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Balakrishna S, Loosli T, Zaheri M, Frischknecht P, Huber M, Kusejko K, Yerly S, Leuzinger K, Perreau M, Ramette A, Wymant C, Fraser C, Kellam P, Gall A, Hirsch HH, Stoeckle M, Rauch A, Cavassini M, Bernasconi E, Notter J, Calmy A, Günthard HF, Metzner KJ, Kouyos RD. Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. J Antimicrob Chemother 2023; 78:656-664. [PMID: 36738248 DOI: 10.1093/jac/dkac430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds. METHODS To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds. RESULTS We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%. CONCLUSIONS We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.
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Affiliation(s)
- Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Karoline Leuzinger
- Clinical Virology Division, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Chris Wymant
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Astrid Gall
- Excellence in Life Sciences (EMBO), Heidelberg, Germany
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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2
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Raymond S, Jeanne N, Nicot F, Dimeglio C, Carcenac R, Harter A, Ranger N, Martin-Blondel G, Delobel P, Izopet J. HIV-1 resistance genotyping by ultra-deep sequencing and 6-month virological response to first-line treatment. J Antimicrob Chemother 2023; 78:346-353. [PMID: 36449383 DOI: 10.1093/jac/dkac391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVES To evaluate the routine use of the Sentosa ultra-deep sequencing (UDS) system for HIV-1 polymerase resistance genotyping in treatment-naïve individuals and to analyse the virological response (VR) to first-line antiretroviral treatment. METHODS HIV drug resistance was determined on 237 consecutive samples from treatment-naïve individuals using the Sentosa UDS platform with two mutation detection thresholds (3% and 20%). VR was defined as a plasma HIV-1 virus load <50 copies/mL after 6 months of treatment. RESULTS Resistance to at least one antiretroviral drug with a mutation threshold of 3% was identified in 29% and 16% of samples according to ANRS and Stanford algorithms, respectively. The ANRS algorithm also revealed reduced susceptibility to at least one protease inhibitor (PI) in 14.3% of samples, to one reverse transcriptase inhibitor in 12.7%, and to one integrase inhibitor (INSTI) in 5.1%. For a mutation threshold of 20%, resistance was identified in 24% and 13% of samples according to ANRS and Stanford algorithms, respectively. The 6 months VR was 87% and was similar in the 58% of patients given INSTI-based treatment, in the 16% given PI-based treatment and in the 9% given NNRTI-based treatment. Multivariate analysis indicated that the VR was correlated with the baseline HIV virus load and resistance to at least one PI at both 3% and 20% mutation detection thresholds (ANRS algorithm). CONCLUSIONS The Vela UDS platform is appropriate for determining antiretroviral resistance in patients on a first-line antiretroviral treatment. Further studies are needed on the use of UDS for therapeutic management.
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Affiliation(s)
- Stéphanie Raymond
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Guillaume Martin-Blondel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300France
| | - Pierre Delobel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300France
| | - Jacques Izopet
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
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Wadden J, Ravi K, John V, Babila CM, Koschmann C. Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy. Front Immunol 2022; 13:882452. [PMID: 35464472 PMCID: PMC9018987 DOI: 10.3389/fimmu.2022.882452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are tumors derived from mutations in glial brain cells. Gliomas cause significant morbidity and mortality and development of precision diagnostics and novel targeted immunotherapies are critically important. Radiographic imaging is the most common technique to diagnose and track response to treatment, but is an imperfect tool. Imaging does not provide molecular information, which is becoming critically important for identifying targeted immunotherapies and monitoring tumor evolution. Furthermore, immunotherapy induced inflammation can masquerade as tumor progression in images (pseudoprogression) and confound clinical decision making. More recently, circulating cell free tumor DNA (cf-tDNA) has been investigated as a promising biomarker for minimally invasive glioma diagnosis and disease monitoring. cf-tDNA is shed by gliomas into surrounding biofluids (e.g. cerebrospinal fluid and plasma) and, if precisely quantified, might provide a quantitative measure of tumor burden to help resolve pseudoprogression. cf-tDNA can also identify tumor genetic mutations to help guide targeted therapies. However, due to low concentrations of cf-tDNA, recovery and analysis remains challenging. Plasma cf-tDNA typically represents <1% of total cf-DNA due to the blood-brain barrier, limiting their usefulness in practice and motivating the development and use of highly sensitive and specific detection methods. This mini review summarizes the current and future trends of various approaches for cf-tDNA detection and analysis, including new methods that promise more rapid, lower-cost, and accessible diagnostics. We also review the most recent clinical case studies for longitudinal disease monitoring and highlight focus areas, such as novel accurate detection methodologies, as critical research priorities to enable translation to clinic.
