILITY AND IMPLEMENTATION Binaries are freely available for download at https://github.com/viro-tls/THETA. It was implemented in Matlab and supported on MS Windows platform. The sequence data used in this work are available from GenBank under the accession numbers MK618182-MK618417.
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Affiliation(s)
- Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Stéphanie Raymond
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Christelle Reynes
- Institut de Génomique Fonctionnelle, 34090 Montpellier, France.,UM-Université de Montpellier, 34090 Montpellier, France.,Faculté de Pharmacie, 34090 Montpellier, France
| | | | | | | | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Pierre Delobel
- CHU de Toulouse, Service de Maladies Infectieuses et Tropicales, 31059 Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
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6
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Gartner MJ, Gorry PR, Tumpach C, Zhou J, Dantanarayana A, Chang JJ, Angelovich TA, Ellenberg P, Laumaea AE, Nonyane M, Moore PL, Lewin SR, Churchill MJ, Flynn JK, Roche M. Longitudinal analysis of subtype C envelope tropism for memory CD4 + T cell subsets over the first 3 years of untreated HIV-1 infection. Retrovirology 2020; 17:24. [PMID: 32762760 PMCID: PMC7409430 DOI: 10.1186/s12977-020-00532-2] [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: 06/02/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background HIV-1 infects a wide range of CD4+ T cells with different phenotypic properties and differing expression levels of entry coreceptors. We sought to determine the viral tropism of subtype C (C-HIV) Envelope (Env) clones for different CD4+ T cell subsets and whether tropism changes during acute to chronic disease progression. HIV-1 envs were amplified from the plasma of five C-HIV infected women from three untreated time points; less than 2 months, 1-year and 3-years post-infection. Pseudoviruses were generated from Env clones, phenotyped for coreceptor usage and CD4+ T cell subset tropism was measured by flow cytometry. Results A total of 50 C-HIV envs were cloned and screened for functionality in pseudovirus infection assays. Phylogenetic and variable region characteristic analysis demonstrated evolution in envs between time points. We found 45 pseudoviruses were functional and all used CCR5 to mediate entry into NP2/CD4/CCR5 cells. In vitro infection assays showed transitional memory (TM) and effector memory (EM) CD4+ T cells were more frequently infected (median: 46% and 25% of total infected CD4+ T cells respectively) than naïve, stem cell memory, central memory and terminally differentiated cells. This was not due to these subsets contributing a higher proportion of the CD4+ T cell pool, rather these subsets were more susceptible to infection (median: 5.38% EM and 2.15% TM cells infected), consistent with heightened CCR5 expression on EM and TM cells. No inter- or intra-participant changes in CD4+ T cell subset tropism were observed across the three-time points. Conclusions CD4+ T cell subsets that express more CCR5 were more susceptible to infection with C-HIV Envs, suggesting that these may be the major cellular targets during the first 3 years of infection. Moreover, we found that viral tropism for different CD4+ T cell subsets in vitro did not change between Envs cloned from acute to chronic disease stages. Finally, central memory, naïve and stem cell memory CD4+ T cell subsets were susceptible to infection, albeit inefficiently by Envs from all time-points, suggesting that direct infection of these cells may help establish the latent reservoir early in infection.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Carolin Tumpach
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jingling Zhou
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Ashanti Dantanarayana
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - J Judy Chang
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Thomas A Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,Life Sciences, Burnet Institute, Melbourne, VIC, Australia
| | - Paula Ellenberg
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Annemarie E Laumaea
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Molati Nonyane
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia. .,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia. .,School of Clinical Sciences, Monash University, Melbourne, VIC, Australia.
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Melbourne, VIC, Australia. .,The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia.
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Distefano M, Lanzarotti E, Fernández MF, Mangano A, Martí M, Aulicino P. Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences. Sci Rep 2020; 10:12583. [PMID: 32724045 PMCID: PMC7387458 DOI: 10.1038/s41598-020-69408-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/30/2020] [Indexed: 02/05/2023] Open
Abstract
HIV-1 determinants of coreceptor usage within the gp120 V3 loop have been broadly studied over the past years. This information has led to the development of state-of the-art bioinformatic tools that are useful to predict co-receptor usage based on the V3 loop sequence mainly of subtypes B, C and A. However, these methods show a poor performance for subtype F V3 loops, which are found in an increasing number of HIV-1 strains worldwide. In the present work we investigated determinants of viral tropisms in the understudied subtype F by looking at genotypic and structural information of coreceptor:V3 loop interactions in a novel group of 40 subtype F V3 loops obtained from HIV-1 strains phenotypically characterized either as syncytium inducing or non-syncytium inducing by the MT-2 assay. We provide novel information about estimated interactions energies between a set of V3 loops with known tropism in subtype F, that allowed us to improve predictions of the coreceptor usage for this subtype. Understanding genetic and structural features underlying HIV coreceptor usage across different subtypes is relevant for the rational design of preventive and therapeutic strategies aimed at limiting the HIV-1 epidemic worldwide.
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Affiliation(s)
- Maximiliano Distefano
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Departamento de Computación, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Fernández
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Aulicino
- Laboratorio de Biología Celular Y Retrovirus- CONICET, Hospital de Pediatría "J.P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina.
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Comparative analyses of error handling strategies for next-generation sequencing in precision medicine. Sci Rep 2020; 10:5750. [PMID: 32238883 PMCID: PMC7113248 DOI: 10.1038/s41598-020-62675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/18/2020] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) offers the opportunity to sequence millions and billions of DNA sequences in a short period, leading to novel applications in personalized medicine, such as cancer diagnostics or antiviral therapy. Nevertheless, sequencing technologies have different error rates, which occur during the sequencing process. If the NGS data is used for diagnostics, these sequences with errors are typically neglected or a worst-case scenario is assumed. In the current study, we focused on the impact of ambiguous bases on therapy recommendations for Human Immunodeficiency Virus 1 (HIV-1) patients. Concretely, we analyzed the treatment recommendation with entry blockers based on prediction models for co-receptor tropism. We compared three different error handling strategies that have been used in the literature, namely (i) neglection, (ii) worst-case assumption, and (iii) deconvolution with a majority vote. We could show that for two or more ambiguous positions per sequence a reliable prediction is generally no longer possible. Moreover, also the position of ambiguity plays a crucial role. Thus, we analyzed the error probability distributions of existing sequencing technologies, e.g., Illumina MiSeq or PacBio, with respect to the aforementioned error handling strategies and it turned out that neglection outperforms the other strategies in the case where no systematic errors are present. In other cases, the deconvolution strategy with the majority vote should be preferred.
