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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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Montagna C, De Crignis E, Bon I, Re MC, Mezzaroma I, Turriziani O, Graziosi C, Antonelli G. V3 net charge: additional tool in HIV-1 tropism prediction. AIDS Res Hum Retroviruses 2014; 30:1203-12. [PMID: 25322170 DOI: 10.1089/aid.2014.0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genotype-based algorithms are valuable tools for the identification of patients eligible for CCR5 inhibitors administration in clinical practice. Among the available methods, geno2pheno[coreceptor] (G2P) is the most used online tool for tropism prediction. This study was conceived to assess if the combination of G2P prediction with V3 peptide net charge (NC) value could improve the accuracy of tropism prediction. A total of 172 V3 bulk sequences from 143 patients were analyzed by G2P and NC values. A phenotypic assay was performed by cloning the complete env gene and tropism determination was assessed on U87_CCR5(+)/CXCR4(+) cells. Sequences were stratified according to the agreement between NC values and G2P results. Of sequences predicted as X4 by G2P, 61% showed NC values higher than 5; similarly, 76% of sequences predicted as R5 by G2P had NC values below 4. Sequences with NC values between 4 and 5 were associated with different G2P predictions: 65% of samples were predicted as R5-tropic and 35% of sequences as X4-tropic. Sequences identified as X4 by NC value had at least one positive residue at positions known to be involved in tropism prediction and positive residues in position 32. These data supported the hypothesis that NC values between 4 and 5 could be associated with the presence of dual/mixed-tropic (DM) variants. The phenotypic assay performed on a subset of sequences confirmed the tropism prediction for concordant sequences and showed that NC values between 4 and 5 are associated with DM tropism. These results suggest that the combination of G2P and NC could increase the accuracy of tropism prediction. A more reliable identification of X4 variants would be useful for better selecting candidates for Maraviroc (MVC) administration, but also as a predictive marker in coreceptor switching, strongly associated with the phase of infection.
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Affiliation(s)
- Claudia Montagna
- Virology Section, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Elisa De Crignis
- Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Isabella Bon
- Microbiology Section, Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
| | - Maria Carla Re
- Microbiology Section, Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
| | - Ivano Mezzaroma
- Department of Clinical Medicine, Sapienza University, Rome, Italy
| | - Ombretta Turriziani
- Virology Section, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Cecilia Graziosi
- Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Guido Antonelli
- Virology Section, Department of Molecular Medicine, Sapienza University, Rome, Italy
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Arruda LB, Araújo MLD, Martinez ML, Gonsalez CR, Duarte AJDS, Coakley E, Lie Y, Casseb J. Determination of viral tropism by genotyping and phenotyping assays in Brazilian HIV-1-infected patients. Rev Inst Med Trop Sao Paulo 2014; 56:287-90. [PMID: 25076427 PMCID: PMC4131812 DOI: 10.1590/s0036-46652014000400003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 01/30/2014] [Indexed: 12/03/2022] Open
Abstract
The clinical application of CCR5 antagonists involves first determining
the coreceptor usage by the infecting viral strain. Bioinformatics programs that
predict coreceptor usage could provide an alternative method to screen candidates for
treatment with CCR5 antagonists, particularly in countries with limited financial
resources. Thus, the present study aims to identify the best approach using
bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice.
Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under
clinical monitoring were analyzed in this study. Based on the Trofile results, the
viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of
tropism using a Geno2pheno[coreceptor] analysis with a false positive rate
of 10% gave the most suitable performance in this sampling: the R5 and X4 strains
were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6%
concordance between the phenotypic and genotypic results. Further studies are needed
to clarify how genetic diversity amongst virus strains affects bioinformatics-driven
approaches for determining tropism. Although this strategy could be useful for
screening patients in developing countries, some limitations remain that restrict the
wider application of coreceptor usage tests in clinical practice.
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Affiliation(s)
- Liã Bárbara Arruda
- Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Marilia Ladeira de Araújo
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Maira Luccia Martinez
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Claudio Roberto Gonsalez
- HIV Out-clinic, Ambulatory of Secondary Immunodeficiencies, ADEE3002, Department of Dermatology, Hospital of Clinics at School of Medicine, University of São Paulo
| | - Alberto José da Silva Duarte
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Eoin Coakley
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Yolanda Lie
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Jorge Casseb
- Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, SP, Brazil
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Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrob Agents Chemother 2014; 58:2167-85. [PMID: 24468782 DOI: 10.1128/aac.02710-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3' end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new antiretroviral drugs and, more importantly, will aid in the treatment and management of HIV-infected individuals.