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Affiliation(s)
- Jack Wadden
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| | | | | | | | - Carl Koschmann
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
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Tachbele E, Kyobe S, Katabazi FA, Kigozi E, Mwesigwa S, Joloba M, Messele A, Amogne W, Legesse M, Pieper R, Ameni G. Genetic Diversity and Acquired Drug Resistance Mutations Detected by Deep Sequencing in Virologic Failures among Antiretroviral Treatment Experienced Human Immunodeficiency Virus-1 Patients in a Pastoralist Region of Ethiopia. Infect Drug Resist 2021; 14:4833-4847. [PMID: 34819737 PMCID: PMC8607991 DOI: 10.2147/idr.s337485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/03/2021] [Indexed: 01/15/2023] Open
Abstract
Purpose This study was conducted to investigate the drug resistance mutations and genetic diversity of HIV-1 in ART experienced patients in South Omo, Ethiopia. Patients and Methods A cross-sectional study conducted on 253 adult patients attending ART clinics for ≥6 months in South Omo. Samples with VL ≥1000 copies/mL were considered as virological failures (VF) and their reverse transcriptase gene codons 90–234 were sequenced using Illumina MiSeq. MinVar was used for the identification of the subtypes and drug resistance mutations. Phylogenetic tree was constructed by neighbor-joining method using the maximum likelihood model. Results The median duration of ART was 51 months and 18.6% (47/253) of the patients exhibited VF. Of 47 viraemic patients, the genome of 41 were sequenced and subtype C was dominant (87.8%) followed by recombinant subtype BC (4.9%), M-09-CPX (4.9) and BF1 (2.4%). Of 41 genotyped subjects, 85.4% (35/41) had at least one ADR mutation. Eighty-one percent (33/41) of viraemic patients harbored NRTI resistance mutations, and 48.8% (20/41) were positive for NNRTI resistance mutations, with 43.9% dual resistance mutations. Among NRTI resistance mutations, M184V (73.2%), K219Q (63.4%) and T215 (56.1%) complex were the most mutated positions, while the most common NNRTI resistance mutations were K103N (24.4%), K101E, P225H and V108I 7.5% each. Active tuberculosis (aOR=13, 95% CI= 3.46–29.69), immunological failure (aOR=3.61, 95% CI=1.26–10.39), opportunistic infections (aOR=8.39, 95% CI= 1.75–40.19), and poor adherence were significantly associated with virological failure, while rural residence (aOR 2.37; 95% CI: 1.62–9.10, P= 0.05), immunological failures (aOR 2.37; 95% CI: 1.62–9.10, P= 0.05) and high viral load (aOR 16; 95% CI: 5.35 51.59, P <0.001) were predictors of ADR mutation among the ART experienced and viraemic study subjects. Conclusion The study revealed considerable prevalence of VF and ADR mutation with the associated risk indicators. Regular virological monitoring and drug resistance genotyping methods should be implemented for better ART treatment outcomes of the nation.
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Affiliation(s)
- Erdaw Tachbele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.,College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Edgar Kigozi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Moses Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wondwossen Amogne
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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5
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Tekin D, Gokengin D, Onay H, Erensoy S, Sertoz R. Investigation of drug resistance against protease, reverse transcriptase, and integrase inhibitors by next-generation sequencing in HIV-positive patients. J Med Virol 2021; 93:3627-3633. [PMID: 33026651 DOI: 10.1002/jmv.26582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
Our aim was to investigate the mutations in protease (PR), reverse transcriptase (RT), and integrase (IN) gene regions in human immunodeficiency virus (HIV) using a single amplicon via next-generation sequencing (NGS). The study included plasma samples from 49 HIV-1-positive patients, which were referred for HIV-1 drug resistance testing during 2017. A nested polymerase chain reaction (PCR) was performed after the RNA extraction and one-step reverse transcription stages. The sequencing of the HIV genome in the PR, RT, and IN gene regions was carried out using MiSeq NGS technology. Sanger sequencing (SS) was used to analyze resistance mutations in the PR and RT gene regions using a ViroSeq HIV-1 Genotyping System. PCR products were analyzed with an ABI3500 GeneticAnalyzer (Applied Biosystems). Resistance mutations detected with NGS at frequencies above 20% were identical to the SS results. Resistance to at least one antiretroviral (ARV) drug was 22.4% (11 of 49) with NGS and 10.2% (5 of 49) with SS. At least one low-frequency resistance mutation was detected in 18.3% (9 of 49) of the samples. Low-frequency resistance mutations resulted in virological failure in only one patient. The cost of the analyses was reduced by sample pooling and multiplex analysis using the MiSeq system. This is the first study in Turkey to use NGS technologies for the detection of resistance mutations in all three gene (PR, RT, IN) regions using a single amplicon. Our findings suggest that NGS is more sensitive and cost-effective than the SS method.