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9
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Gartner MJ, Roche M, Churchill MJ, Gorry PR, Flynn JK. Understanding the mechanisms driving the spread of subtype C HIV-1. EBioMedicine 2020; 53:102682. [PMID: 32114391 PMCID: PMC7047180 DOI: 10.1016/j.ebiom.2020.102682] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C (C-HIV) is the most prevalent form of HIV-1 globally, accounting for approximately 50% of infections worldwide. C-HIV is the predominant and near-exclusive subtype in the low resource regions of India and Southern Africa. Given the vast diversity of HIV-1 subtypes, it is curious as to why C-HIV constitutes such a large proportion of global infections. This enriched prevalence may be due to phenotypic differences between C-HIV isolates and other viral strains that permit enhanced transmission efficiency or, pathogenicity, or might due to the socio-demographics of the regions where C-HIV is endemic. Here, we compare the mechanisms of C-HIV pathogenesis to less prominent HIV-1 subtypes, including viral genetic and phenotypic characteristics, and host genetic variability, to understand whether evolutionary factors drove C-HIV to predominance.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia.
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10
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Löchel HF, Riemenschneider M, Frishman D, Heider D. SCOTCH: subtype A coreceptor tropism classification in HIV-1. Bioinformatics 2019; 34:2575-2580. [PMID: 29554213 DOI: 10.1093/bioinformatics/bty170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/14/2018] [Indexed: 01/25/2023] Open
Abstract
Motivation The V3 loop of the gp120 glycoprotein of the Human Immunodeficiency Virus 1 (HIV-1) is considered to be responsible for viral coreceptor tropism. gp120 interacts with the CD4 receptor of the host cell and subsequently V3 binds either CCR5 or CXCR4. Due to the fact that the CCR5 coreceptor is targeted by entry inhibitors, a reliable prediction of the coreceptor usage of HIV-1 is of great interest for antiretroviral therapy. Although several methods for the prediction of coreceptor tropism are available, almost all of them have been developed based on only subtype B sequences, and it has been shown in several studies that the prediction of non-B sequences, in particular subtype A sequences, are less reliable. Thus, the aim of the current study was to develop a reliable prediction model for subtype A viruses. Results Our new model SCOTCH is based on a stacking approach of classifier ensembles and shows a significantly better performance for subtype A sequences compared to other available models. In particular for low false positive rates (between 0.05 and 0.2, i.e. recommendation in the German and European Guidelines for tropism prediction), SCOTCH shows significantly better prediction performances in terms of partial area under the curves and diagnostic odds ratios compared to existing tools, and thus can be used to reliably predict coreceptor tropism for subtype A sequences. Availability and implementation SCOTCH can be downloaded/accessed at http://www.heiderlab.de.
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Affiliation(s)
- Hannah F Löchel
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
| | | | - Dmitrij Frishman
- Department of Genome-Oriented Bioinformatics, Technical University of Munich, Freising, Germany.,Laboratory of Bioinformatics, St. Petersburg State Polytechnic University, St. Petersburg, Russia
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
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Banin AN, Tuen M, Bimela JS, Tongo M, Zappile P, Khodadadi‐Jamayran A, Nanfack AJ, Okonko IO, Meli J, Wang X, Mbanya D, Ngogang J, Gorny MK, Heguy A, Fokunang C, Duerr R. Near full genome characterization of HIV-1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns. J Int AIDS Soc 2019; 22:e25362. [PMID: 31353798 PMCID: PMC6661401 DOI: 10.1002/jia2.25362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION In Cameroon, a manifold diversity of HIV strains exists with CRF02_AG and unique recombinant forms (URFs) being the predominant strains. In recent years, a steady increase in URFs and clade F2 viruses has been monitored through partial genome sequencing. There is an information gap in the characterization of emerging URFs along the full genome, which is needed to address the challenges URFs pose towards diagnosis, treatment and HIV-1 vaccine design. METHOD Eighteen Cameroonian URFs from samples collected between the years 2000 and 2015 were studied using a newly developed near full genome sequencing (NFGS) protocol based on variable nested RT-PCRs with a versatile primer set. Near full genomes were characterized for recombination patterns and sequence signatures with possible impact on antiretroviral treatment or Env-directed immune responses. Third-generation sequencing (3GS) of near full or half genomes (HGs) gave insight into intra-patient URF diversity. RESULTS The characterized URFs were composed of a broad variety of subtypes and recombinants including A, F, G, CRF01_AE, CRF02_AG and CRF22_01A1. Phylogenetic analysis unveiled dominant CRF02_AG and F2 recombination patterns. 3GS indicated a high intra-patient URF diversity with up to four distinct viral sub-populations present in plasma at the same time. URF pol genomic analysis revealed a number of accessory drug resistance mutations (DRMs) in the ART-naïve participants. Genotypic env analysis suggests CCR5 usage in 14/18 samples and identified deviations at residues, critical for gp120/gp41 interphase and CD4 binding site broadly neutralizing antibodies in more than half of the studied URFs. V1V2 sites of immune pressure in the human RV144 vaccine study varied in more than a third of URFs. CONCLUSIONS This study identified novel mosaic patterns in URFs in Cameroon. In line with the regional predominance of CRF_02AG and the increased prevalence of clade F2, prominent CRF_02AG and F2 background patterns were observed underlying the URFs. In the context of the novel mosaic genomes, the impact of the identified accessory DRMs and Env epitope variations on treatment and immune control remains elusive. The evolving diversity of HIV-1 URFs in Cameroon requires continuous monitoring to respond to the increasing challenges for diagnosis, antiretroviral treatment and prevention.
