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Chrysostomou AC, Topcu C, Stylianou DC, Hezka J, Kostrikis LG. Development of a new comprehensive HIV-1 genotypic drug resistance assay for all commercially available reverse transcriptase, protease and integrase inhibitors in patients infected with group M HIV-1 strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104243. [PMID: 32061896 DOI: 10.1016/j.meegid.2020.104243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/28/2022]
Abstract
Comprehensive PCR assays for the genotypic drug resistance analysis of all HIV-1 antiretroviral agents (reverse transcriptase, protease and integrase inhibitors) are increasingly in demand due to introduction of integrase inhibitors in the first line regimens and the increasing presence of non-B HIV-1 clades around the world. This study focused on the development and evaluation of a new PCR-based assay for the amplification and sequencing of the entire HIV-1 pol region of major circulating group M HIV-1 strains in Europe for genotypic drug resistance analysis. The comprehensive touchdown PCR assay developed in this study utilized HIV-1 RNA extracted from the plasma of blood samples of consenting HIV-1 infected patients in Cyprus, collected from 2017 to 2019. The HIV-1 pol region was amplified by touchdown PCR for both the primary RT-PCR and the secondary PCR steps. Successful PCR amplicons were determined by population DNA sequencing, using the Sanger method and the genotypic drug resistance analysis was performed with the Stanford University HIV Drug Resistance Database Program. The newly developed assay successfully amplified the entire HIV-1 pol region (2844 nucleotides long) of 141 out of 144 samples of group M HIV-1 subtypes and recombinant strains of the Cyprus HIV-1 Transmission Cohort Study (CHICS) isolated from 2017 to 2019 and genotypic analyses were conducted for all currently available HIV-1 reverse transcriptase, protease and integrase inhibitors. The drug resistance, epidemiological and demographic data of these study subjects will be expanded upon in the CHICS (L.G. Kostrikis et al., manuscript in preparation for publication). The newly developed HIV-1 genotypic drug resistance assay would benefit clinical settings, and research focusing on the world-wide spread of HIV-1 drug-resistant strains, especially in geographic regions characterized by polyphyletic HIV-1 infections.
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Affiliation(s)
- Andreas C Chrysostomou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Dora C Stylianou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus.
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Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering. J Clin Microbiol 2015; 53:2581-92. [PMID: 26041893 DOI: 10.1128/jcm.00756-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838-3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective-the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)-and has the potential to enable the scale up of public health HIV prevention interventions.
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Mouafo LCM, Péré H, Ndjoyi-Mbiguino A, Koyalta D, Longo JDD, Mbopi-Kéou FX, Kane CT, Bélec L. LETTER TO THE EDITOR Performance of the ViroSeq® HIV-1 Genotyping System v2.0 in Central Africa. Open AIDS J 2015; 9:9-13. [PMID: 25767633 PMCID: PMC4353127 DOI: 10.2174/1874613601509010009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/01/2015] [Accepted: 01/12/2015] [Indexed: 11/22/2022] Open
Abstract
Resistance genotypes in pol gene of HIV-1 were obtained by the ViroSeq® HIV-1 Genotyping System v2.0 (Celera Diagnostics, Alameda, CA, USA) in 138 of 145 (95%) antiretroviral treatment-experienced adults in virological failure living in Central Africa (Cameroon, Central African Republic, Chad, Gabon). HIV-1 group M exhibited broad genetic diversity. Performance of the 7 ViroSeq® sequencing primers showed high failure rate, from 3% to 76% (D: 76%; F: 17%; A and H: 15%; G and B: 4%; C: 3%). These findings emphasize the need of updating the ViroSeq® HIV-1 genotyping system for non-B subtypes HIV-1.
