1
|
Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting. Viruses 2022; 14:v14102208. [PMID: 36298763 PMCID: PMC9608942 DOI: 10.3390/v14102208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022] Open
Abstract
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar's test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.
Collapse
|
2
|
HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
Collapse
|
3
|
Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase. Nat Commun 2020; 11:5922. [PMID: 33262331 PMCID: PMC7708638 DOI: 10.1038/s41467-020-19801-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 12/05/2022] Open
Abstract
Little is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <1000 copies/mL from 12 weeks onwards, <200 copies/mL from 24 weeks onwards, and <50 copies/mL after 48 weeks. Here we report how this outcome was impacted by PDR, defined by the World Health Organization (WHO) mutation list. Of 1053 trial participants, 874 (83%) have successful sequencing, including 289 (33%) randomized to EFV-based therapy and 585 (67%) randomized to DTG-based therapy. Fourteen percent (122/874) have ≥1 WHO-defined mutation, of which 98% (120/122) are NNRTI mutations. Rates of virologic suppression are lower in the total cohort among those with PDR 65% (73/112) compared to those without PDR (85% [605/713], P < 0.001), and for those on EFV-based treatment (60% [12/20] vs 86% [214/248], P = 0.002) and for those on DTG-based treatment (61/92 [66%] vs 84% [391/465] P < 0.001, P for interaction by regimen 0.49). Results are similar in multivariable models adjusted for clinical characteristics and adherence. NNRTI resistance prior to treatment is associated with long-term failure of integrase inhibitor-containing first-line regimens, and portends high rates of first-line failure in sub Saharan Africa. Here the authors combine next generation sequencing on plasma from participants of the ADVANCE clinical trial with virological and follow-up data to investigate the impact of pre-treatment drug resistance (PDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) on the efficacy of second-generation integrase inhibitors and find an association between NNRTI resistance prior to treatment and long-term treatment.
Collapse
|
4
|
Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Viruses 2020; 12:v12070694. [PMID: 32605062 PMCID: PMC7411816 DOI: 10.3390/v12070694] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4-99; reverse transcriptase 38-247). The concordance among laboratories' sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1-100%), compared to 15% (99.4%, 88.5-100%), 10% (99.2%, 87.4-100%), or 5% (98.5%, 86.4-100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.
Collapse
|
5
|
Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
Collapse
Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| |
Collapse
|
6
|
Raymond S, Nicot F, Pallier C, Bellecave P, Maillard A, Trabaud MA, Morand-Joubert L, Rodallec A, Amiel C, Mourez T, Bocket L, Beby-Defaux A, Bouvier-Alias M, Lambert-Niclot S, Charpentier C, Malve B, Mirand A, Dina J, Le Guillou-Guillemette H, Marque-Juillet S, Signori-Schmuck A, Barin F, Si-Mohamed A, Avettand Fenoel V, Roussel C, Calvez V, Saune K, Marcelin AG, Rodriguez C, Descamps D, Izopet J. Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen. Clin Infect Dis 2019; 66:1588-1594. [PMID: 29244143 DOI: 10.1093/cid/cix1070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Background Minority resistant variants of human immunodeficiency virus type 1 (HIV-1) could influence the virological response to treatment based on nonnucleoside reverse transcriptase inhibitors (NNRTIs). Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harboring minority resistant variants to nucleos(t)ide reverse transcriptase inhibitors and NNRTIs and to assess their influence on the virological response (VR). Methods All the subjects, 541 HIV-1-infected patients started a first-line regimen containing rilpivirine. VR was defined as a HIV-1 RNA load <50 copies/mL at month 6 with continued suppression at month 12. NGS was performed at baseline (retrospectively) on the 454 GS-FLX platform (Roche). Results NGS revealed resistance-associated mutations accounting for 1% to <5% of variants in 17.2% of samples, for 5%-20% in 5.7% of samples, and for >20% in 29% of samples. We identified 43 (8.8%) and 36 (7.4%) patients who harbored rilpivirine-resistant variants with a 1% sensitivity threshold according to the French National Agency for Research on AIDS and Viral Hepatitis and Stanford algorithms, respectively. The VR was 96.9% at month 12. Detection of minority rilpivirine resistant variants was not associated with virological failure (VF). Multivariate analysis indicated that VF at month 12 was associated with a CD4 count <250 cells/µL at baseline, a slower decrease in viral load at month 3, and rilpivirine resistance at baseline using the Stanford algorithm with a 20% threshold. Conclusions Minority resistant variants had no impact on the VR of treatment-naive patients to a rilpivirine-based regimen.
Collapse
Affiliation(s)
- Stéphanie Raymond
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
| | - Florence Nicot
- Laboratoire de Virologie, Centre Hospitalier Universitaire (CHU) de Toulouse
| | | | | | | | - Mary Anne Trabaud
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon
| | | | | | | | | | | | | | | | | | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Unité Mixte de Recherche 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris.,Laboratoire de Virologie, Hôpital Bichat-Claude Bernard
| | | | | | | | | | | | | | | | | | | | | | - Vincent Calvez
- Laboratoire de Virologie, Hôpital de la Pitié-Salpêtrière
| | - Karine Saune
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
| | | | | | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Unité Mixte de Recherche 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris.,Laboratoire de Virologie, Hôpital Bichat-Claude Bernard
| | - Jacques Izopet
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
| | | |
Collapse
|
7
|
Nguyen T, Fofana DB, Lê MP, Charpentier C, Peytavin G, Wirden M, Lambert-Niclot S, Desire N, Grude M, Morand-Joubert L, Flandre P, Katlama C, Descamps D, Calvez V, Todesco E, Marcelin AG. Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing. J Antimicrob Chemother 2019; 73:2485-2492. [PMID: 29873733 DOI: 10.1093/jac/dky198] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are recommended by international guidelines as first-line therapy in antiretroviral-naive and -experienced HIV-1-infected patients. Objectives This study aimed at evaluating the prevalence at failure of INSTI-resistant variants and the impact of baseline minority resistant variants (MiRVs) on the virological response to an INSTI-based regimen. Methods Samples at failure of 134 patients failing a raltegravir-containing (n = 65), an elvitegravir-containing (n = 20) or a dolutegravir-containing (n = 49) regimen were sequenced by Sanger sequencing and ultra-deep sequencing (UDS). Baseline samples of patients with virological failure (VF) (n = 34) and of those with virological success (VS) (n = 31) under INSTI treatment were sequenced by UDS. Data were analysed using the SmartGene platform, and resistance was interpreted according to the ANRS algorithm version 27. Results At failure, the prevalence of at least one INSTI-resistant variant was 39.6% by Sanger sequencing and 57.5% by UDS, changing the interpretation of resistance in 17/134 (13%) patients. Among 53 patients harbouring at least one resistance mutation detected by both techniques, the most dominant INSTI resistance mutations were N155H (45%), Q148H/K/R (23%), T97A (19%) and Y143C (11%). There was no difference in prevalence of baseline MiRVs between patients with VF and those with VS. MiRVs found at baseline in patients with VF were not detected at failure either in majority or minority mutations. Conclusions UDS is more sensitive than Sanger sequencing at detecting INSTI MiRVs at treatment failure. The presence of MiRVs at failure could be important to the decision to switch to other INSTIs. However, there was no association between the presence of baseline MiRVs and the response to INSTI-based therapies in our study.