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Affiliation(s)
- Andrew N Banin
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
- Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Michael Tuen
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
| | - Jude S Bimela
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
- Faculty of ScienceDepartment of BiochemistryUniversity of Yaoundé 1YaoundéCameroon
| | - Marcel Tongo
- Center of Research for Emerging and Re‐Emerging Diseases (CREMER)Institute of Medical Research and Study of Medicinal PlantsYaoundéCameroon
| | - Paul Zappile
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
| | - Alireza Khodadadi‐Jamayran
- Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC)Division of Advanced Research Technologies (DART)New York University Langone Medical CenterNew YorkNYUSA
| | - Aubin J Nanfack
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
- Medical Diagnostic CenterYaoundéCameroon
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and ManagementYaoundéCameroon
| | - Iheanyi O Okonko
- Virus Research UnitDepartment of MicrobiologyUniversity of Port HarcourtPort HarcourtNigeria
| | | | - Xiaohong Wang
- Manhattan Veterans Affairs Harbor Healthcare SystemsNew YorkNYUSA
| | - Dora Mbanya
- Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Jeanne Ngogang
- Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Miroslaw K Gorny
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
| | - Adriana Heguy
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
| | - Charles Fokunang
- Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Ralf Duerr
- Department of PathologyNew York University School of MedicineNew YorkNYUSA
- Manhattan Veterans Affairs Harbor Healthcare SystemsNew YorkNYUSA
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12
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Hongjaisee S, Nantasenamat C, Carraway TS, Shoombuatong W. HIVCoR: A sequence-based tool for predicting HIV-1 CRF01_AE coreceptor usage. Comput Biol Chem 2019; 80:419-432. [PMID: 31146118 DOI: 10.1016/j.compbiolchem.2019.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Determination of HIV-1 coreceptor usage is strongly recommended before starting the coreceptor-specific inhibitors for HIV treatment. Currently, the genotypic assays are the most interesting tools due to they are more feasible than phenotypic assays. However, most of prediction models were developed and validated by data set of HIV-1 subtype B and C. The present study aims to develop a powerful and reliable model to accurately predict HIV-1 coreceptor usage for CRF01_AE subtype called HIVCoR. HIVCoR utilized random forest and support vector machine as the prediction model, together with amino acid compositions, pseudo amino acid compositions and relative synonymous codon usage frequencies as the input feature. The overall success rate of 93.79% was achieved from the external validation test on the objective benchmark dataset. Comparison results indicated that HIVCoR was superior to other bioinformatics tools and genotypic predictors. For the convenience of experimental scientists, a user-friendly webserver has been established at http://codes.bio/hivcor/.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiangmai 50200, Thailand; Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai 50200, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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13
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Kalu AW, Telele NF, Aralaguppe SG, Gebre-Selassie S, Fekade D, Marrone G, Sonnerborg A. Coreceptor Tropism and Maraviroc Sensitivity of Clonally Derived Ethiopian HIV-1C Strains Using an in-house Phenotypic Assay and Commonly Used Genotypic Methods. Curr HIV Res 2019; 16:113-120. [PMID: 29766813 DOI: 10.2174/1570162x16666180515124836] [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: 01/04/2018] [Revised: 04/23/2018] [Accepted: 05/07/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C. METHODS Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line. RESULTS The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond's method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc. CONCLUSION There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Ethiopia
| | - Gaetano Marrone
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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14
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Abstract
HIV-1 env sequencing enables predictions of viral coreceptor tropism and phylogenetic investigations of transmission events. The aim of the study was to estimate the contribution of non-R5 strains to the viral spread in Poland. Partial proviral env sequences were retrieved from baseline blood samples of patients with newly diagnosed HIV-1 infection between 2008-2014, including 46 patients with recent HIV-1 infection (RHI), and 246 individuals with long-term infection (LTHI). These sequences were subjected to the genotypic coreceptor tropism predictions and phylogenetic analyses to identify transmission clusters. Overall, 27 clusters with 57 sequences (19.5%) were detected, including 15 sequences (26.3%) from patients with RHI. The proportion of non-R5 strains among all study participants was 23.3% (68/292), and was comparable between patients with RHI and LTHI (11/46, 23.9% vs 57/246, 23.2%; p = 1.000). All 11 patients with non-R5 strains and RHI were men having sex with men (MSM). Among these patients, 4 had viral sequences grouped within phylogenetic cluster with another sequence of non-R5 strain obtained from patient with LTHI, indicating potential acquisition of non-R5 HIV-1 for at least 4/46 (8.7%) patients with RHI. We were unable to confirm the contribution of patients with RHI to the forward transmission of non-R5 strains, but a relatively high proportion of non-R5 strains among them deserves attention due to the limited susceptibility to CCR5 antagonists.
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15
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Morton SP, Phillips JB, Phillips JL. The Molecular Basis of pH-Modulated HIV gp120 Binding Revealed. Evol Bioinform Online 2019; 15:1176934319831308. [PMID: 30872918 PMCID: PMC6407167 DOI: 10.1177/1176934319831308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/17/2018] [Indexed: 01/31/2023] Open
Abstract
Decades of research has yet to provide a vaccine for HIV, the virus which causes AIDS. Recent theoretical research has turned attention to mucosa pH levels over systemic pH levels. Previous research in this field developed a computational approach for determining pH sensitivity that indicated higher potential for transmission at mucosa pH levels present during intercourse. The process was extended to incorporate a principal component analysis (PCA)-based machine learning technique for classification of gp120 proteins against a known transmitted variant called Biomolecular Electro-Static Indexing (BESI). The original process has since been extended to the residue level by a process we termed Electrostatic Variance Masking (EVM) and used in conjunction with BESI to determine structural differences present among various subspecies across Clades A1 and C. Results indicate that structures outside of the core selected by EVM may be responsible for binding affinity observed in many other studies and that pH modulation of select substructures indicated by EVM may influence specific regions of the viral envelope protein (Env) involved in protein-protein interactions.
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Affiliation(s)
- Scott P Morton
- Center for Computational Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA
| | | | - Joshua L Phillips
- Center for Computational Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA.,Department of Computer Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA
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16
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Sojane K, Kangethe RT, Chang CC, Moosa MYS, Lewin SR, French MA, Ndung'u T. Individuals with HIV-1 Subtype C Infection and Cryptococcal Meningitis Exhibit Viral Genetic Intermixing of HIV-1 Between Plasma and Cerebrospinal Fluid and a High Prevalence of CXCR4-Using Variants. AIDS Res Hum Retroviruses 2018; 34:607-620. [PMID: 29658309 PMCID: PMC6314437 DOI: 10.1089/aid.2017.0209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genotypic properties of human immunodeficiency virus type 1 (HIV-1) subtype C in individuals presenting with cryptococcal meningitis (CM) are not well established. Employing single-genome amplification as well as bulk PCR, cloning and sequencing strategies, we evaluated the genetic properties of HIV-1 subtype C env in 16 antiretroviral therapy-naive study participants with CM. Eleven of the 16 participants had matched blood plasma and cerebrospinal fluid (CSF) evaluated, with the rest having either a plasma or CSF sample evaluated. Before antiretroviral therapy initiation, matched plasma and CSF-derived env sequences of all 11 participants displayed genetic intermixing between the two compartments. Overall, 7 of the 16 (∼43.8%) participants harbored CXCR4-using variants in plasma and/or CSF, according to coreceptor usage prediction algorithms. This study suggests that HIV-1 subtype C genetic intermixing between peripheral blood and the central nervous system is common in individuals presenting with CM, and that CXCR4 usage is present in one or both compartments in approximately 44% of individuals.