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Affiliation(s)
- Linda Chapdeleine Mekue Mouafo
- University of Dschang, Dschang, Cameroon ; Assistance Publique - Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Hélène Péré
- Assistance Publique - Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France ; Faculté de Médecine Paris Descartes, Université Paris Descartes (Paris V), Sorbonne Paris Cité, Paris, France
| | | | | | - Jean De Dieu Longo
- Centre National de Référence des Maladies Sexuellement Transmissibles, et de la Thérapie Antirétrovirale, and Unité de Recherches et d'Intervention sur les Maladies Sexuellement Transmissibles et le SIDA, Département de Santé Publique, Faculté des Sciences de la Santé de Bangui, Bangui, Central African Republic
| | - François-Xavier Mbopi-Kéou
- Laboratoire National de Santé Hygiène Mobile, Ministry of Public Health, and Université de Yaoundé I, Yaoundé, Cameroon
| | - Coumba Toure Kane
- Laboratoire de Bactériologie-virologie, CHU Aristide Le Dantec, Dakar, Senegal
| | - Laurent Bélec
- Assistance Publique - Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France ; Faculté de Médecine Paris Descartes, Université Paris Descartes (Paris V), Sorbonne Paris Cité, Paris, France
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Alemán Y, Vinken L, Kourí V, Pérez L, Álvarez A, Abrahantes Y, Fonseca C, Pérez J, Correa C, Soto Y, Schrooten Y, Vandamme AM, Van Laethem K. Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba. PLoS One 2015; 10:e0117176. [PMID: 25671421 PMCID: PMC4324769 DOI: 10.1371/journal.pone.0117176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/19/2014] [Indexed: 11/20/2022] Open
Abstract
As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.
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Affiliation(s)
- Yoan Alemán
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lore Vinken
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Vivian Kourí
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lissette Pérez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Alina Álvarez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yeissel Abrahantes
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Carlos Fonseca
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Jorge Pérez
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Consuelo Correa
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yudira Soto
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yoeri Schrooten
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universida de Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- * E-mail:
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Li G, Verheyen J, Theys K, Piampongsant S, Van Laethem K, Vandamme AM. HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes. Retrovirology 2014; 11:79. [PMID: 25253273 PMCID: PMC4189171 DOI: 10.1186/s12977-014-0079-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/01/2014] [Indexed: 11/19/2022] Open
Abstract
HIV-1 Gag amino acid substitutions associated with protease inhibitor (PI) treatment have mainly been reported in subtype B, while information on other subtypes is scarce. Using sequences from 11613 patients infected with different HIV-1 subtypes, we evaluated the prevalence of 93 Gag amino acid substitutions and their association with genotypic PI resistance. A significant association was found for 13 Gag substitutions, including A431V in both subtype B and CRF01_AE. K415R in subtype C and S451G in subtype B were newly identified. Most PI-associated Gag substitutions are located in the flexible C-terminal domain, revealing the key role this region plays in PI resistance.
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Pineda-Peña AC, Schrooten Y, Vinken L, Ferreira F, Li G, Trovão NS, Khouri R, Derdelinckx I, De Munter P, Kücherer C, Kostrikis LG, Nielsen C, Littsola K, Wensing A, Stanojevic M, Paredes R, Balotta C, Albert J, Boucher C, Gomez-Lopez A, Van Wijngaerden E, Van Ranst M, Vercauteren J, Vandamme AM, Van Laethem K. Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic. PLoS One 2014; 9:e101738. [PMID: 25003369 PMCID: PMC4086934 DOI: 10.1371/journal.pone.0101738] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 06/10/2014] [Indexed: 11/23/2022] Open
Abstract
We aimed to study epidemic trends and predictors for transmitted drug resistance (TDR) in our region, its clinical impact and its association with transmission clusters. We included 778 patients from the AIDS Reference Center in Leuven (Belgium) diagnosed from 1998 to 2012. Resistance testing was performed using population-based sequencing and TDR was estimated using the WHO-2009 surveillance list. Phylogenetic analysis was performed using maximum likelihood and Bayesian techniques. The cohort was predominantly Belgian (58.4%), men who have sex with men (MSM) (42.8%), and chronically infected (86.5%). The overall TDR prevalence was 9.6% (95% confidence interval (CI): 7.7-11.9), 6.5% (CI: 5.0-8.5) for nucleoside reverse transcriptase inhibitors (NRTI), 2.2% (CI: 1.4-3.5) for non-NRTI (NNRTI), and 2.2% (CI: 1.4-3.5) for protease inhibitors. A significant parabolic trend of NNRTI-TDR was found (p = 0.019). Factors significantly associated with TDR in univariate analysis were male gender, Belgian origin, MSM, recent infection, transmission clusters and subtype B, while multivariate and Bayesian network analysis singled out subtype B as the most predictive factor of TDR. Subtype B was related with transmission clusters with TDR that included 42.6% of the TDR patients. Thanks to resistance testing, 83% of the patients with TDR who started therapy had undetectable viral load whereas half of the patients would likely have received a suboptimal therapy without this test. In conclusion, TDR remained stable and a NNRTI up-and-down trend was observed. While the presence of clusters with TDR is worrying, we could not identify an independent, non-sequence based predictor for TDR or transmission clusters with TDR that could help with guidelines or public health measures.