Collapse
Affiliation(s)
- T Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - D B Fofana
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - M P Lê
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - C Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - G Peytavin
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - M Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - S Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - N Desire
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - M Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - L Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - P Flandre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - C Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de maladies infectieuses, F-75013 Paris, France
| | - D Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - V Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - E Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - A G Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| |
Collapse
|
8
|
MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors. Viruses 2019; 11:v11090806. [PMID: 31480341 PMCID: PMC6784143 DOI: 10.3390/v11090806] [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: 08/15/2019] [Accepted: 08/24/2019] [Indexed: 01/01/2023] Open
Abstract
The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRMpol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM.
Collapse
|
9
|
Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
Collapse
|
10
|
Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V, Shomron N, Vignuzzi M, van der Werf S. Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol 2018; 9:2596. [PMID: 30429836 PMCID: PMC6220372 DOI: 10.3389/fmicb.2018.02596] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.
Collapse
Affiliation(s)
- Cyril Barbezange
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Louis Jones
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, The Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| |
Collapse
|
11
|
Ekoru K, Young EH, Dillon DG, Gurdasani D, Stehouwer N, Faurholt-Jepsen D, Levitt NS, Crowther NJ, Nyirenda M, Njelekela MA, Ramaiya K, Nyan O, Adewole OO, Anastos K, Compostella C, Dave JA, Fourie CM, Friis H, Kruger IM, Longenecker CT, Maher DP, Mutimura E, Ndhlovu CE, Praygod G, Pefura Yone EW, Pujades-Rodriguez M, Range N, Sani MU, Sanusi M, Schutte AE, Sliwa K, Tien PC, Vorster EH, Walsh C, Gareta D, Mashili F, Sobngwi E, Adebamowo C, Kamali A, Seeley J, Smeeth L, Pillay D, Motala AA, Kaleebu P, Sandhu MS. HIV treatment is associated with a two-fold higher probability of raised triglycerides: Pooled Analyses in 21 023 individuals in sub-Saharan Africa. Glob Health Epidemiol Genom 2018; 3:e7. [PMID: 29881632 PMCID: PMC5985947 DOI: 10.1017/gheg.2018.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Anti-retroviral therapy (ART) regimes for HIV are associated with raised levels of circulating triglycerides (TG) in western populations. However, there are limited data on the impact of ART on cardiometabolic risk in sub-Saharan African (SSA) populations. METHODS Pooled analyses of 14 studies comprising 21 023 individuals, on whom relevant cardiometabolic risk factors (including TG), HIV and ART status were assessed between 2003 and 2014, in SSA. The association between ART and raised TG (>2.3 mmol/L) was analysed using regression models. FINDINGS Among 10 615 individuals, ART was associated with a two-fold higher probability of raised TG (RR 2.05, 95% CI 1.51-2.77, I2=45.2%). The associations between ART and raised blood pressure, glucose, HbA1c, and other lipids were inconsistent across studies. INTERPRETATION Evidence from this study confirms the association of ART with raised TG in SSA populations. Given the possible causal effect of raised TG on cardiovascular disease (CVD), the evidence highlights the need for prospective studies to clarify the impact of long term ART on CVD outcomes in SSA.
Collapse
Affiliation(s)
- K. Ekoru
- Department of Medicine, University of Cambridge, Cambridge, UK
- Global Health and Populations Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - E. H. Young
- Department of Medicine, University of Cambridge, Cambridge, UK
- Global Health and Populations Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - D. G. Dillon
- Weill Cornell Medical College, New York City, New York, USA
| | - D. Gurdasani
- Department of Medicine, University of Cambridge, Cambridge, UK
- Global Health and Populations Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - N. Stehouwer
- University Hospitals Case Medical Center, Cleveland, Ohio, USA
| | - D. Faurholt-Jepsen
- Department of Infectious Diseases, University of Copenhagen (Rigshospitalet), Copenhagen, Denmark
| | - N. S. Levitt
- Division of Diabetic Medicine and Endocrinology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - N. J. Crowther
- Department of Chemical Pathology, National Health Laboratory Service, University of the Witwatersrand Medical School, Johannesburg, South Africa
| | - M. Nyirenda
- Malawi Epidemiology and Intervention Research Unit, Malawi, Lilongwe
| | - M. A. Njelekela
- Department of Physiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - K. Ramaiya
- Shree Hindu Mandal Hospital, Dar es Salaam, Tanzania
| | - O. Nyan
- Royal Victoria Teaching Hospital, School of Medicine, University of The Gambia, Banjul, The Gambia
| | - O. O. Adewole
- Department of Medicine, Obafemi Awolowo University, Ile Ife, Nigeria
| | - K. Anastos
- Albert Einstein College of Medicine, Bronx NY, USA
| | - C. Compostella
- Department of Medicine, University of Padua, Padua, Italy
| | - J. A. Dave
- Division of Diabetic Medicine and Endocrinology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - C. M. Fourie
- HART (Hypertension in Africa Research Team), North-West University, Potchefstroom, South Africa
| | - H. Friis
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Denmark
| | - I. M. Kruger
- Africa Unit for Transdisciplinary Health Research (AUTHeR), North-West University, Potchefstroom, South Africa
| | | | - D. P. Maher
- Special Programme for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - E. Mutimura
- Albert Einstein College of Medicine, Bronx NY, USA
| | - C. E. Ndhlovu
- Clinical Epidemiology Resource Training Centre, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - G. Praygod
- National Institute for Medical Research, Tanzania, Dar es Salaam
| | | | - M. Pujades-Rodriguez
- Epicentre, Médecins Sans Frontières, Paris, France
- Department of Epidemiology and Public Health, University College of London, Clinical Epidemiology Group, London, UK
| | - N. Range
- National Institute for Medical Research, Tanzania, Dar es Salaam
| | - M. U. Sani
- Cardiology Unit, Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - M. Sanusi
- Cardiology Unit, Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A. E. Schutte
- HART (Hypertension in Africa Research Team), North-West University, Potchefstroom, South Africa
- MRC Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - K. Sliwa
- Soweto Cardiovascular Research Unit, Chris Hani Baragwanath Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - P. C. Tien
- Department of Medicine, University of California, San Francisco, USA
| | - E. H. Vorster
- Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - C. Walsh
- Department of Nutrition and Dietetics, University of the Free State, Bloemfontein, South Africa
| | - D. Gareta
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - F. Mashili
- National Institute for Medical Research, Tanzania, Dar es Salaam
| | - E. Sobngwi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Cameroon, Yaoundé
| | - C. Adebamowo
- Institute of Human Virology, Abuja, Nigeria
- Department of Epidemiology and Public Health, Institute of Human Virology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, USA
| | - A. Kamali
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | - J. Seeley
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | - L. Smeeth
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - D. Pillay
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - A. A. Motala
- Department of Diabetes and Endocrinology, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - P. Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | - M. S. Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK
- Global Health and Populations Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| |
Collapse
|
12
|
Gibson RM, Nickel G, Crawford M, Kyeyune F, Venner C, Nankya I, Nabulime E, Ndashimye E, Poon AFY, Salata RA, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries. Infect Dis Poverty 2017; 6:163. [PMID: 29202874 PMCID: PMC5716384 DOI: 10.1186/s40249-017-0377-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
Background Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country. Methods We examined the drug resistance genotypes by Sanger sequencing of 262 HIV-infected patients failing a first line combined antiretroviral treatment containing either AZT or d4T, which represents approximately 5% of the patients at the Joint Clinical Research Center receiving a AZT or d4T containing treatment. Next generation sequencing (DEEPGEN™HIV) and multiplex oligonucleotide ligation assays (AfriPOLA) were then performed on a subset of patient samples to detect low frequency drug resistant mutations. CD4 cell counts, viral RNA loads, and treatment changes were analyzed in a cohort of treatment success and failures. Results Over 80% of patients failing first line AZT/d4T-containing cART had predicted drug resistance to 3TC (Lamivudine) and non-nucleoside RT inhibitors (NNRTIs) in the treatment regimen but only 45% had resistance AZT/d4T associated resistance mutations (TAMs). TAMs were however detected at low frequency within the patients HIV quasispecies (1–20%) in 21 of 34 individuals who were failing first-line AZT-containing cART and lacked TAMs by Sanger. Due to lack of TAMs by Sanger, AZT was typically maintained in second-line therapies and these patients had a low frequency of subsequent virologic success. Conclusions Our findings suggest that continued use of AZT and d4T in first-line treatment in low-to-middle income countries may lead to misdiagnosis of HIV-1 drug resistance and possibly enhance a succession of second- and third-line treatment failures. Electronic supplementary material The online version of this article (doi: 10.1186/s40249-017-0377-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Richard M Gibson
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Crawford
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Colin Venner
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Immaculate Nankya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.,Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Emmanuel Ndashimye
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Robert A Salata
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada. .,TREAT, Joint Clinical Research Centre, Kampala, Uganda.