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Affiliation(s)
- Katlego Sojane
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Richard T Kangethe
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Christina C Chang
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
| | - Mahomed-Yunus S Moosa
- 3 Department of Infectious Diseases, King Edward VIII Hospital, University of KwaZulu-Natal , Durban, South Africa
| | - Sharon R Lewin
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
- 4 The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital , Melbourne, Australia
| | - Martyn A French
- 5 Medical School and School of Biomedical Sciences, University of Western Australia , Perth, Australia
- 6 Department of Clinical Immunology, Royal Perth Hospital and PathWest Laboratory Medicine , Perth, Australia
| | - Thumbi Ndung'u
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
- 7 Africa Health Research Institute , Durban, South Africa
- 8 Ragon Institute of MGH, MIT and Harvard University , Cambridge, Massachusetts
- 9 Max Planck Institute for Infection Biology , Berlin, Germany
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17
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Novel Strategy To Adapt Simian-Human Immunodeficiency Virus E1 Carrying env from an RV144 Volunteer to Rhesus Macaques: Coreceptor Switch and Final Recovery of a Pathogenic Virus with Exclusive R5 Tropism. J Virol 2018; 92:JVI.02222-17. [PMID: 29743361 DOI: 10.1128/jvi.02222-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/17/2018] [Indexed: 02/06/2023] Open
Abstract
The phase III RV144 human immunodeficiency virus (HIV) vaccine trial conducted in Thailand remains the only study to show efficacy in decreasing the HIV acquisition risk. In Thailand, circulating recombinant forms of HIV clade A/E (CRF01_AE) predominate; in such viruses, env originates from clade E (HIV-E). We constructed a simian-human immunodeficiency virus (SHIV) chimera carrying env isolated from an RV144 placebo recipient in the SHIV-1157ipd3N4 backbone. The latter contains long terminal repeats (LTRs) with duplicated NF-κB sites, thus resembling HIV LTRs. We devised a novel strategy to adapt the parental infectious molecular clone (IMC), R5 SHIV-E1, to rhesus macaques: the simultaneous depletion of B and CD8+ cells followed by the intramuscular inoculation of proviral DNA and repeated administrations of cell-free virus. High-level viremia and CD4+ T-cell depletion ensued. Passage 3 virus unexpectedly caused acute, irreversible CD4+ T-cell loss; the partially adapted SHIV had become dual tropic. Virus and IMCs with exclusive R5 tropism were reisolated from earlier passages, combined, and used to complete adaptation through additional macaques. The final isolate, SHIV-E1p5, remained solely R5 tropic. It had a tier 2 neutralization phenotype, was mucosally transmissible, and was pathogenic. Deep sequencing revealed 99% Env amino acid sequence conservation; X4-only and dual-tropic strains had evolved independently from an early branch of parental SHIV-E1. To conclude, our primate model data reveal that SHIV-E1p5 recapitulates important aspects of HIV transmission and pathobiology in humans.IMPORTANCE Understanding the protective principles that lead to a safe, effective vaccine against HIV in nonhuman primate (NHP) models requires test viruses that allow the evaluation of anti-HIV envelope responses. Reduced HIV acquisition risk in RV144 has been linked to nonneutralizing IgG antibodies with a range of effector activities. Definitive experiments to decipher the mechanisms of the partial protection observed in RV144 require passive-immunization studies in NHPs with a relevant test virus. We have generated such a virus by inserting env from an RV144 placebo recipient into a SHIV backbone with HIV-like LTRs. The final SHIV-E1p5 isolate, grown in rhesus monkey peripheral blood mononuclear cells, was mucosally transmissible and pathogenic. Earlier SHIV-E passages showed a coreceptor switch, again mimicking HIV biology in humans. Thus, our series of SHIV-E strains mirrors HIV transmission and disease progression in humans. SHIV-E1p5 represents a biologically relevant tool to assess prevention strategies.
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Fokam J, Bellocchi MC, Armenia D, Nanfack AJ, Carioti L, Continenza F, Takou D, Temgoua ES, Tangimpundu C, Torimiro JN, Koki PN, Fokunang CN, Cappelli G, Ndjolo A, Colizzi V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Next-generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV-1 vertically infected children. Medicine (Baltimore) 2018; 97:e0176. [PMID: 29595649 PMCID: PMC5895385 DOI: 10.1097/md.0000000000010176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
With limited and low-genetic barrier drugs used for the prevention of mother-to-child transmission (PMTCT) of HIV in sub-Saharan Africa, vertically transmitted HIV-1 drug-resistance (HIVDR) is concerning and might prompt optimal pediatric strategies.The aim of this study was to ascertain HIVDR and viral-tropism in majority and minority populations among Cameroonian vertically infected children.A comparative analysis among 18 HIV-infected children (7 from PMTCT-exposed mothers and 11 from mothers without PMTCT-exposure) was performed. HIVDR and HIV-1 co-receptor usage was evaluated by analyzing sequences obtained by both Sanger sequencing and ultra-deep 454-pyrosequencing (UDPS), set at 1% threshold.Overall, median (interquartile range) age, viremia, and CD4 count were 6 (4-10) years, 5.5 (4.9-6.0) log10 copies/mL, and 526 (282-645) cells/mm, respectively. All children had wild-type viruses through both Sanger sequencing and UDPS, except for 1 PMTCT-exposed infant harboring minority K103N (8.31%), born to a mother exposed to AZT+3TC+NVP. X4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS). Rate of X4-tropic viruses was 0% (0/6) below 5 years (also as minority species), and became relatively high above 5 years (55.6% [5/9], P = .040. X4-tropic viruses were higher with CD4 ≤15% (4/9 [44.4%]) versus CD4 >15% (1/6 [16.7%], P = .580); similarly for CD4 ≤200 (3/4 [75%]) versus CD4 >200 (2/11 [18.2%] cells/mm, P = .077.NGS has the ability of excluding NRTI- and NNRTI-mutations as minority species in all but 1 children, thus supporting the safe use of these drug-classes in those without such mutations, henceforth sparing ritonavir-boosted protease inhibitors or integrase inhibitors for the few remaining cases. In children under five years, X4-tropic variants would be rare, suggesting vertical-transmission with CCR5-tropic viruses and possible maraviroc usage at younger ages.