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Affiliation(s)
- Andrea-Clemencia Pineda-Peña
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
| | - Yoeri Schrooten
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Lore Vinken
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Fossie Ferreira
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Guangdi Li
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Nídia Sequeira Trovão
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Ricardo Khouri
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Inge Derdelinckx
- Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Paul De Munter
- Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | | | | | | | - Kirsi Littsola
- National Institute of health and welfare, Helsinki, Finland
| | - Annemarie Wensing
- Department of Virology, University Medical Center Utrecht, The Netherlands
| | - Maja Stanojevic
- University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | | | | | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Charles Boucher
- Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Arley Gomez-Lopez
- Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
| | - Eric Van Wijngaerden
- Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
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Megens S, Laethem KV. HIV-1 genetic variation and drug resistance development. Expert Rev Anti Infect Ther 2014; 11:1159-78. [PMID: 24151833 DOI: 10.1586/14787210.2013.844649] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Up until 10 years ago, basic and clinical HIV-1 research was mainly performed on HIV-1 subtype B that predominated in resource-rich settings. Over the past decade, HIV-1 care and therapy has been scaled up substantially in Latin America, Africa and Asia. These regions are largely dominated by non-B subtype infections, and especially the African continent is affected by the HIV pandemic. Insight on the potency of antiviral drugs and regimens as well as on the emergence of drug resistance in non-B subtypes was lacking triggering research in this field, also partly driven by the introduction and spreading of HIV-1 non-B subtypes in Europe. The scope of this article was to review and discuss the state-of-the-art on the impact of HIV-1 genetic variation on the in vitro activity of antiviral drugs and in vivo response to antiviral therapy; as well as on the in vitro and in vivo emergence of drug resistance.
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Affiliation(s)
- Sarah Megens
- Department Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Vinken L, Megens S, Schrooten Y, Vandamme AM, Van Laethem K. Evaluation of the automatic editing tool RECall for HIV-1 pol and V3 loop sequences. J Virol Methods 2013; 193:135-9. [PMID: 23748120 DOI: 10.1016/j.jviromet.2013.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/14/2013] [Accepted: 05/28/2013] [Indexed: 11/24/2022]
Abstract
Genotypic drug resistance testing is routine practice in HIV-1 clinical care. The visual interpretation of sequencing electropherograms is labour-intensive and subject to intra- and inter-assay variability because decisions are based on operators' judgments. In this study the performance of the automatic editing tool RECall was compared to the current standard of editing manually and editing using the tool ViroSeq. Using RECall a consensus sequence could be generated for 97% of the V3 loop and for 79% of the pol experiments. By comparison, using manual editing a consensus sequence could be reached for 87% of the V3 and 87% of the pol experiments. Using ViroSeq, a consensus sequence was generated for 68% of the pol experiments. On a predefined dataset, manual editing displayed the highest probability to accurately assign mixtures (0.91 vs. 0.88 by ViroSeq vs. 0.76 by RECall) and the lowest probability to inaccurately assign a mixture to a pure base call (0.002 vs. 0.019 by ViroSeq vs. 0.002 by RECall). As differences in base calling have little impact on drug resistance interpretation and hands-on-time could be substantially reduced, RECall could be a valuable tool for the standardization and acceleration of the editing process.