| |
Collapse
|
13
|
SahBandar IN, Samonte G, Telan E, Siripong N, Belcaid M, Schanzenbach D, Leano S, Chagan-Yasutan H, Hattori T, Shikuma CM, Ndhlovu LC. Ultra-Deep Sequencing Analysis on HIV Drug-Resistance-Associated Mutations Among HIV-Infected Individuals: First Report from the Philippines. AIDS Res Hum Retroviruses 2017; 33:1099-1106. [PMID: 28569550 DOI: 10.1089/aid.2016.0151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A sharp increase in the number of people living with HIV has been documented in the Philippines. In response, the government has instituted antiretroviral therapy (ART) nationwide through HIV treatment hubs. However, no data presently exist on the status of ART drug-resistance-associated mutations (DRMs). In this study, we aim at analyzing DRM profiles in the Philippines and at providing comprehensive data on DRMs to guide treatment decisions and prevent viral failures. We conducted a cross-sectional study in 119 volunteers who tested positive for HIV from more than 8,000 participants screened for HIV across the nation through the 2013 Integrated HIV Behavioral and Serologic Surveillance (IHBSS) program. Amplicons were generated from plasma RNA by using primers designed to analyze diverse HIV-1 isolates targeting the reverse transcriptase region and sequenced on a 454 ultra-deep sequencing (UDS) platform to assess DRMs. DRMs were defined by using the Stanford HIV drug resistance database, and we found only 2 from 110 evaluable individuals with major HIV variants (>20% prevalence) that were highly resistant to the non-nucleoside reverse transcriptase inhibitor (NNRTI: efavirenz and nevirapine). However, a larger fraction of individuals harbored minority drug-resistant HIV variants (0.5%-20% prevalence) and they were highly resistant to NNRTI nevirapine (89/110), rilpivirine (5/110), and efavirenz (49/110). This study is the first report on the presence of HIV drug resistance in the Philippines and demonstrates the utility of UDS in assisting the detection of HIV minor variants. Monitoring for ART-DRMs will assist in improving HIV management strategies in curtailing the evolving epidemic in the Philippines.
Collapse
Affiliation(s)
- Ivo N. SahBandar
- Hawaii Center for AIDS, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
| | - Genesis Samonte
- Department of Health, National Epidemiology Center, Manila, Philippines
| | - Elizabeth Telan
- National Reference Laboratory, STD AIDS Cooperative Central Laboratory, Manila, Philippines
| | - Nalyn Siripong
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mahdi Belcaid
- Pacific Center for Emerging Infectious Diseases Research, University of Hawaii, Honolulu, Hawaii
| | - David Schanzenbach
- Pacific Center for Emerging Infectious Diseases Research, University of Hawaii, Honolulu, Hawaii
| | - Susan Leano
- National Reference Laboratory, STD AIDS Cooperative Central Laboratory, Manila, Philippines
| | - Haorile Chagan-Yasutan
- International Research Institute of Disaster Science (IRIDeS), Tohoku University, Sendai, Japan
| | - Toshio Hattori
- Department of Occupational Therapy, KIBI International University, Takahashi, Japan
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
| | - Lishomwa C. Ndhlovu
- Hawaii Center for AIDS, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii Manoa, Honolulu, Hawaii
| |
Collapse
|
14
|
Etta EM, Mavhandu L, Manhaeve C, McGonigle K, Jackson P, Rekosh D, Hammarskjold ML, Bessong PO, Tebit DM. High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa. AIDS Res Ther 2017; 14:36. [PMID: 28750647 PMCID: PMC5531022 DOI: 10.1186/s12981-017-0161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Background Combination antiretroviral therapy (cART) has significantly reduced HIV morbidity and mortality in both developed and developing countries. However, the sustainability of cART may be compromised by the emergence of viral drug resistance mutations (DRM) and the cellular persistence of proviruses carrying these DRM. This is potentially a more serious problem in resource limited settings. Methods DRM were evaluated in individuals with unsuppressed viral loads after first or multiple lines of cART at two sites in rural Limpopo, South Africa. Seventy-two patients with viral loads of >1000 copies/ml were recruited between March 2014 and December 2015. Complete protease (PR) and partial Reverse Transcriptase (RT) sequences were amplified from both plasma RNA and paired proviral DNA from 35 of these subjects. Amplicons were directly sequenced to determine subtype and DRM using the Stanford HIV Drug Resistance Interpretation algorithm. Results Among the 72 samples, 69 could be PCR amplified from RNA and 35 from both RNA and DNA. Sixty-five (94.2%) viruses were subtype C, while one was subtype B (1.4%), one recombinant K/C, one recombinant C/B and one unclassified. Fifty-eight (84%) sequences carried at least one DRM, while 11 (15.9%) displayed no DRM. DRM prevalence according to drug class was: NRTI 60.8% NNRTI 65.2%, and PI 5.8%. The most common DRMs were; M184V (51.7%), K103N (50%), V106M (20.6%), D67N (13.3%), K65R (12%). The frequency of the DRM tracked well with the frequency of use of medications to which the mutations were predicted to confer resistance. Interestingly, a significant number of subjects showed predicted resistance to the newer NNRTIs, etravirine (33%) and rilpivirine (42%), both of which are not yet available in this setting. The proportion of DRM in RNA and DNA were mostly similar with the exception of the thymidine analogue mutations (TAMs) D67N, K70R, K219QE; and K103N which were slightly more prevalent in DNA than RNA. Subjects who had received cART for at least 5 years were more likely to harbour >2 DRM (p < 0.05) compared to those treated for a shorter period. DRM were more prevalent in this rural setting compared to a neighbouring urban setting. Conclusion We found a very high prevalence of NRTI and NNRTI DRM in patients from rural Limpopo settings with different durations of treatment. The prevalence was significantly higher than those reported in urban settings in South Africa. The dominance of NNRTI based mutations late in treatment supports the use of PI based regimens for second line treatment in this setting. The slight dominance of TAMs in DNA from infected PBMCs compared to plasma virus requires further studies that should include cART subjects with suppressed virus. Such studies will improve our understanding of the pattern of drug resistance and dynamics of viral persistence in these rural settings.