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Affiliation(s)
- Joseph Fokam
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- University of Yaounde I
- National HIV Drug Resistance Prevention and Surveillance Working Group, Yaounde, Cameroon
| | | | | | - Aubin J. Nanfack
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- New York University School of Medicine, New York, NY
| | | | - Fabio Continenza
- National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Desire Takou
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Edith S. Temgoua
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Charlotte Tangimpundu
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Judith N. Torimiro
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Yaounde I
- National HIV Drug Resistance Prevention and Surveillance Working Group, Yaounde, Cameroon
| | - Paul N. Koki
- University of Yaounde I
- Mother-Child Center, Chantal BIYA Foundation, Yaounde
| | | | | | - Alexis Ndjolo
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Yaounde I
| | - Vittorio Colizzi
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- UNESCO Board of Multidisciplinary Biotechnology, Rome, Italy
| | | | - Carlo-Federico Perno
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
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19
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Matume ND, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Bessong PO. Next generation sequencing reveals a high frequency of CXCR4 utilizing viruses in HIV-1 chronically infected drug experienced individuals in South Africa. J Clin Virol 2018; 103:81-87. [PMID: 29661652 DOI: 10.1016/j.jcv.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Entry inhibitors, such as Maraviroc, bind to CCR5 inhibiting entry of CCR5 utilizing viruses (R5 viruses). In the course of HIV infection, CXCR4 utilizing viruses (X4 viruses) may emerge and outgrow R5 viruses, and potentially limit the effectiveness of Maraviroc. The use of Maraviroc is reserved for salvage therapy in South Africa. OBJECTIVE In this study, we examined the frequency of R5 and X4 viruses, using next generation sequencing, in patients under treatment to draw inferences on the utility of Maraviroc in a South African population. STUDY DESIGN Proviral DNA was isolated from peripheral blood mononuclear cells (PBMC) of 72 chronically HIV infected patients on antiretroviral treatment. HIV V3 loop gene was amplified and sequenced on an Illumina MiniSeq platform. Viral subtypes were determined by the jumping profile Hidden Markov Model (jpHMM) and REGA genotyping tools. De Novo consensus sequences were derived for the majority and minority populations for each patient using Geneious® software version 8.1.5. HIV-1 tropism was inferred using PSSMsinsi, Geno2pheno and Phenoseq-C web-based tools. RESULTS Quality V3 loop sequences were obtained from 72 patients, with 5 years (range: 0-16) median duration on treatment. Subtypes A1, B and C viruses were identified at frequencies of 4% (3/72), 4% (3/72) and 92% (66/72) respectively. Fifty four percent (39/72) of patients exclusively harboured R5 viral quasispecies; and 21% (15/72) exclusively harbored X4 viral quasispecies. Twenty five percent of patients (18/72) harbored dual/mixture of R5X4 quasispecies. Of these 18 patients, about 28% (5/18) harbored the R5+X4, a mixture with a majority R5 and minority X4 viruses, while about 72% (13/18) harbored the R5X4+ mixture with a majority X4 and minority R5 viruses. The proportion of all patients who harbored X4 viruses either exclusively or dual/mixture was 46% (33/72). Thirty-five percent (23/66) of the patients who were of HIV-1 subtype C harboured X4 viruses (χ2 = 3.58; p = .058), and 57% of these (13/23) harbored X4 viruses exclusively. CD4+ cell count less than 350 cell/μl was associated with the presence of X4 viruses (χ2 = 4.99; p = .008). CONCLUSION The effectiveness of Maraviroc as a component in salvage therapy may be compromised for a significant number of chronically infected patients harboring CXCR4 utilizing viruses.
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Affiliation(s)
- Nontokozo D Matume
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa.
| | - Denis M Tebit
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA.
| | - Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA.
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA.
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA.
| | - Pascal O Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa.
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20
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Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa. Sci Rep 2018; 8:2363. [PMID: 29403064 PMCID: PMC5799384 DOI: 10.1038/s41598-018-20814-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/24/2018] [Indexed: 11/08/2022] Open
Abstract
Genotypic tropism testing (GTT) for co-receptor usage is a recommended tool for clinical practice before administration of the CCR5-antagonist maraviroc. For some isolates, phenotypic tropism testing (PTT) revealed discordant results with GTT. In this study, we performed a comparative study between GTT and PTT in HIV-1C from East Africa (HIV-1CEA) and compared the data with HIV-1B and 01_AE and described the maraviroc susceptibility in the CCR5-tropic strains. Patient-derived HIV-1 envgp120 region was cloned into a modified pNL4-3 plasmid expressing the luciferase gene. rPhenotyping dissected single clones from 31 HIV-1CEA infected patients and four strains with known phenotype. Additionally, 68 clones from 18 patients (HIV-1B: 5, 01_AE: 7, HIV-1CEA: 6) were used to determine the PTT in GHOST cell line. The respective V3-sequences were used for GTT. R5-tropic strains from HIV-1CEA (n = 20) and non-C (n = 12) were tested for maraviroc sensitivity in TZMbl cell line. The GTT falsely called a higher proportion of X4-tropic strains in HIV-1CET compared to PTT by both rPhenotyping and the GHOST-cell assay. When multiple clones were tested in a subset of patients’ samples, both dual-tropic and R5-tropic strains were identified for HIV-1C. Relatively higher EC50 values were observed in HIV-1C strains than the non-C strains (p = 0.002).