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Affiliation(s)
- Lore Vinken
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Thiam M, Diop-Ndiaye H, Kebe K, Vidal N, Diakhate-Lô R, Diouara AAM, Leye N, Ndiaye O, Sow A, Ngom-Gueye NF, Mboup S, Toure-Kane C. Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal. J Virol Methods 2012; 188:97-103. [PMID: 23266258 DOI: 10.1016/j.jviromet.2012.11.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 11/22/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
The objective of this study was to investigate the performance of the ViroSeq HIV-1 Genotyping System v2.0 on HIV-1 non-B strains identified in Senegalese patients. The study involved 150 patients, and genotyping was performed using the ViroSeq HIV-1 Genotyping System v2.0 or an in-house method developed by the French National Agency on AIDS Research AC11 when the ViroSeq HIV-1 Genotyping System v2.0 failed. The sequences were edited to assess the performance of sequencing primers at their presumed binding regions. The Polymorphism was studied in the regions between the sequences of Senegalese patients and the subtype B strains used as references. The phylogenetic analysis showed a predominance of CRF02_AG (88/150; 58.7%) and the circulation of 11 subtypes/CRFs, 16 unique recombinant forms (URFs) and one unclassified sample. The amplification and sequencing rates were 98% (147/150) and 96.6% (142/147), respectively. This study showed that only primer B exhibited 100% success, while the failure rate ranged from 1.4% to 71.4% for the other primers (D: 71.4%, A and H: 12.2%, F: 7.5%, G: 5.5% and C: 1.4%). These findings suggest the need for an alternative method or alternative primers for non-B strains that were not sequenced successfully using the ViroSeq HIV-1 Genotyping System v2.0.
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Affiliation(s)
- Moussa Thiam
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Dakar, Senegal
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Xu S, Li J, Bao Z, Xing H, Zhong P, Li H, Zhou H, Li X, Wu S, Song A, Li X, Nie J, Wang Y. Development and Evaluation of a National Reference Panel of HIV-1 Protease and Reverse Transcriptase Drug-Resistance Mutations for HIV-1 Genotypic Resistance Assays in China. Mol Diagn Ther 2012; 14:31-41. [DOI: 10.1007/bf03256351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xu S, Zhong P, Li J, Song A, Li H, Nie J, Li X, Wang Y. Comparative evaluation of the ViroSeq™ HIV-1 genotyping system and an in-house method for analysis of HIV-1 drug-resistance mutations in China. Mol Diagn Ther 2011; 15:41-52. [PMID: 21469769 DOI: 10.1007/bf03257192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND OBJECTIVE With the introduction of the ViroSeq™ HIV-1 Genotyping System (ViroSeq™ assay) into China, it is important to evaluate the impact of the diversity of HIV-1 genotypes found in China on the performance of the ViroSeq™ assay compared with an in-house method. MATERIALS AND METHODS A total of 318 plasma samples, collected from 206 HIV-1-infected patients receiving antiretroviral therapy and 112 treatment-naïve HIV-1-infected patients, were used for evaluating the concordance of genotypes, genotypic resistance mutations, and phenotypic resistance between the ViroSeq™ assay and an in-house method for analyzing HIV-1 drug resistance in China. RESULTS A concordance of genotypes between the ViroSeq™ assay and the in-house method was observed for the 313 samples (98.4%), using the Stanford University HIV Drug Resistance Database (Version 6.0.5). The overall concordances of drug-resistance-related mutations (DRRMs) in the HIV-1 protease (PR) and reverse transcriptase (RT) coding sequences within the HIV-1 pol gene, scored by the ViroSeq™ assay and the in-house method, were 99.5% and 98.1%, respectively. Discrepancies between the two methods were found in 38 samples assayed for protease inhibitor (PI) DRRMs, 36 samples assayed for nucleoside reverse transcriptase inhibitor (NRTI) DRRMs, and 72 samples assayed for non-nucleoside reverse transcriptase inhibitor (NNRTI) DRRMs, and 100%, 88.9%, and 87.5% of the samples with discrepancies for PI, NRTI, and NNRTI DRRMs, respectively, were genotyped as subtype B. One NNRTI mutation (the RT mutation Y318F) was reported only by the ViroSeq™ assay, and this discrepancy resulted from the difference in the pol gene lengths generated by the two systems. Furthermore, the overall concordance of phenotypic resistance was 94.7% (301/318) between the two methods. CONCLUSION The ViroSeq™ assay will be a useful tool for monitoring clinical drug resistance and for better management of HIV-1 patients receiving antiretroviral therapy in China.