Collapse
|
15
|
Martín V, Perales C, Fernández-Algar M, Dos Santos HG, Garrido P, Pernas M, Parro V, Moreno M, García-Pérez J, Alcamí J, Torán JL, Abia D, Domingo E, Briones C. An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies. PLoS One 2016; 11:e0166902. [PMID: 27959928 PMCID: PMC5154500 DOI: 10.1371/journal.pone.0166902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.
Collapse
Affiliation(s)
- Verónica Martín
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona. Barcelona, Spain
| | - María Fernández-Algar
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Helena G. Dos Santos
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Patricia Garrido
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - María Pernas
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Alcamí
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Luis Torán
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - David Abia
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
- * E-mail:
| |
Collapse
|
16
|
Darcissac E, Nacher M, Adriouch L, Berlioz-Arthaud A, Boukhari R, Couppié P, Djossou F, Donato D, El Guedj M, Lavergne A, Papot E, Pouliquen JF, Tanguy E, Vantilcke V, Lacoste V. HIV-1 Pol Gene Polymorphism and Antiretroviral Resistance Mutations in Treatment-Naive Adult Patients in French Guiana Between 2006 and 2012. AIDS Res Hum Retroviruses 2016; 32:801-11. [PMID: 27009561 DOI: 10.1089/aid.2016.0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little information is available on the molecular epidemiologic profile of HIV-1 in French Guiana, the French department with the highest HIV/AIDS incidence. To follow the evolution of HIV-1 diversity, we carried out a molecular analysis of HIV-1 isolates from 305 treatment-naive patients between 2006 and 2012. Protease and reverse-transcriptase sequences were obtained for subtype characterization, polymorphism analysis, and identification of drug resistance mutations. Of 305 HIV-1 strains, 95.1% were subtype B viruses. The overall prevalence of transmitted drug-resistance mutations (TDRMs) was 4.6% (14/305), ranging from 1.9% to 7.1% depending on the year. This study shows a low level of HIV-1 genetic diversity and a moderate prevalence of TDRMs with no evidence of an increasing trend over the study period. Nevertheless, the strong genetic polymorphism observed on both genes may be of concern for long-term treatment of people living with HIV-1 and thus deserves continuous monitoring.
Collapse
Affiliation(s)
- Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Mathieu Nacher
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
- Centre d'Investigation Clinique—Epidemiologie Clinique (CIC-EC) Antilles Guyane, INSERM CIE 802, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Leila Adriouch
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Alain Berlioz-Arthaud
- Laboratoire de Biologie Médicale, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Rachida Boukhari
- Service de Biologie Médicale, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Pierre Couppié
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Felix Djossou
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Myriam El Guedj
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Emmanuelle Papot
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Jean-François Pouliquen
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Edouard Tanguy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Vincent Vantilcke
- Hôpital de Jour Adultes, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| |
Collapse
|
17
|
Presence of Minority Resistant Variants After Failure of a Tenofovir, Emtricitabine, and Rilpivirine Regimen. J Acquir Immune Defic Syndr 2016; 72:e43-5. [DOI: 10.1097/qai.0000000000000935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
18
|
Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure. Antimicrob Agents Chemother 2016; 60:3380-97. [PMID: 27001818 DOI: 10.1128/aac.00038-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/11/2016] [Indexed: 12/27/2022] Open
Abstract
Most patients failing antiretroviral treatment in Uganda continue to fail their treatment regimen even if a dominant drug-resistant HIV-1 genotype is not detected. In a recent retrospective study, we observed that approximately 30% of HIV-infected individuals in the Joint Clinical Research Centre (Kampala, Uganda) experienced virologic failure with a susceptible HIV-1 genotype based on standard Sanger sequencing. Selection of minority drug-resistant HIV-1 variants (not detectable by Sanger sequencing) under antiretroviral therapy pressure can lead to a shift in the viral quasispecies distribution, becoming dominant members of the virus population and eventually causing treatment failure. Here, we used a novel HIV-1 genotyping assay based on deep sequencing (DeepGen) to quantify low-level drug-resistant HIV-1 variants in 33 patients failing a first-line antiretroviral treatment regimen in the absence of drug-resistant mutations, as screened by standard population-based Sanger sequencing. Using this sensitive assay, we observed that 64% (21/33) of these individuals had low-frequency (or minority) drug-resistant variants in the intrapatient HIV-1 population, which correlated with treatment failure. Moreover, the presence of these minority HIV-1 variants was associated with higher intrapatient HIV-1 diversity, suggesting a dynamic selection or fading of drug-resistant HIV-1 variants from the viral quasispecies in the presence or absence of drug pressure, respectively. This study identified low-frequency HIV drug resistance mutations by deep sequencing in Ugandan patients failing antiretroviral treatment but lacking dominant drug resistance mutations as determined by Sanger sequencing methods. We showed that these low-abundance drug-resistant viruses could have significant consequences for clinical outcomes, especially if treatment is not modified based on a susceptible HIV-1 genotype by Sanger sequencing. Therefore, we propose to make clinical decisions using more sensitive methods to detect minority HIV-1 variants.
Collapse
|
19
|
HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China. PLoS One 2016; 11:e0149215. [PMID: 26895182 PMCID: PMC4760947 DOI: 10.1371/journal.pone.0149215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Objective Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF). Methods 29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels. Results DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS. Conclusions DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
Collapse
|
20
|
Bellecave P, Recordon-Pinson P, Fleury H. Evaluation of Automatic Analysis of Ultradeep Pyrosequencing Raw Data to Determine Percentages of HIV Resistance Mutations in Patients Followed-Up in Hospital. AIDS Res Hum Retroviruses 2016; 32:85-92. [PMID: 26529549 DOI: 10.1089/aid.2015.0201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A major obstacle to using next generation sequencing (NGS) technology in clinical routine practice is reliable data analysis. Thousands of sequences need to be aligned and validated, to exclude sequencing artifacts and generate accurate results. We compared two analysis pipelines for Roche 454 ultradeep pyrosequencing (UDPS) raw data generated from HIV-1 clinical samples: a commercial and fully automated Web-based software NGS HIV-1 Module (SmartGene, Zug, Switzerland) vs. the Amplicon Variant Analyzer software (AVA, 454 Life Sciences; Roche). Results were also compared to those obtained with Sanger sequencing. HIV-1 reverse transcriptase and protease genes from 34 plasma samples were submitted to Sanger sequencing and GS Junior UDPS. Raw UDPS data (sff files) from all samples were analyzed with AVA 2.7 software plus manual review of the alignments and the fully automated SmartGene NGS HIV-1 Module prototype (SMG). Results obtained with both analysis pipelines showed good correlation (85.0%). Divergent results were mainly observed at homopolymer positions, such as K101, where the frame-aware alignment and error corrections of the automated approach were more efficient and more accurate, both in terms of detecting and quantifying drug resistance mutations. Our study shows that NGS data can easily be analyzed via a fully automated analysis pipeline, here the SmartGene NGS HIV-1 Module, thus minimizing the need for manual review of alignments by the user, otherwise essential to ensure accurate results. Such automated analysis pipelines may facilitate the adoption of NGS platforms in the routine clinical laboratory.