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Affiliation(s)
- Duygu Tekin
- Department of Medical Microbiology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Deniz Gokengin
- Department of Clinical Microbiology and Infectious Diseases, Ege University Medical School, Izmir, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Ege University Medical School, Izmir, Turkey
| | - Selda Erensoy
- Department of Medical Microbiology, Ege University Medical School, Izmir, Turkey
| | - Ruchan Sertoz
- Department of Medical Microbiology, Ege University Medical School, Izmir, Turkey
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Su B, Zheng X, Liu Y, Liu L, Xin R, Lu H, Huang C, Bai L, Mammano F, Zhang T, Wu H, Sun L, Dai L. Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. J Antimicrob Chemother 2020; 74:1408-1416. [PMID: 30668734 DOI: 10.1093/jac/dky561] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/24/2018] [Accepted: 12/10/2018] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Ultra-deep sequencing (UDS) is a powerful tool for exploring the impact on virological outcome of minority variants with low frequencies, some even <1% of the virus population. Here, we compared HIV-1 minority variants at baseline, through plasma RNA and PBMC DNA analyses, and the dominant variants at the virological failure (VF) point, to evaluate the impact of minority drug-resistant variants (MDRVs) on virological outcomes. METHODS Single-molecule real-time sequencing (SMRTS) was performed on baseline RNA and DNA. The Stanford HIV-1 drug resistance database was used for the identification and evaluation of drug resistance-associated mutations (DRAMs). RESULTS We classified 50 patients into virological success (VS) and VF groups. We found that the rates of reverse transcriptase inhibitor (RTI) DRAMs determined by SMRTS did not differ significantly within or between groups, whether based on RNA or DNA analyses. There was no significant difference in the level of resistance to specific drugs between groups, in either DNA or RNA analyses, except for the DNA-based analysis of lamivudine, for which there was a trend towards a higher prevalence of intermediate/high-level resistance in the VF group. The RNA MDRVs corresponded to DNA MDRVs, except for M100I and Y188H. Sequencing from DNA appeared to be more sensitive than from RNA to detect MDRVs. CONCLUSIONS Detection of pretreatment minority HIV-1 RTI-resistant variants by UDS showed that MDRVs at baseline were not significantly associated with virological outcome. However, HIV-1 DNA sequencing by UDS was useful for detecting pretreatment drug resistance mutations in patients, potentially affecting virological responses, suggesting a potential clinical relevance for ultra-deep DNA sequencing.
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Affiliation(s)
- Bin Su
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | | | - Yan Liu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Lifeng Liu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Ruolei Xin
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hongyan Lu
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Chun Huang
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lishi Bai
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Fabrizio Mammano
- INSERM U941, Genetics and Ecology of Viruses, Hospital Saint Louis, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Tong Zhang
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Lijun Sun
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lili Dai
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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Dimeglio C, Raymond S, Nicot F, Jeanne N, Carcenac R, Lefebvre C, Izopet J. Impact of the mutational load on the virological response to a first-line rilpivirine-based regimen. J Antimicrob Chemother 2020; 74:718-721. [PMID: 30535228 DOI: 10.1093/jac/dky495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 11/08/2018] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To determine how the load of rilpivirine-resistant variants (mutational load) influences the virological response (VR) of HIV-1-infected patients to a rilpivirine-based first-line regimen. PATIENTS AND METHODS Four hundred and eighty-nine patients infected with HIV-1 whose reverse transcriptase gene had been successfully resistance genotyped using next-generation sequencing were given a first-line regimen containing rilpivirine. Variables associated with the VR at 12 months were identified using a logistic model. The results were used to build a multivariate model for each mutational load threshold and the R2 variations were analysed to identify the mutational load threshold that best predicted the VR. RESULTS The mutational load at baseline was the only variable linked to the VR at 12 months (P < 0.01). The VR at 12 months decreased from 96.9% to 83.4% when the mutational load was >1700 copies/mL and to 50% when the mutational load was > 9000 copies/mL. The threshold of 9000 copies/mL was associated with the VR at 12 months with an OR of 36.7 (95% CI 4.7-285.1). The threshold of 1700 copies/mL was associated with the VR at 12 months with an OR of 7.2 (95% CI 1.4-36.8). CONCLUSIONS There is quantifiable evidence that determining a mutational load threshold can be used to identify those patients on a first-line regimen containing rilpivirine who are at risk of virological failure. The clinical management of HIV-infected patients can be improved by evaluating the frequency of mutant variants at a threshold of < 20% together with the plasma HIV-1 viral load at the time of resistance genotyping.