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Affiliation(s)
- Sihong Xu
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing, PR China
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Peeters M, Aghokeng AF, Delaporte E. Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays. Clin Microbiol Infect 2011; 16:1525-31. [PMID: 20649800 DOI: 10.1111/j.1469-0691.2010.03300.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and prevention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains. We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.
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Affiliation(s)
- M Peeters
- UMR 145 VIH et Maladies Associées Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France.
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Fokam J, Salpini R, Santoro MM, Cento V, D’Arrigo R, Gori C, Perno CF, Colizzi V, Nanfack A, Gwom LC, Cappelli G, Takou D. Performance evaluation of an in-house human immunodeficiency virus type-1 protease-reverse transcriptase genotyping assay in Cameroon. Arch Virol 2011; 156:1235-43. [DOI: 10.1007/s00705-011-0982-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 03/14/2011] [Indexed: 11/29/2022]
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14
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High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. J Clin Microbiol 2011; 49:1635-41. [PMID: 21270223 DOI: 10.1128/jcm.01478-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.
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Magnetic-silica based nucleic acid extraction for Human Immunodeficiency Virus Type-1 drug-resistance testing in low viremic patients. J Clin Virol 2010; 47:8-12. [DOI: 10.1016/j.jcv.2009.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 09/29/2009] [Accepted: 10/12/2009] [Indexed: 11/18/2022]
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16
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Aghokeng AF, Vergne L, Mpoudi-Ngole E, Mbangue M, Deoudje N, Mokondji E, Nambei WS, Peyou-Ndi MM, Moka JJL, Delaporte E, Peeters M. Evaluation of transmitted HIV drug resistance among recently-infected antenatal clinic attendees in four Central African countries. Antivir Ther 2009; 14:401-11. [DOI: 10.1177/135965350901400313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background The rapid expansion of antiretroviral treatment in resource-limited settings is raising concerns regarding the emergence and transmission of HIV drug resistance (HIVDR). We evaluated the extent of transmission of drug-resistant HIV strains in four Central African countries: the Republic of Congo, Central African Republic, Chad and Cameroon. Methods The World Health Organization (WHO) HIVDR threshold survey was implemented in major treatment areas in each country. Pregnant women who were aged <25 years, who were at first pregnancy and who were HIV type-1-positive were enrolled at each site in 2006–2007 for geno-typing. HIVDR prevalence was categorized using the WHO threshold survey binomial sequential sampling method. Results The prevalence of HIVDR in Brazzaville and Bangui sites could not be classified because the eligible sample number was not reached. HIVDR prevalence was low (<5%) in N'Djamena for all drug classes. In Yaoundé, we found one individual with the D67D/N mutation and two with K103N. HIVDR prevalence was categorized as low (<5%) for protease inhibitors (PIs) and nucleoside reverse transcriptase inhibitors (NRTIs), and moderate (≥5-≤15%) for non-NRTIs (NNRTIs). HIVDR prevalence in Douala was low for PIs and NNRTIs, and moderate for NRTIs as we identified one individual with M184V plus K101E plus G190A mutations and a second with D67D/N. Conclusions The moderate HIVDR prevalence found in Yaoundé and Douala indicate that efforts should be made in Cameroon to prevent HIVDR; however, additional surveys are needed to confirm this trend. This study highlighted challenges presented by the WHO methodology, such as additional costs, workload, difficulties in acquiring even small sample numbers and the necessity for better quality assurance of HIV testing and record keeping at antenatal clinics.