Collapse
Affiliation(s)
- Pantxika Bellecave
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
| | - Patricia Recordon-Pinson
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
| | - Hervé Fleury
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
| |
Collapse
|
21
|
Porter DP, Daeumer M, Thielen A, Chang S, Martin R, Cohen C, Miller MD, White KL. Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study. Viruses 2015; 7:6360-70. [PMID: 26690199 PMCID: PMC4690866 DOI: 10.3390/v7122943] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023] Open
Abstract
At Week 96 of the Single-Tablet Regimen (STaR) study, more treatment-naïve subjects that received rilpivirine/emtricitabine/tenofovir DF (RPV/FTC/TDF) developed resistance mutations compared to those treated with efavirenz (EFV)/FTC/TDF by population sequencing. Furthermore, more RPV/FTC/TDF-treated subjects with baseline HIV-1 RNA >100,000 copies/mL developed resistance compared to subjects with baseline HIV-1 RNA ≤100,000 copies/mL. Here, deep sequencing was utilized to assess the presence of pre-existing low-frequency variants in subjects with and without resistance development in the STaR study. Deep sequencing (Illumina MiSeq) was performed on baseline and virologic failure samples for all subjects analyzed for resistance by population sequencing during the clinical study (n = 33), as well as baseline samples from control subjects with virologic response (n = 118). Primary NRTI or NNRTI drug resistance mutations present at low frequency (≥2% to 20%) were detected in 6.6% of baseline samples by deep sequencing, all of which occurred in control subjects. Deep sequencing results were generally consistent with population sequencing but detected additional primary NNRTI and NRTI resistance mutations at virologic failure in seven samples. HIV-1 drug resistance mutations emerging while on RPV/FTC/TDF or EFV/FTC/TDF treatment were not present at low frequency at baseline in the STaR study.
Collapse
Affiliation(s)
| | - Martin Daeumer
- Seq-IT GmbH & Co. KG, Pfaffplatz 10, 67655 Kaiserslautern, Germany.
| | | | - Silvia Chang
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Ross Martin
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Cal Cohen
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Michael D Miller
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Kirsten L White
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| |
Collapse
|
22
|
Clinical value of ultradeep HIV-1 genotyping and tropism testing in late presenters with advanced disease. AIDS 2015; 29:1493-504. [PMID: 26244389 DOI: 10.1097/qad.0000000000000748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This article aims to investigate if the detection of preexisting drug-resistant minority variant (DRMV) and/or X4 HIV-1 variants could improve the efficacy of first-line combined antiretroviral therapy (ART) in late presenters. DESIGN Post-hoc, combined analysis of two open-label, prospective, randomized clinical trials comparing first-line ART with efavirenz (EFV) vs. ritonavir-boosted protease inhibitor (PI/r)-based regimens in ART-naive, HIV-1-infected patients, with CD4 T-cell counts less than 100 cells/μl and wild-type HIV-1 by bulk sequencing. METHODS Pre-ART samples were reanalyzed for the presence of DRMVs and X4 HIV-1 using 454 sequencing. Kaplan-Meier curves and Cox regression were used to evaluate the association between X4 HIV and DRMVs and risk of virological failure. RESULTS From 141 evaluable patients, 57 received EFV, and 84 received PI/r, including first-line ART. Median pre-ART CD4 T-cell counts and HIV-1 RNA levels were 39 cells/μl and 257 424 copies/ml, respectively; 35.5% of patients had X4 HIV variants. Detection of DRMVs leading to an ART-specific cumulative HIVdb score of at least 10 increased the risk of virological failure in patients initiating EFV [log-rank P = 0.048, hazard ratio = 4.3 (95% confidence interval: 0.8, 25.0), P = 0.074], but not in those starting PI/r. Presence of X4 HIV did not affect virological outcomes, but was associated with impaired CD4 T-cell count recovery over 2 years (214 vs. 315 cells/μl with X4 vs. R5 HIV-1 tropism, respectively, P = 0.017). CONCLUSION Accounting for preexisting DRMVs may improve the outcomes of first-line nonnucleoside reverse transcriptase inhibitor-based ART in late presenters with advanced immune suppression. Presence of X4 HIV-1 at diagnosis predicts impaired immune restoration under ART.
Collapse
|
23
|
Todesco E, Rodriguez C, Morand-Joubert L, Mercier-Darty M, Desire N, Wirden M, Girard PM, Katlama C, Calvez V, Marcelin AG. Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing. J Antimicrob Chemother 2015; 70:1503-6. [PMID: 25614045 DOI: 10.1093/jac/dku557] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/12/2014] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Resistant minority variants present before ART can be a source of virological failure. This has been shown for NRTIs, NNRTIs and CCR5 inhibitors. However, very few data are available for the detection of such minority resistant variants that could be selected at virological failure and not detected using classical Sanger sequencing. METHODS We studied 26 patients treated with tenofovir, emtricitabine and efavirenz with their first virological failure (defined as two consecutive viral loads >50 copies/mL). We performed standard Sanger sequencing and ultradeep sequencing (UDS; Roche 454(®) Life Sciences) in plasma at failure. For UDS, mutations >1% were considered. We compared the presence of reverse transcriptase mutations between the two techniques, using the latest ANRS algorithm. RESULTS UDS detected more resistance mutations in 38.5% of cases (10/26 patients) and the genotypic sensitivity score (GSS) was reduced for 6 of them (23.1%). The GSS was impacted more often for NRTIs than for NNRTIs, for which most mutations were already detected by Sanger sequencing. Resistant minority variants were detected even in patients with low viral load at failure. CONCLUSIONS These results strongly argue for the use of next-generation sequencing in patients failing on an NRTI+NNRTI regimen, as UDS has the potential to modify the choice of the subsequent regimen.
Collapse
Affiliation(s)
- Eve Todesco
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France INSERM U955, Créteil, France
| | - Laurence Morand-Joubert
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Saint Antoine, AP-HP Paris, France
| | | | - Nathalie Desire
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Marc Wirden
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Pierre-Marie Girard
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Saint Antoine, AP-HP Paris, France
| | - Christine Katlama
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| |
Collapse
|
24
|
Emerging antiretroviral drug resistance in sub-Saharan Africa: novel affordable technologies are needed to provide resistance testing for individual and public health benefits. AIDS 2014; 28:2643-8. [PMID: 25493592 DOI: 10.1097/qad.0000000000000502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
25
|
Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol 2014; 62:48-53. [PMID: 25542470 DOI: 10.1016/j.jcv.2014.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 11/08/2014] [Indexed: 11/21/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) allows the detection of minor variant HIV drug resistance mutations (DRMs). However data from new NGS platforms after Prevention-of-Mother-to-Child-Transmission (PMTCT) regimen failure are limited. OBJECTIVE To compare major and minor variant HIV DRMs with Illumina MiSeq and Life Technologies Ion Personal Genome Machine (PGM) in infants infected despite a PMTCT regimen. STUDY DESIGN We conducted a cross-sectional study of NGS for detecting DRMs in infants infected despite a zidovudine (AZT) and Nevirapine (NVP) regimen, before initiation of combination antiretroviral therapy. Sequencing was performed on PCR products from plasma samples on PGM and MiSeq platforms. Bioinformatic analyses were undertaken using a codon-aware version of the Smith-Waterman mapping algorithm and a mixture multinomial error filtering statistical model. RESULTS Of 15 infants, tested at a median age of 3.4 months after birth, 2 (13%) had non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs (K103N and Y181C) by bulk sequencing, whereas PGM detected 4 (26%) and MiSeq 5 (30%). NGS enabled the detection of additional minor variant DRMs in the infant with K103N. Coverage and instrument quality scores were higher with MiSeq, increasing the confidence of minor variant calls. CONCLUSIONS NGS followed by bioinformatic analyses detected multiple minor variant DRMs in HIV-1 RT among infants where PMTCT failed. The high coverage of MiSeq and high read quality improved the confidence of identified DRMs and may make this platform ideal for minor variant detection.