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21
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort. PLoS One 2017; 12:e0182384. [PMID: 28841646 PMCID: PMC5571954 DOI: 10.1371/journal.pone.0182384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Background Genotypic tropism testing (GTT) has been developed largely on HIV-1 subtype B. Although a few reports have analysed the utility of GTT in other subtypes, more studies using HIV-1 subtype C (HIV-1C) are needed, considering the huge contribution of HIV-1C to the global epidemic. Methods Plasma was obtained from 420 treatment-naïve HIV-1C infected Ethiopians recruited 2009–2011. The V3 region was sequenced and the coreceptor usage was predicted by five tools: Geno2Pheno clinical–and clonal–models, PhenoSeq-C, C-PSSM and Raymond’s algorithm. The impact of baseline tropism on antiretroviral treatment (ART) outcome was evaluated. Results Of 352 patients with successful baseline V3 sequences, the proportion of predicted R5 virus varied between the methods by 12.5% (78.1%-90.6%). However, only 58.2% of the predictions were concordant and only 1.7% were predicted to be X4-tropic across the five methods. Compared pairwise, the highest concordance was between C-PSSM and Geno2Pheno clonal (86.4%). In bivariate intention to treat (ITT) analysis, R5 infected patients achieved treatment success more frequently than X4 infected at month six as predicted by Geno2Pheno clinical (77.8% vs 58.7%, P = 0.004) and at month 12 by C-PSSM (61.9% vs 46.6%, P = 0.038). However, in the multivariable analysis adjusted for age, gender, baseline CD4 and viral load, only tropism as predicted by C-PSSM showed an impact on month 12 (P = 0.04, OR 2.47, 95% CI 1.06–5.79). Conclusion Each of the bioinformatics models predicted R5 tropism with comparable frequency but there was a large discordance between the methods. Baseline tropism had an impact on outcome of first line ART at month 12 in multivariable ITT analysis but only based on prediction by C-PSSM which thus possibly could be used for predicting outcome of ART in HIV-1C infected Ethiopians.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail: ,
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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22
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Xu Y, Phetsouphanh C, Suzuki K, Aggrawal A, Graff-Dubois S, Roche M, Bailey M, Alcantara S, Cashin K, Sivasubramaniam R, Koelsch KK, Autran B, Harvey R, Gorry PR, Moris A, Cooper DA, Turville S, Kent SJ, Kelleher AD, Zaunders J. HIV-1 and SIV Predominantly Use CCR5 Expressed on a Precursor Population to Establish Infection in T Follicular Helper Cells. Front Immunol 2017; 8:376. [PMID: 28484447 PMCID: PMC5399036 DOI: 10.3389/fimmu.2017.00376] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/15/2017] [Indexed: 01/28/2023] Open
Abstract
Background T follicular helper (Tfh) cells are increasingly recognized as a major reservoir of HIV infection that will likely need to be addressed in approaches to curing HIV. However, Tfh express minimal CCR5, the major coreceptor for HIV-1, and the mechanism by which they are infected is unclear. We have previously shown that macaque Tfh lack CCR5, but are infected in vivo with CCR5-using SIV at levels comparable to other memory CD4+ T cells. Similarly, human splenic Tfh cells are highly infected with HIV-1 DNA. Therefore, we set out to examine the mechanism of infection of Tfh cells. Methodology Tfh and other CD4+ T cell subsets from macaque lymph nodes and spleens, splenic Tfh from HIV+ subjects, and tonsillar Tfh from HIV-uninfected subjects were isolated by cell sorting prior to cell surface and molecular characterization. HIV proviral gp120 sequences were submitted to genotypic and phenotypic tropism assays. Entry of CCR5- and CXCR4-using viruses into Tfh from uninfected tonsillar tissue was measured using a fusion assay. Results Phylogenetic analysis, genotypic, and phenotypic analysis showed that splenic Tfh cells from chronic HIV+ subjects were predominantly infected with CCR5-using viruses. In macaques, purified CCR5+PD-1intermediate(int)+ memory CD4+ T cells were shown to include pre-Tfh cells capable of differentiating in vitro to Tfh by upregulation of PD-1 and Bcl6, confirmed by qRT-PCR and single-cell multiplex PCR. Infected PD-1int cells survive, carry SIV provirus, and differentiate into PD-1hi Tfh after T cell receptor stimulation, suggesting a pathway for SIV infection of Tfh. In addition, a small subset of macaque and human PD-1hi Tfh can express low levels of CCR5, which makes them susceptible to infection. Fusion assays demonstrated CCR5-using HIV-1 entry into CCR5+ Tfh and pre-Tfh cells from human tonsils. Conclusion The major route of infection of Tfh in macaques and humans appears to be via a CCR5-expressing pre-Tfh population. As the generation of Tfh are important for establishing effective immune responses during primary infections, Tfh are likely to be an early target of HIV-1 following transmission, creating an important component of the reservoir that has the potential to expand over time.
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Affiliation(s)
- Yin Xu
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | | | - Kazuo Suzuki
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
| | - Anu Aggrawal
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - Stephanie Graff-Dubois
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Michael Roche
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Center for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia
| | - Michelle Bailey
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Kieran Cashin
- Center for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia
| | - Rahuram Sivasubramaniam
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
| | - Kersten K Koelsch
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - Brigitte Autran
- Sorbonne Universités, UPMC University Paris 06, INSERM U1135, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France.,AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - Richard Harvey
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
| | - Paul R Gorry
- Center for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,School of Health and Biomedical Sciences, College of Science, Engineering and Health, RMIT University, Bundoora, VIC, Australia
| | - Arnaud Moris
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France.,AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - David A Cooper
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
| | - Stuart Turville
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Anthony D Kelleher
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
| | - John Zaunders
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW, Australia
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23
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Kitawi RC, Hunja CW, Aman R, Ogutu BR, Muigai AWT, Kokwaro GO, Ochieng W. Partial HIV C2V3 envelope sequence analysis reveals association of coreceptor tropism, envelope glycosylation and viral genotypic variability among Kenyan patients on HAART. Virol J 2017; 14:29. [PMID: 28196510 PMCID: PMC5310022 DOI: 10.1186/s12985-017-0703-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/08/2017] [Indexed: 01/18/2023] Open
Abstract
Background HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antiviral immunity and treatment. The aim of this study was to assess if HIV subtype differences were associated with variations in glycosylation patterns and co-receptor tropism among HAART patients experiencing different virologic treatment outcomes. Methods A total of 118 HIV env C2V3 sequence isolates generated previously from 59 Kenyan patients receiving highly active antiretroviral therapy (HAART) were examined for tropism and glycosylation patterns. For analysis of Potential N-linked glycosylation sites (PNGs), amino acid sequences generated by the NCBI’s Translate tool were applied to the HIVAlign and the N-glycosite tool within the Los Alamos Database. Viral tropism was assessed using Geno2Pheno (G2P), WebPSSM and Phenoseq platforms as well as using Raymond’s and Esbjörnsson’s rules. Chi square test was used to determine independent variables association and ANOVA applied on scale variables. Results At respective False Positive Rate (FPR) cut-offs of 5% (p = 0.045), 10% (p = 0.016) and 20% (p = 0.005) for CXCR4 usage within the Geno2Pheno platform, HIV-1 subtype and viral tropism were significantly associated in a chi square test. Raymond’s rule (p = 0.024) and WebPSSM (p = 0.05), but not Phenoseq or Esbjörnsson showed significant associations between subtype and tropism. Relative to other platforms used, Raymond’s and Esbjörnsson’s rules showed higher proportions of X4 variants, while WebPSSM resulted in lower proportions of X4 variants across subtypes. The mean glycosylation density differed significantly between subtypes at positions, N277 (p = 0.034), N296 (p = 0.036), N302 (p = 0.034) and N366 (p = 0.004), with HIV-1D most heavily glycosylated of the subtypes. R5 isolates had fewer PNGs than X4 isolates, but these differences were not significant except at position N262 (p = 0.040). Cell-associated isolates from virologic treatment success subjects were more glycosylated than cell-free isolates from virologic treatment failures both for the NXT (p = 0.016), and for all the patterns (p = 0.011). Conclusion These data reveal significant associations of HIV-1 subtype diversity, viral co-receptor tropism, viral suppression and envelope glycosylation. These associations have important implications for designing therapy and vaccines against HIV. Heavy glycosylation and preference for CXCR4 usage of HIV-1D may explain rapid disease progression in patients infected with these strains.