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Affiliation(s)
- Avelin F Aghokeng
- Virology Laboratory CRESAR/IMPM/Institut de Recherche pour le Développement (IRD), Yaoundé, Cameroon
| | - Laurence Vergne
- UMR145, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| | - Eitel Mpoudi-Ngole
- Virology Laboratory CRESAR/IMPM/Institut de Recherche pour le Développement (IRD), Yaoundé, Cameroon
| | | | - Noe Deoudje
- Programme National de lutte contre le Sida/IST, N'Djamena, Chad
| | - Etienne Mokondji
- Laboratoire National de la Santé Publique, Brazzaville, Republic of Congo
| | - Wilfrid S Nambei
- Laboratoire National de Biologie, Bangui, Central African Republic
| | - Marlyse M Peyou-Ndi
- Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Yaoundé, Cameroon
| | - Jean-Jacques L Moka
- Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Yaoundé, Cameroon
| | - Eric Delaporte
- UMR145, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| | - Martine Peeters
- UMR145, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
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Hirsch MS, Günthard HF, Schapiro JM, Brun-Vézinet F, Clotet B, Hammer SM, Johnson VA, Kuritzkes DR, Mellors JW, Pillay D, Yeni PG, Jacobsen DM, Richman DD. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 2008; 47:266-85. [PMID: 18549313 DOI: 10.1086/589297] [Citation(s) in RCA: 350] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Resistance to antiretroviral drugs remains an important limitation to successful human immunodeficiency virus type 1 (HIV-1) therapy. Resistance testing can improve treatment outcomes for infected individuals. The availability of new drugs from various classes, standardization of resistance assays, and the development of viral tropism tests necessitate new guidelines for resistance testing. The International AIDS Society-USA convened a panel of physicians and scientists with expertise in drug-resistant HIV-1, drug management, and patient care to review recently published data and presentations at scientific conferences and to provide updated recommendations. Whenever possible, resistance testing is recommended at the time of HIV infection diagnosis as part of the initial comprehensive patient assessment, as well as in all cases of virologic failure. Tropism testing is recommended whenever the use of chemokine receptor 5 antagonists is contemplated. As the roll out of antiretroviral therapy continues in developing countries, drug resistance monitoring for both subtype B and non-subtype B strains of HIV will become increasingly important.
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Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Deforche K, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, van den Heuvel A, van der Gucht B, van Ranst M, van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Vandamme AM, van Laethem K. Prevalence and epidemiology of HIV type 1 drug resistance among newly diagnosed therapy-naive patients in Belgium from 2003 to 2006. AIDS Res Hum Retroviruses 2008; 24:355-62. [PMID: 18327983 DOI: 10.1089/aid.2007.0212] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study is the first prospective study to assess the prevalence, epidemiology, and risk factors of HIV-1 drug resistance in newly diagnosed HIV-infected patients in Belgium. In January 2003 it was initiated as part of the pan-European SPREAD program, and continued thereafter for four inclusion rounds until December 2006. Epidemiological, clinical, and behavioral data were collected using a standardized questionnaire and genotypic resistance testing was done on a sample taken within 6 months of diagnosis. Two hundred and eighty-five patients were included. The overall prevalence of transmitted HIV-1 drug resistance in Belgium was 9.5% (27/285, 95% CI: 6.6-13.4). Being infected in Belgium, which largely coincided with harboring a subtype B virus, was found to be significantly associated with transmission of drug resistance. The relatively high rate of baseline resistance might jeopardize the success of first line treatment as more than 1 out of 10 (30/285, 10.5%) viruses did not score as fully susceptible to one of the recommended first-line regimens, i.e., zidovudine, lamivudine, and efavirenz. Our results support the implementation of genotypic resistance testing as a standard of care in all treatment-naive patients in Belgium.