Collapse
|
26
|
Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Paredes R, Metzner KJ. Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing. J Antimicrob Chemother 2014; 70:930-40. [PMID: 25336166 PMCID: PMC4319483 DOI: 10.1093/jac/dku426] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives It is still debated if pre-existing minority drug-resistant HIV-1 variants (MVs) affect the virological outcomes of first-line NNRTI-containing ART. Methods This Europe-wide case–control study included ART-naive subjects infected with drug-susceptible HIV-1 as revealed by population sequencing, who achieved virological suppression on first-line ART including one NNRTI. Cases experienced virological failure and controls were subjects from the same cohort whose viraemia remained suppressed at a matched time since initiation of ART. Blinded, centralized 454 pyrosequencing with parallel bioinformatic analysis in two laboratories was used to identify MVs in the 1%–25% frequency range. ORs of virological failure according to MV detection were estimated by logistic regression. Results Two hundred and sixty samples (76 cases and 184 controls), mostly subtype B (73.5%), were used for the analysis. Identical MVs were detected in the two laboratories. 31.6% of cases and 16.8% of controls harboured pre-existing MVs. Detection of at least one MV versus no MVs was associated with an increased risk of virological failure (OR = 2.75, 95% CI = 1.35–5.60, P = 0.005); similar associations were observed for at least one MV versus no NRTI MVs (OR = 2.27, 95% CI = 0.76–6.77, P = 0.140) and at least one MV versus no NNRTI MVs (OR = 2.41, 95% CI = 1.12–5.18, P = 0.024). A dose–effect relationship between virological failure and mutational load was found. Conclusions Pre-existing MVs more than double the risk of virological failure to first-line NNRTI-based ART.
Collapse
Affiliation(s)
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Rob Schuurman
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserslautern, Germany
| | - Sue Aitken
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | | | - Antonella D'Arminio Monforte
- Department of Health Sciences, Clinic of Infectious Diseases, 'San Paolo' Hospital, University of Milan, Milan, Italy
| | - Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Clare L Booth
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Claudia Michalik
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany Clinical Trial Centre (ZKS), University of Cologne, Cologne, Germany
| | - Klaus Jansen
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany
| | - Bernard Masquelier
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Erika Castro
- Addiction Medicine, Service of Community Psychiatry, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Roger Paredes
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
27
|
Chabria SB, Gupta S, Kozal MJ. Deep Sequencing of HIV: Clinical and Research Applications. Annu Rev Genomics Hum Genet 2014; 15:295-325. [DOI: 10.1146/annurev-genom-091212-153406] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shiven B. Chabria
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
| | - Shaili Gupta
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
| | - Michael J. Kozal
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
| |
Collapse
|
28
|
Contribution of human immunodeficiency virus type 1 minority variants to reduced drug susceptibility in patients on an integrase strand transfer inhibitor-based therapy. PLoS One 2014; 9:e104512. [PMID: 25110880 PMCID: PMC4128663 DOI: 10.1371/journal.pone.0104512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
The role of HIV-1 minority variants on transmission, pathogenesis, and virologic failure to antiretroviral regimens has been explored; however, most studies of low-level HIV-1 drug-resistant variants have focused in single target regions. Here we used a novel HIV-1 genotypic assay based on deep sequencing, DEEPGEN (Gibson et al 2014 Antimicrob Agents Chemother 58∶2167) to simultaneously analyze the presence of minority variants carrying mutations associated with reduced susceptibility to protease (PR), reverse transcriptase (RT), and integrase strand transfer integrase inhibitors (INSTIs), as well as HIV-1 coreceptor tropism. gag-p2/NCp7/p1/p6/pol-PR/RT/INT and env/C2V3 PCR products were obtained from twelve heavily treatment-experienced patients experiencing virologic failure while participating in a 48-week dose-ranging study of elvitegravir (GS-US-183-0105). Deep sequencing results were compared with (i) virological response to treatment, (ii) genotyping based on population sequencing, (iii) phenotyping data using PhenoSense and VIRALARTS, and (iv) HIV-1 coreceptor tropism based on the phenotypic test VERITROP. Most patients failed the antiretroviral regimen with numerous pre-existing mutations in the PR and RT, and additionally newly acquired INSTI-resistance mutations as determined by population sequencing (mean 9.4, 5.3, and 1.4 PI- RTI-, and INSTI-resistance mutations, respectively). Interestingly, since DEEPGEN allows the accurate detection of amino acid substitutions at frequencies as low as 1% of the population, a series of additional drug resistance mutations were detected by deep sequencing (mean 2.5, 1.5, and 0.9, respectively). The presence of these low-abundance HIV-1 variants was associated with drug susceptibility, replicative fitness, and coreceptor tropism determined using sensitive phenotypic assays, enhancing the overall burden of resistance to all four antiretroviral drug classes. Further longitudinal studies based on deep sequencing tests will help to clarify (i) the potential impact of minority HIV-1 drug resistant variants in response to antiretroviral therapy and (ii) the importance of the detection of HIV minority variants in the clinical practice.
Collapse
|
29
|
Jeulin H, Foissac M, Boyer L, Agrinier N, Perrier P, Kennel A, Velay A, Goehringer F, Henard S, Rabaud C, May T, Schvoerer E. Real-life rilpivirine resistance and potential emergence of an E138A-positive HIV strain in north-eastern France. J Antimicrob Chemother 2014; 69:3095-102. [PMID: 25006240 DOI: 10.1093/jac/dku256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVES To assess the prevalence of resistance to rilpivirine and mutations at position 138 in reverse transcriptase and to identify associated epidemiological and biological characteristics. METHODS This retrospective study included 238 patients with available HIV-1 nucleotide sequences analysed at the Laboratory of Virology at the University Hospital of Nancy between January 2011 and June 2013. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) was evaluated according to the ANRS algorithm (version 23) and correlated with clinico-epidemiological and therapeutic data. The virus strains were analysed by evaluating the distance and distribution of the phylogenetic tree (MEGAv5). RESULTS Among previously treated patients (111/238, 46.6%), 68/111 (61.3%) had received NNRTIs; all were rilpivirine-naive. The prevalence of rilpivirine resistance in the whole cohort was 12.6% (30/238), and was 10.2% (13/127) and 15.3% (17/111) in naive and pre-treated patients, respectively. The E138A mutation was the most frequent mutation associated with resistance to rilpivirine (P < 0.0001). The prevalence of the E138A mutation tended to increase over time, from 3.6% (2/55) during the first half of 2011 to 9.3% (4/43) during the first half of 2013 (P = 0.0614). Seven viral strains from seven naive male patients positive for the E138A mutation appeared in the same cluster. CONCLUSIONS In our cohort of patients, we observed significantly increased resistance to rilpivirine, mostly because of the E138A mutation, probably due to an E138A strain circulating in newly diagnosed men who have sex with men. Taken together, our results emphasize the need to investigate the prevalence of rilpivirine resistance-associated mutations in the coming years both in France and abroad.