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Affiliation(s)
- Rose C Kitawi
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya
| | - Carol W Hunja
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,South Eastern Kenya University, P.O Box 170-90200, Kitui, Kenya
| | - Rashid Aman
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,African Center for Clinical Trials, P.O. Box 2288-00202, Nairobi, Kenya.,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Bernhards R Ogutu
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Anne W T Muigai
- Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya
| | - Gilbert O Kokwaro
- Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Washingtone Ochieng
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. .,Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. .,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya. .,Immunology and Infectious Diseases Dept, Harvard School of Public Health, Boston, MA, USA.
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24
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort. BMC Infect Dis 2017; 17:37. [PMID: 28061826 PMCID: PMC5219668 DOI: 10.1186/s12879-016-2163-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background CCR5 coreceptor using HIV-1 subtype C (HIV-1C) has been reported to dominate the Ethiopian epidemic. However, almost all data have been obtained from two large cities in the central and north-west regions and recent data is lacking. Methods Plasma were obtained from 420 treatment-naïve patients recruited 2009–2011 to a large country-wide Ethiopian cohort. The V3 region was sequenced and the co-receptor tropism was predicted by the clinical and clonal models of the geno2pheno tool at different false positive rates (fpr) and for subtype. In an intention to treat analysis the impact of baseline tropism on outcome of antiretroviral therapy was evaluated. Results V3 loop sequencing was successful in 352 (84%) patients. HIV-1C was found in 350 (99.4%) and HIV-1A in two (0.6%) patients. When comparing the geno2pheno fpr10% clonal and clinical models, 24.4% predictions were discordant. X4-virus was predicted in 17.0 and 19.0%, respectively, but the predictions were concordant in only 6%. At fpr5%, concordant X4-virus predictions were obtained in 3.1%. The proportion of X4-tropic virus (clonal fpr10%) increased from 5.6 to 17.3% (p < 0.001) when 387 Ethiopian V3 loop sequences dated from 1984 to 2003 were compared with ours. In an intention to treat analysis, 67.9% reached treatment success at month 6 and only 50% at month 12. Only age and not tropism predicted therapy outcome and no difference was found in CD4+ cell gain between R5-tropic and X4-tropic infected patients. At viral failure, R5 to X4 switch was rare while X4 to R5 switch occurred more frequently (month 6: p = 0.006; month 12: p = 0.078). Conclusion The HIV-1C epidemic is monophylogenetic in all regions of Ethiopia and R5-tropic virus dominates, even in patients with advanced immunodeficiency, although the proportion of X4-tropic virus seems to have increased over the last two decades. Geno2pheno clinical and clonal prediction models show a large discrepancy at fpr10%, but not at fpr5%. Hence further studies are needed to assess the utility of genotypic tropism testing in HIV-1C. In ITT analysis only age and not tropism influenced the outcome.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden. .,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samir Abdurahman
- Public Health Agency of Sweden, Solna, Sweden.,Department of Science and Technology, Örebro University, Örebro, Sweden
| | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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25
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Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda. AIDS 2016; 30:1781-8. [PMID: 27124899 DOI: 10.1097/qad.0000000000001128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Previous studies suggest that infection with non-R5-tropic subtype B HIV-1, compared with R5, is associated with a more rapid decline in CD4 cell count, but does not affect PI/(N)NRTI therapy outcome. Here, we explored clinical correlates associated with viral tropism in subtype A1 and D infections. METHODS HIV-1 subtype A1 (n = 196) and D (n = 143) pretherapy plasma samples and up to 7.5 years of posttherapy virologic and CD4 data were collected from a cross-sectional cohort in Mbarara, Uganda. Tropism and subtype were inferred using env V3 (geno2pheno) and gp41 (RIP) Sanger sequences. For each subtype, R5 infection was compared with non-R5 in terms of: pretherapy viral load and CD4 cell count (Mann-Whitney tests), and therapy outcomes, including time to virologic suppression, postsuppression virologic rebound, CD4 decline and CD4 recovery (log-rank tests). RESULTS A 94% of all patients in this study achieved virologic suppression within median 3 months posttherapy. In both subtypes, non-R5 infection was associated with lower pretherapy CD4 cell count (non-R5 vs. R5; A: median 57 vs. 147 cells/μl P = 0.005; D: 80 vs. 128 cells/μl P = 0.006). Multivariable linear regression confirmed that tropism, not subtype nor the interaction between subtype and tropism, was a significant predictor of pretherapy CD4 cell count (P < 0.0001). None of pretherapy viral load, time to virologic suppression, virologic rebound, CD4 decline nor CD4 recovery was significantly different (all P > 0.09). CONCLUSION Regardless of HIV-1 subtype or tropism, the majority of patients in this Ugandan cohort responded to therapy, even though non-R5 infection was associated with lower pretherapy CD4 cell count.