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Affiliation(s)
- Jurgen Vercauteren
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Inge Derdelinckx
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - André Sasse
- Scientific Institute of Public Health, Brussels, Belgium
| | | | - Helga Ceunen
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ann De Roo
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Koen Deforche
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Katrien Fransen
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Patrick Goubau
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Jean-Cyr Yombi
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Corinne Liesnard
- Cliniques Universitaires de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Michel Moutschen
- Liège AIDS Reference Center, University of Liège, Liège, Belgium
| | | | - Roeland Rens
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Yoeri Schrooten
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dolores Vaira
- Liège AIDS Reference Center, University of Liège, Liège, Belgium
| | | | | | - Marc van Ranst
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eric van Wijngaerden
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Bernard Vandercam
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Marc Vekemans
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Anne-Mieke Vandamme
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Kristel van Laethem
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Leuven, Belgium
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High concordance between HIV-1 drug resistance genotypes generated from plasma and dried blood spots in antiretroviral-experienced patients. AIDS 2007; 21:2503-11. [PMID: 18025887 DOI: 10.1097/qad.0b013e3281c618db] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Dried blood spots (DBS) are a convenient alternative to plasma for drug resistance testing in resource-limited settings. We investigated the correlation between resistance genotypes generated from DBS and plasma. DESIGN Sixty DBS specimens from HIV-1 subtype B-infected antiretroviral-experienced (n = 58) and naive patients (n = 2) were tested. DBS were prepared using 50 mul blood and were stored with desiccant at -20 degrees C. METHODS Resistance genotypes from DBS were obtained using the ViroSeq HIV-1 assay and were compared with genotypes derived from plasma. The frequency of amplification of proviral DNA from DBS was evaluated using an in-house nested polymerase chain reaction assay. RESULTS : Fifty of the 60 DBS specimens were successfully genotyped including all 38 specimens collected from patients with plasma viral loads greater than 2000 copies/ml and 12 of 22 DBS (54.5%) from patients with viral loads less than 2000 copies/ml. HIV-1 DNA was detected in 44.4% of the DBS. Despite the presence of DNA, genotypes from DBS and plasma were highly concordant. Of the 316 mutations found in plasma sequences, 306 (96.8%) were also found in DBS. Discrepancies were mostly caused by mixtures at minor protease positions or unusual amino acid changes, and in only two cases were caused by major protease (M46L) or reverse transcriptase (K103N) mutations absent in DBS sequences. CONCLUSION : We demonstrated a high concordance between resistance genotypes from plasma and DBS, and that resistance testing from DBS can achieve sensitive levels similar to those seen using plasma. Our results indicate that DBS may represent a feasible alternative to plasma for drug resistance testing in treated individuals.
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Ribas SG, Heyndrickx L, Ondoa P, Fransen K. Performance evaluation of the two protease sequencing primers of the Trugene HIV-1 genotyping kit. J Virol Methods 2006; 135:137-42. [PMID: 16777242 DOI: 10.1016/j.jviromet.2006.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 04/11/2006] [Accepted: 05/02/2006] [Indexed: 11/26/2022]
Abstract
This article describes the performance of the two protease sequencing modules available in the Trugene HIV-1 genotyping Kit on a sample population with a high prevalence of HIV-1 non-B subtypes (n=110). The relevance of the algorithm recommended by the kit was also evaluated. The results indicated a high sequencing failure rate of the PR module (34%). Forty-five percent of the failed sequences derived from non-B subtype viruses. Furthermore, no PR sequence could be obtained from any of the HIV-1 subtype A and C infected samples that were tested. In contrast, a sequence could be obtained from the entire panel using the P2 module. The data indicated that the high rate of sequencing failures of the PR module was related to both the HIV-1 non-B subtypes as well as lower levels of RNA viral load. In six out of the 73 samples for which both protease modules were successful, discrepancies between the two protease sequences were observed, which led to discordant resistance reports in two cases. The data highlight the problems and the clinical implications that may occur during resistance genotyping of clinical samples with a high prevalence of HIV-1 non-B subtypes.
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Snoeck J, Kantor R, Shafer RW, Van Laethem K, Deforche K, Carvalho AP, Wynhoven B, Soares MA, Cane P, Clarke J, Pillay C, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, Rodrigues R, Bouzas MB, Brun-Vézinet F, Reid C, Cahn P, Brigido LF, Grossman Z, Soriano V, Sugiura W, Phanuphak P, Morris L, Weber J, Pillay D, Tanuri A, Harrigan RP, Camacho R, Schapiro JM, Katzenstein D, Vandamme AM. Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. Antimicrob Agents Chemother 2006; 50:694-701. [PMID: 16436728 PMCID: PMC1366873 DOI: 10.1128/aac.50.2.694-701.2006] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The major limitation of drug resistance genotyping for human immunodeficiency virus remains the interpretation of the results. We evaluated the concordance in predicting therapy response between four different interpretation algorithms (Rega 6.3, HIVDB-08/04, ANRS [07/04], and VGI 8.0). Sequences were gathered through a worldwide effort to establish a database of non-B subtype sequences, and demographic and clinical information about the patients was gathered. The most concordant results were found for nonnucleoside reverse transcriptase (RT) inhibitors (93%), followed by protease inhibitors (84%) and nucleoside RT inhibitor (NRTIs) (76%). For therapy-naive patients, for nelfinavir, especially for subtypes C and G, the discordances were driven mainly by the protease (PRO) mutational pattern 82I/V + 63P + 36I/V for subtype C and 82I + 63P + 36I + 20I for subtype G. Subtype F displayed more discordances for ritonavir in untreated patients due to the combined presence of PRO 20R and 10I/V. In therapy-experienced patients, subtype G displayed a lot of discordances for saquinavir and indinavir due to mutational patterns involving PRO 90 M and 82I. Subtype F had more discordance for nelfinavir attributable to the presence of PRO 88S and 82A + 54V. For the NRTIs lamivudine and emtricitabine, CRF01_AE had more discordances than subtype B due to the presence of RT mutational patterns 65R + 115 M and 118I + 215Y, respectively. Overall, the different algorithms agreed well on the level of resistance scored, but some of the discordances could be attributed to specific (subtype-dependent) combinations of mutations. It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype.