Collapse
Affiliation(s)
- H Jeulin
- CHU Nancy, Laboratoire de Virologie, Nancy, F-54000, France Université Lorraine, Faculté de Médecine, EA 7300, Vandoeuvre-les-Nancy, F-54500, France
| | - M Foissac
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - L Boyer
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - N Agrinier
- CHU Nancy, Service d'épidémiologie clinique, Nancy, F-54000, France
| | - P Perrier
- CHU Nancy, Laboratoire d'histocompatibilité, Nancy, F-54000, France
| | - A Kennel
- CHU Nancy, Laboratoire d'histocompatibilité, Nancy, F-54000, France
| | - A Velay
- CHU Nancy, Laboratoire de Virologie, Nancy, F-54000, France Université Lorraine, Faculté de Médecine, EA 7300, Vandoeuvre-les-Nancy, F-54500, France
| | - F Goehringer
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - S Henard
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - C Rabaud
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - T May
- CHU Nancy, Service de Maladies Infectieuses et Tropicales, Nancy, F-54000, France
| | - E Schvoerer
- CHU Nancy, Laboratoire de Virologie, Nancy, F-54000, France Université Lorraine, Faculté de Médecine, EA 7300, Vandoeuvre-les-Nancy, F-54500, France
| |
Collapse
|
30
|
Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
Collapse
Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| |
Collapse
|
31
|
Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure. AIDS 2014; 28:1315-24. [PMID: 24698843 DOI: 10.1097/qad.0000000000000267] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Drug-resistance mutations are routinely detected using standard Sanger sequencing, which does not detect minor variants with a frequency below 20%. The impact of detecting minor variants generated by ultra-deep sequencing (UDS) on HIV drug-resistance interpretations has not yet been studied. DESIGN Fifty HIV-1 patients who experienced virological failure were included in this retrospective study. METHODS The HIV-1 UDS protocol allowed the detection and quantification of HIV-1 protease and reverse transcriptase variants related to genotypes A, B, C, F and G. DeepChek-HIV simplified drug-resistance interpretation software was used to compare Sanger sequencing and UDS. RESULTS The total time required for the UDS protocol was found to be approximately three times longer than Sanger sequencing with equivalent reagent costs. UDS detected all of the mutations found by population sequencing and identified additional resistance variants in all patients. An analysis of drug resistance revealed a total of 643 and 224 clinically relevant mutations by UDS and Sanger sequencing, respectively. Three resistance mutations with more than 20% prevalence were detected solely by UDS: A98S (23%), E138A (21%) and V179I (25%). A significant difference in the drug-resistance interpretations for 19 antiretroviral drugs was observed between the UDS and Sanger sequencing methods. Y181C and T215Y were the most frequent mutations associated with interpretation differences. CONCLUSION A combination of UDS and DeepChek software for the interpretation of drug resistance results would help clinicians provide suitable treatments. A cut-off of 1% allowed a better characterization of the viral population by identifying additional resistance mutations and improving the drug-resistance interpretation.
Collapse
|
32
|
Pou C, Noguera-Julian M, Pérez-Álvarez S, García F, Delgado R, Dalmau D, Álvarez-Tejado M, Gonzalez D, Sayada C, Chueca N, Pulido F, Ibáñez L, Rodríguez C, Casadellà M, Santos JR, Ruiz L, Clotet B, Paredes R. Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing. Clin Infect Dis 2014; 59:578-88. [PMID: 24879788 DOI: 10.1093/cid/ciu287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The clinical relevance of ultrasensitive human immunodeficiency virus type 1 (HIV-1) genotypic resistance testing in antiretroviral treatment (ART)-experienced individuals remains unknown. METHODS This was a retrospective, multicentre, cohort study in ART-experienced, HIV-1-infected adults who initiated salvage ART including, at least 1 ritonavir-boosted protease inhibitor, raltegravir or etravirine. Presalvage ART Sanger and 454 sequencing of plasma HIV-1 were used to generate separate genotypic sensitivity scores (GSS) using the HIVdb, ANRS, and REGA algorithms. Virological failure (VF) was defined as 2 consecutive HIV-1 RNA levels ≥200 copies/mL at least 12 weeks after salvage ART initiation, whereas subjects remained on the same ART. The ability of Sanger and 454-GSS to predict VF was assessed by receiver operating characteristic (ROC) curves and survival analyses. RESULTS The study included 132 evaluable subjects; 28 (21%) developed VF. Using HIVdb, 454 predicted VF better than Sanger sequencing in the ROC curve analysis (area under the curve: 0.69 vs 0.60, Delong test P = .029). Time to VF was shorter for subjects with 454-GSS < 3 vs 454-GSS ≥ 3 (Log-rank P = .003) but not significantly different between Sanger-GSS < 3 and ≥3. Factors independently associated with increased risk of VF in multivariate Cox regression were a 454-GSS < 3 (HR = 4.6, 95 CI, [1.5, 14.0], P = .007), and the number of previous antiretrovirals received (HR = 1.2 per additional drug, 95 CI, [1.1, 1.3], P = .001). Equivalent findings were obtained with the ANRS and REGA algorithms. CONCLUSIONS Ultrasensitive HIV-1 genotyping improves GSS-based predictions of virological outcomes of salvage ART relative to Sanger sequencing. This may improve the clinical management of ART-experienced subjects living with HIV-1. CLINICAL TRIALS REGISTRATION NCT01346878.
Collapse
Affiliation(s)
- Christian Pou
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic
| | - Susana Pérez-Álvarez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Federico García
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - David Dalmau
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa Universitat de Barcelona, Terrassa
| | | | | | - Chalom Sayada
- ABL SA, Barcelona, Spain ABL SA, Luxembourg, Luxembourg
| | - Natalia Chueca
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Federico Pulido
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - Laura Ibáñez
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa
| | - Cristina Rodríguez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - José R Santos
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Lidia Ruiz
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| |
Collapse
|
33
|
|
34
|
Clinically relevant transmitted drug resistance to first line antiretroviral drugs and implications for recommendations. PLoS One 2014; 9:e90710. [PMID: 24637804 PMCID: PMC3956602 DOI: 10.1371/journal.pone.0090710] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/03/2014] [Indexed: 11/28/2022] Open
Abstract
Background The aim was to analyse trends in clinically relevant resistance to first-line antiretroviral drugs in Spain, applying the Stanford algorithm, and to compare these results with reported Transmitted Drug Resistance (TDR) defined by the 2009 update of the WHO SDRM list. Methods We analysed 2781 sequences from ARV naive patients of the CoRIS cohort (Spain) between 2007–2011. Using the Stanford algorithm “Low-level resistance”, “Intermediate resistance” and “High-level resistance” categories were considered as “Resistant”. Results 70% of the TDR found using the WHO list were relevant for first-line treatment according to the Stanford algorithm. A total of 188 patients showed clinically relevant resistance to first-line ARVs [6.8% (95%Confidence Interval: 5.8–7.7)], and 221 harbored TDR using the WHO list [7.9% (6.9–9.0)]. Differences were due to a lower prevalence in clinically relevant resistance for NRTIs [2.3% (1.8–2.9) vs. 3.6% (2.9–4.3) by the WHO list] and PIs [0.8% (0.4–1.1) vs. 1.7% (1.2–2.2)], while it was higher for NNRTIs [4.6% (3.8–5.3) vs. 3.7% (3.0–4.7)]. While TDR remained stable throughout the study period, clinically relevant resistance to first line drugs showed a significant trend to a decline (p = 0.02). Conclusions Prevalence of clinically relevant resistance to first line ARVs in Spain is decreasing, and lower than the one expected looking at TDR using the WHO list. Resistance to first-line PIs falls below 1%, so the recommendation of screening for TDR in the protease gene should be questioned in our setting. Cost-effectiveness studies need to be carried out to inform evidence-based recommendations.