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Watters SA, Mlcochova P, Maldarelli F, Goonetilleke N, Pillay D, Gupta RK. Sequential CCR5-Tropic HIV-1 Reactivation from Distinct Cellular Reservoirs following Perturbation of Elite Control. PLoS One 2016; 11:e0158854. [PMID: 27403738 PMCID: PMC4942039 DOI: 10.1371/journal.pone.0158854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/22/2016] [Indexed: 12/31/2022] Open
Abstract
Background HIV Elite Controllers may reveal insights into virus persistence given they harbour small reservoir sizes, akin to HIV non-controllers treated early with combination antiretroviral therapy. Both groups of patients represent the most promising candidates for interventions aimed at sustained remission or ‘cure’. Analytic treatment interruption (ATI) in the latter group leads to stochastic rebound of virus, though it is unclear whether loss of elite control is also associated with similar rebound characteristics. Methods We studied three discrete periods of virus rebound during myeloma related immune disruption over 2.5 years in an elite controller who previously underwent autologous stem cell transplantation (ASCT) in the absence of any antiretroviral therapy. Single genome sequencing of the V1-V4 region of env in PBMC and plasma was performed and phylogenies reconstructed. Average pairwise distance (APD) was calculated and non-parametric methods used to assess compartmentalisation. Coreceptor usage was predicted based on genotypic algorithms. Results 122 single genome sequences were obtained (median 26 sequences per rebound). The initial rebounding plasma env sequences following ASCT represented two distinct lineages, and clustered with proviral DNA sequences isolated prior to ASCT. One of the lineages was monophyletic, possibly indicating reactivation from clonally expanded cells. The second rebound occurred 470 days after spontaneous control of the first rebound and was phylogenetically distinct from the first, confirmed by compartmentalisation analysis, with a different cellular origin rather than ongoing replication. By contrast, third rebound viruses clustered with second rebound viruses, with evidence for ongoing evolution that was associated with lymphopenia and myeloma progression. Following ASCT a shift in tropism from CXCR4-tropic viruses to a CCR5-tropic population was observed to persist through to the third rebound. Conclusions Our data highlight similarities in the viral reservoir between elite and non-controllers undergoing ATI following allogeneic transplantation. The lack of propagation of CXCR4 using viruses following transplantation warrants further study.
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Affiliation(s)
- Sarah A. Watters
- Division of Infection and Immunity, University College London, London, United Kingdom
- HIV Dynamics and Replication Program, NCI, Frederick, Maryland, United States of America
| | - Petra Mlcochova
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, Frederick, Maryland, United States of America
| | - Nilu Goonetilleke
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, United Kingdom
- Africa Centre for Health and Population Studies, Durban, KwaZulu-Natal, South Africa
| | - Ravindra K. Gupta
- Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail:
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27
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Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sönnerborg A, Neogi U. Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster. AIDS Res Hum Retroviruses 2016; 32:471-4. [PMID: 26881451 DOI: 10.1089/aid.2015.0380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In this study, we characterize HIV-1 subtype C (HIV-1C) strains at the near full-length genome (NFLG) level and perform genotypic drug resistance testing (GRT) and genotypic tropism testing (GTT) from Ethiopia (HIV-1CET). Plasma samples (n = 150) were obtained from therapy-naive individuals residing in Addis Ababa, Ethiopia in 2008. HIV-NFLG was performed in a subset of patients (n = 30). GRT (pol) and GTT (V3 env) were performed using in-house methods. GTT was analyzed by PhenoSeq-C. The phylogenetic analysis of the NLFG identified two separate clusters of HIV-1CET, although all strains formed one large overarching cluster together. At NFLG, greater diversity was found among HIV-1CET strains compared to HIV-1C strains from other geographical locations. The geographic clustering was weak in the small subgenomic (pol and env) regions. The primary drug-resistant mutations were identified at a low level (<5%). GTT identified that 12% (12/102) of the patients were predicted to be harboring X4-tropic or both R5/X4-tropic viruses.
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Affiliation(s)
- Wondwossen Amogne
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Irene Bontell
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Grossmann
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Getachew Aderaye
- Department of Medicine, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lars Lindquist
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C. Sci Rep 2016; 6:24883. [PMID: 27126912 PMCID: PMC4850382 DOI: 10.1038/srep24883] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/07/2016] [Indexed: 02/06/2023] Open
Abstract
Antiretroviral treatment of Human Immunodeficiency Virus type-1 (HIV-1) infections with CCR5-antagonists requires the co-receptor usage prediction of viral strains. Currently available tools are mostly designed based on subtype B strains and thus are in general not applicable to non-B subtypes. However, HIV-1 infections caused by subtype B only account for approximately 11% of infections worldwide. We evaluated the performance of several sequence-based algorithms for co-receptor usage prediction employed on subtype A V3 sequences including circulating recombinant forms (CRFs) and subtype C strains. We further analysed sequence profiles of gp120 regions of subtype A, B and C to explore functional relationships to entry phenotypes. Our analyses clearly demonstrate that state-of-the-art algorithms are not useful for predicting co-receptor tropism of subtype A and its CRFs. Sequence profile analysis of gp120 revealed molecular variability in subtype A viruses. Especially, the V2 loop region could be associated with co-receptor tropism, which might indicate a unique pattern that determines co-receptor tropism in subtype A strains compared to subtype B and C strains. Thus, our study demonstrates that there is a need for the development of novel algorithms facilitating tropism prediction of HIV-1 subtype A to improve effective antiretroviral treatment in patients.
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Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. PLoS One 2016; 11:e0148974. [PMID: 26859389 PMCID: PMC4747591 DOI: 10.1371/journal.pone.0148974] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/26/2016] [Indexed: 01/21/2023] Open
Abstract
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.
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Affiliation(s)
- Chris A Kieslich
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Yannis A Guzman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States of America
| | - Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
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Dauwe K, Mortier V, Schauvliege M, Van Den Heuvel A, Fransen K, Servais JY, Bercoff DP, Seguin-Devaux C, Verhofstede C. Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate. BMC Infect Dis 2015; 15:524. [PMID: 26572861 PMCID: PMC4647655 DOI: 10.1186/s12879-015-1217-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.
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Affiliation(s)
- Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Annelies Van Den Heuvel
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Katrien Fransen
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
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