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Affiliation(s)
- Joke Snoeck
- Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Snoeck J, Riva C, Steegen K, Schrooten Y, Maes B, Vergne L, Van Laethem K, Peeters M, Vandamme AM. Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes. J Virol Methods 2005; 128:47-53. [PMID: 15871907 DOI: 10.1016/j.jviromet.2005.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/23/2005] [Accepted: 04/04/2005] [Indexed: 12/23/2022]
Abstract
Genotypic assays are used often to guide clinicians in decisions concerning the treatment of patients. An optimized sequence-based genotypic assay was used to determine the whole protease and reverse transcriptase (RT) gene, including the gag cleavage site region and RNase H region. Since non-B subtypes are increasing in countries where subtype B was the most prevalent subtype, and treatment becomes more available in developing countries where the epidemic is characterized by a high prevalence of non-B subtypes, it was important that the genotypic test was evaluated using a panel of different subtypes. Amplification was successful for different subtypes: A, B, C, D, F, G, H, J, CRF01_AE, CRF02_AG, CRF11_cpx, CRF13_cpx and an uncharacterized recombinant sample. The detection limit of the PCR was 1000 copies/ml, except for 1 subtype C sample (PL3) and 1 CRF02_AG sample (PL8). The detection limit for these samples was 5000 copies/ml. A sequence could be obtained in both directions for most of the samples.
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Affiliation(s)
- J Snoeck
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Thomson MM, Casado G, Posada D, Sierra M, Nájera R. Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba. AIDS 2005; 19:1155-63. [PMID: 15990568 DOI: 10.1097/01.aids.0000176215.95119.1d] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Analysis of partial pol and env sequences have indicated a high diversity of HIV-1 genetic forms in Cuba, including two potential novel circulating recombinant forms (CRF): U/H and D/A. OBJECTIVES To determine whether U/H recombinant viruses from Cuba, detected in 7% of samples, represent a novel HIV-1 CRF, and to identify non-Cuban viruses related to this recombinant form. METHODS Near full-length genome amplification was carried out by nested polymerase chain reaction in four overlapping DNA segments of two epidemiologically unlinked viruses in uncultured peripheral blood mononuclear cells. The sequences were analysed phylogenetically. Recombinant structures and phylogenetic relationships were analysed by bootscanning and by maximum likelihood. Searches for related viruses in databases were initially based on sequence homology and sharing of signature nucleotides. RESULTS Both Cuban viruses clustered uniformly in bootscans all along the genome with each other and with a virus from Cameroon, CM53379, indicating that all three represent the same recombinant form. Their genome comprised multiple segments clustering with subtypes A1, F, G, H and K, as well as segments failing to cluster with recognized subtypes. The newly defined CRF, designated CRF18_cpx, was phylogenetically related in partial segments to CRF13_cpx, CRF04_cpx and 36 additional viruses, most of them from Central Africa. One of the viruses from Cameroon, sequenced in the near full-length genome, was a CRF18_cpx/subtype G secondary recombinant. CONCLUSIONS A novel HIV-1 complex circulating recombinant form (CRF18_cpx) has been identified that is circulating in Cuba and Central Africa.
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Affiliation(s)
- Michael M Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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