Collapse
|
35
|
Raffi F, Pozniak AL, Wainberg MA. Has the time come to abandon efavirenz for first-line antiretroviral therapy? J Antimicrob Chemother 2014; 69:1742-7. [PMID: 24603962 DOI: 10.1093/jac/dku058] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Efavirenz has been recommended as a preferred third agent together with two nucleos(t)ides for first-line combination antiretroviral therapy (ART) for >15 years. The availability of efavirenz in a fixed-dose combination makes it very attractive. However, because of (i) adverse events associated with efavirenz, (ii) a poorer overall efficacy of efavirenz compared with newer antiretrovirals, (iii) the ranking of efavirenz as FDA Pregnancy Category D and (iv) the relatively high prevalence of transmitted drug-resistance mutations, there is a need to reconsider the role of efavirenz in first-line ART. We review the available evidence that challenges efavirenz's current position in first-line HIV treatment guidelines. Apart from its animal teratogenic potential, and moderate neuropsychiatric adverse events associated with its use, efavirenz has recently been associated with an increased risk of suicidality when compared with other antiretroviral drugs. Most importantly, efavirenz has demonstrated overall inferior efficacy to various comparator drugs, which include rilpivirine, raltegravir and dolutegravir, in antiretroviral-naive patients. Furthermore, epidemiological data indicate that the prevalence of non-nucleoside reverse transcriptase inhibitor resistance has reached 5%-8% in various parts of the world, and minority transmitted non-nucleoside reverse transcriptase inhibitor resistance-associated mutations can have a negative impact on the outcome of first-line efavirenz-based ART. Based on considerations of efficacy, toxicity and resistance, it is time to reconsider the routine use of efavirenz in ART. This, of course, presupposes that other antiretrovirals will be available in place of efavirenz, and may not be applicable in certain developing country settings where this is not the case.
Collapse
Affiliation(s)
- Francois Raffi
- Division of Infectious Diseases, Nantes University Hospital, Nantes, France
| | - Anton L Pozniak
- HIV Department, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Mark A Wainberg
- Departments of Medicine and of Microbiology, Jewish General Hospital, McGill University, Montreal, Canada
| |
Collapse
|
36
|
Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use? Curr Infect Dis Rep 2014; 16:401. [DOI: 10.1007/s11908-014-0401-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
37
|
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.
Collapse
|
38
|
Geretti AM, Conibear T, Hill A, Johnson JA, Tambuyzer L, Thys K, Vingerhoets J, Van Delft Y, Rieger A, Vetter N, Greil R, Pedersen C, Storgaard M, Morlat P, Katlama C, Durant J, Cotte L, Duvivier C, Rey D, Esser S, Stellbrink C, Schmidt W, Stoll M, Stephan C, Fatkenheuer G, Stoehr A, Rockstroh J, Banhegyi D, Itzchak L, Shahar E, Maayan S, Turner D, Lazzarin A, Antinori A, Carosi G, Minoli L, di Perri G, Filice G, Andreoni M, Duiculescu D, Rugina S, Erscoiu S, Streinu A, Pronin A, Pokrovsky V, Gruzdev B, Yakovlev A, Voronin E, Clotet B, Gatell J, Arribas J, Podzamczer D, Domingo P, Alvarez CM, Quero JH, Furrer H, Feher J, Johnson M, Fox J, Nelson M, Fisher M, Orkin C. Sensitive testing of plasma HIV-1 RNA and Sanger sequencing of cellular HIV-1 DNA for the detection of drug resistance prior to starting first-line antiretroviral therapy with etravirine or efavirenz. J Antimicrob Chemother 2013; 69:1090-7. [DOI: 10.1093/jac/dkt474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
39
|
Mohamed S, Ravet S, Camus C, Khiri H, Olive D, Halfon P. Clinical and analytical relevance of NNRTIs minority mutations on viral failure in HIV-1 infected patients. J Med Virol 2013; 86:394-403. [DOI: 10.1002/jmv.23853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Sofiane Mohamed
- Laboratoire Alphabio; Marseille France
- Laboratoire d'Immunologie des Tumeurs et Centre INSERM de Recherche en Cancérologie, Institut Paoli Calmettes; Marseille France
| | | | | | | | - Daniel Olive
- Laboratoire d'Immunologie des Tumeurs et Centre INSERM de Recherche en Cancérologie, Institut Paoli Calmettes; Marseille France
| | - Philippe Halfon
- Laboratoire Alphabio; Marseille France
- Hôpital Européen; Marseille France
| |
Collapse
|
40
|
Garcia-Diaz A, Guerrero-Ramos A, McCormick A, Macartney M, Conibear T, Johnson M, Haque T, Webster D. Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory. J Clin Virol 2013; 58:468-73. [DOI: 10.1016/j.jcv.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 11/28/2022]
|
41
|
Geretti AM, Fox Z, Johnson JA, Booth C, Lipscomb J, Stuyver LJ, Tachedjian G, Baxter J, Touloumi G, Lehmann C, Owen A, Phillips A. Sensitive assessment of the virologic outcomes of stopping and restarting non-nucleoside reverse transcriptase inhibitor-based antiretroviral therapy. PLoS One 2013; 8:e69266. [PMID: 23874928 PMCID: PMC3715458 DOI: 10.1371/journal.pone.0069266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/06/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutants have been shown to emerge after interruption of suppressive NNRTI-based antiretroviral therapy (ART) using routine testing. The aim of this study was to quantify the risk of resistance by sensitive testing and correlate the detection of resistance with NNRTI concentrations after treatment interruption and virologic responses after treatment resumption. METHODS Resistance-associated mutations (RAMs) and NNRTI concentrations were studied in plasma from 132 patients who interrupted suppressive ART within SMART. RAMs were detected by Sanger sequencing, allele-specific PCR, and ultra-deep sequencing. NNRTI concentrations were measured by sensitive high-performance liquid chromatography. RESULTS Four weeks after NNRTI interruption, 19/31 (61.3%) and 34/39 (87.2%) patients showed measurable nevirapine (>0.25 ng/ml) or efavirenz (>5 ng/ml) concentrations, respectively. Median eight weeks after interruption, 22/131 (16.8%) patients showed ≥1 NNRTI-RAM, including eight patients with NNRTI-RAMs detected only by sensitive testing. The adjusted odds ratio (OR) of NNRTI-RAM detection was 7.62 (95% confidence interval [CI] 1.52, 38.30; p = 0.01) with nevirapine or efavirenz concentrations above vs. below the median measured in the study population. Staggered interruption, whereby nucleos(t)ide reverse transcriptase inhibitors (NRTIs) were continued for median nine days after NNRTI interruption, did not prevent NNRTI-RAMs, but increased detection of NRTI-RAMs (OR 4.25; 95% CI 1.02, 17.77; p = 0.03). After restarting NNRTI-based ART (n = 90), virologic suppression rates <400 copies/ml were 8/13 (61.5%) with NNRTI-RAMs, 7/11 (63.6%) with NRTI-RAMs only, and 51/59 (86.4%) without RAMs. The ORs of re-suppression were 0.18 (95% CI 0.03, 0.89) and 0.17 (95% CI 0.03, 1.15) for patients with NNRTI-RAMs or NRTI-RAMs only respectively vs. those without RAMs (p = 0.04). CONCLUSIONS Detection of resistant mutants in the rebound viremia after interruption of efavirenz- or nevirapine-based ART affects outcomes once these drugs are restarted. Further studies are needed to determine RAM persistence in untreated patients and impact on newer NNRTIs.
Collapse
Affiliation(s)
- Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|