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Aiamkitsumrit B, Dampier W, Antell G, Rivera N, Martin-Garcia J, Pirrone V, Nonnemacher MR, Wigdahl B. Bioinformatic analysis of HIV-1 entry and pathogenesis. Curr HIV Res 2014; 12:132-61. [PMID: 24862329 PMCID: PMC4382797 DOI: 10.2174/1570162x12666140526121746] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 03/18/2014] [Accepted: 05/06/2014] [Indexed: 02/07/2023]
Abstract
The evolution of human immunodeficiency virus type 1 (HIV-1) with respect to co-receptor utilization has been shown to be relevant to HIV-1 pathogenesis and disease. The CCR5-utilizing (R5) virus has been shown to be important in the very early stages of transmission and highly prevalent during asymptomatic infection and chronic disease. In addition, the R5 virus has been proposed to be involved in neuroinvasion and central nervous system (CNS) disease. In contrast, the CXCR4-utilizing (X4) virus is more prevalent during the course of disease progression and concurrent with the loss of CD4(+) T cells. The dual-tropic virus is able to utilize both co-receptors (CXCR4 and CCR5) and has been thought to represent an intermediate transitional virus that possesses properties of both X4 and R5 viruses that can be encountered at many stages of disease. The use of computational tools and bioinformatic approaches in the prediction of HIV-1 co-receptor usage has been growing in importance with respect to understanding HIV-1 pathogenesis and disease, developing diagnostic tools, and improving the efficacy of therapeutic strategies focused on blocking viral entry. Current strategies have enhanced the sensitivity, specificity, and reproducibility relative to the prediction of co-receptor use; however, these technologies need to be improved with respect to their efficient and accurate use across the HIV-1 subtypes. The most effective approach may center on the combined use of different algorithms involving sequences within and outside of the env-V3 loop. This review focuses on the HIV-1 entry process and on co-receptor utilization, including bioinformatic tools utilized in the prediction of co-receptor usage. It also provides novel preliminary analyses for enabling identification of linkages between amino acids in V3 with other components of the HIV-1 genome and demonstrates that these linkages are different between X4 and R5 viruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102.
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Nyamache AK, Muigai AW, Ng'ang'a Z, Khamadi SA. Profile of HIV type 1 coreceptor tropism among Kenyan patients from 2009 to 2010. AIDS Res Hum Retroviruses 2013; 29:1105-9. [PMID: 23617327 DOI: 10.1089/aid.2012.0284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A switch of HIV coreceptor usage from CCR5 to CXCR4 occurs in AIDS pathogenesis and may play a critical role in the use of entry inhibitors. To determine the potential usefulness of maraviroc and other CCR5 antagonists among drug-naive and experienced patients in Kenya, the env-C2-V3 gene was successfully sequenced in samples from 176 (98 men and 78 female) consenting subjects between January 2009 and December 2012. In silico CPSSM, webPSSM/, and (ds) Kernel tools were used in predicting coreceptor usage. On the basis of the env V3 loop sequences, 84.1% (148) were reported with R-5 tropism, 4.5% (5) were dual tropic, while 13.4% (23) were of X4 tropism. However, similar to previous studies conducted in Kenya on genetic diversity, HIV-1 subtype A1 (73.9%; 130/176) still remains the most dominant subtype. The high levels of R5 tropism among the studied Kenyan infected populations suggested the potential use of CCR5 antagonists as new therapeutic options in Kenya.
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Affiliation(s)
- Anthony Kebira Nyamache
- Department of Plant and Microbial Sciences, Kenyatta University, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Anne W.T. Muigai
- Department of Botany and Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Zipporah Ng'ang'a
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samoel A. Khamadi
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
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Bon I, Clò A, Borderi M, Colangeli V, Calza L, Morini S, Miserocchi A, Cricca M, Gibellini D, Re MC. Prevalence of R5 strains in multi-treated HIV subjects and impact of new regimens including maraviroc in a selected group of patients with CCR5-tropic HIV-1 infection. Int J Infect Dis 2013; 17:e875-82. [PMID: 23597487 DOI: 10.1016/j.ijid.2013.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/21/2013] [Accepted: 02/19/2013] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Maraviroc currently represents an important antiretroviral drug for multi-experienced and viremic HIV patients. This study focused on two main points: (1) determining the prevalence of R5 and X4 HIV strains in antiretroviral-experienced patients using two main tests currently in use to determine viral tropism, and (2) the follow-up to 3 years of a limited number of patients who started a new antiretroviral protocol including maraviroc. METHODS A group of 56 HIV patients, previously multi-treated, were first analyzed by genotyping assay and Trofile™ to establish their eligibility for maraviroc treatment. In addition, 25 subjects selected to follow a new therapeutic protocol including a CCR5 antagonist were monitored by HIV RNA viral load and CD4+ cell count. RESULTS The determination of viral tropism showed a large percentage of patients with an R5 profile (72% by genotyping assay and 74% by Trofile). The follow-up of most (21 out 25) patients who started the new antiretroviral protocol showed an undetectable viral load throughout the observation period, accompanied by a major improvement in CD4 cell count (cells/mm(3)) (baseline: median CD4 cell count 365, interquartile range (IQR) 204-511; 12 months: median value 501, IQR 349-677, p=0.042; 24 months: median value 503, IQR 386-678, p=0.026; 36 months: median value 601, IQR 517-717, p=0.001). Among the four non-responder subjects, two showed a lack of drug compliance and two switched from R5 to X4. CONCLUSION Although our patient cohort was small, the results showed a high prevalence of R5 viral strains in multi-experienced patients. As well as showing the advantages of genotyping, which can be performed in plasma samples with low viral load replication, the follow-up of HIV patients selected for an alternative drug protocol, including a CCR5 antagonist, showed a persistent undetectable viral replication and a good recovery of CD4 cell count in most treated HIV patients.
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Affiliation(s)
- Isabella Bon
- Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
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Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism. J Clin Microbiol 2013; 51:1517-27. [PMID: 23486708 DOI: 10.1128/jcm.00092-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CCR5 antagonists are a powerful new class of antiretroviral drugs that require a companion assay to evaluate the presence of CXCR4-tropic (non-R5) viruses prior to use in human immunodeficiency virus (HIV)-infected individuals. In this study, we have developed, characterized, verified, and prevalidated a novel phenotypic test to determine HIV-1 coreceptor tropism (VERITROP) based on a sensitive cell-to-cell fusion assay. A proprietary vector was constructed containing a near-full-length HIV-1 genome with the yeast uracil biosynthesis (URA3) gene replacing the HIV-1 env coding sequence. Patient-derived HIV-1 PCR products were introduced by homologous recombination using an innovative yeast-based cloning strategy. The env-expressing vectors were then used in a cell-to-cell fusion assay to determine the presence of R5 and/or non-R5 HIV-1 variants within the viral population. Results were compared with (i) the original version of Trofile (Monogram Biosciences, San Francisco, CA), (ii) population sequencing, and (iii) 454 pyrosequencing, with the genotypic data analyzed using several bioinformatics tools, i.e., the 11/24/25 rule, Geno2Pheno (2% to 5.75%, 3.5%, or 10% false-positive rate [FPR]), and webPSSM. VERITROP consistently detected minority non-R5 variants from clinical specimens, with an analytical sensitivity of 0.3%, with viral loads of ≥1,000 copies/ml, and from B and non-B subtypes. In a pilot study, a 73.7% (56/76) concordance was observed with the original Trofile assay, with 19 of the 20 discordant results corresponding to non-R5 variants detected using VERITROP and not by the original Trofile assay. The degree of concordance of VERITROP and Trofile with population and deep sequencing results depended on the algorithm used to determine HIV-1 coreceptor tropism. Overall, VERITROP showed better concordance with deep sequencing/Geno2Pheno at a 0.3% detection threshold (67%), whereas Trofile matched better with population sequencing (79%). However, 454 sequencing using Geno2Pheno at a 10% FPR and 0.3% threshold and VERITROP more accurately predicted the success of a maraviroc-based regimen. In conclusion, VERITROP may promote the development of new HIV coreceptor antagonists and aid in the treatment and management of HIV-infected individuals prior to and/or during treatment with this class of drugs.
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Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One 2012; 7:e49602. [PMID: 23166726 PMCID: PMC3498215 DOI: 10.1371/journal.pone.0049602] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/27/2012] [Indexed: 12/17/2022] Open
Abstract
HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.
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Mehlotra RK, Dazard JE, John B, Zimmerman PA, Weinberg A, Jurevic RJ. Copy Number Variation within Human β-Defensin Gene Cluster Influences Progression to AIDS in the Multicenter AIDS Cohort Study. ACTA ACUST UNITED AC 2012; 3. [PMID: 23543857 DOI: 10.4172/2155-6113.1000184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
STUDY BACKGROUND DEFB4/103A encoding β-defensin 2 and 3, respectively, inhibit CXCR4-tropic (X4) viruses in vitro. We determined whether DEFB4/103A Copy Number Variation (CNV) influences time-to-X4 and time-to-AIDS outcomes. METHODS We utilized samples from a previously published Multicenter AIDS Cohort Study (MACS), which provides longitudinal account of viral tropism in relation to the full spectrum of rates of disease progression. Using traditional models for time-to-event analysis, we investigated association between DEFB4/103A CNV and the two outcomes, and interaction between DEFB4/103A CNV and disease progression groups, Fast and Slow. RESULTS Time-to-X4 and time-to-AIDS were weakly correlated. There was a stronger relationship between these two outcomes for the fast progressors. DEFB4/103A CNV was associated with time-to-AIDS, but not time-to-X4. The association between higher DEFB4/103A CNV and time-to-AIDS was more pronounced for the slow progressors. CONCLUSION DEFB4/103A CNV was associated with time-to-AIDS in a disease progression group-specific manner in the MACS cohort. Our findings may contribute to enhancing current understanding of how genetic predisposition influences AIDS progression.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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