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Affiliation(s)
- Chloé Dimeglio
- INSERM U1043 - CNRS UMR5282 - Toulouse University Paul Sabatier, CPTP, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Stéphanie Raymond
- INSERM U1043 - CNRS UMR5282 - Toulouse University Paul Sabatier, CPTP, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Jacques Izopet
- INSERM U1043 - CNRS UMR5282 - Toulouse University Paul Sabatier, CPTP, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
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Raymond S, Nicot F, Abravanel F, Minier L, Carcenac R, Lefebvre C, Harter A, Martin-Blondel G, Delobel P, Izopet J. Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance. J Clin Virol 2019; 122:104229. [PMID: 31809945 DOI: 10.1016/j.jcv.2019.104229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Patients on antiretroviral therapy could benefit from HIV-1 DNA resistance genotyping for exploring virological failure with low viral load or to guide treatment simplification. Few new generation sequencing data are available. OBJECTIVE To check that the automated deep sequencing Sentosa platform (Vela DX) detected minority resistant variants well enough for HIV DNA genotyping. STUDY DESIGN We evaluated the Sentosa SQ HIV genotyping assay with automated extraction on 40 DNA longitudinal samples from treatment-experienced patients by comparison with Sanger sequencing. HIV drug resistance was interpreted using the ANRS algorithm (v29) at the threshold of 20 % and 3 %. RESULTS The Sentosa SQ HIV genotyping assay was 100 % successful to amplify and sequence PR and RT and 86 % to amplify and sequence IN when the HIV DNA load was >2.5 log copies/million cells. The Sentosa and Sanger sequencing were concordant for predicting PR-RT resistance at the threshold of 20 % in 14/18 samples successfully sequenced. A higher level of resistance was predicted by Sentosa in three samples and by Sanger in one sample. The prevalence of resistance was 7 % to PI, 59 % to NRTI, 31 % to NNRTI and 20 % to integrase inhibitors using the Sentosa SQ genotyping assay at the threshold of 3 %. Seven additional mutations <20 % were detected using the Sentosa assay. CONCLUSION Automated DNA extraction and sequencing using the Sentosa SQ HIV genotyping assay accurately predicted HIV DNA drug resistance by comparison with Sanger. Prospective studies are needed to evaluate the clinical interest of HIV DNA genotyping.
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Affiliation(s)
- Stéphanie Raymond
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France.
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Florence Abravanel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Luce Minier
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Guillaume Martin-Blondel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Pierre Delobel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Jacques Izopet
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
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9
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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.
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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
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10
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Raymond S, Nicot F, Carcenac R, Lefebvre C, Jeanne N, Saune K, Delobel P, Izopet J. HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform. J Antimicrob Chemother 2019; 73:1152-1157. [PMID: 29444253 DOI: 10.1093/jac/dky003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/29/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples. Results The Vela NGS system detected majority resistance mutations in subtype B and CRF02-AG samples at 500 copies/mL and minority variants with a sensitivity of 5% at 100 000 copies/mL. The Vela NGS system and direct sequencing identified resistance mutations with 97% concordance in 46 clinical samples. Vela identified 1/20 of the 1%-5% mutations identified by 454, 5/12 of the 5%-20% mutations and 60/61 of the >20% mutations. Vela identified 3/14 of the 1%-5% mutations identified by MiSeq, 0/2 of the 5%-20% mutations and 47/47 of the >20% mutations. The resistance mutation quantifications by Vela and 454 were concordant (bias: 2.31%), as were those by Vela and MiSeq (bias: 1.06%). Conclusions The Vela NGS system provides automated nucleic acid extraction, PCR reagent distribution, library preparation and bioinformatics analysis. The analytical performance was very good when compared with direct sequencing, but was less sensitive than two other NGS platforms for detecting minority variants.
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Affiliation(s)
- Stéphanie Raymond
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Karine Saune
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse F-31300, France.,Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France
| | - Jacques Izopet
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
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11
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Gopalan BP, D'Souza RR, Rajnala N, Arumugam K, Dias M, Ranga U, Shet A. Viral evolution in the cell-associated HIV-1 DNA during early ART can lead to drug resistance and virological failure in children. J Med Virol 2019; 91:1036-1047. [PMID: 30695102 DOI: 10.1002/jmv.25413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 11/07/2022]
Abstract
Using cell-associated DNA and cell-free RNA of human immunodeficiency virus type-1 (HIV-1), we investigated the role of drug-resistant viral variants that emerged during early antiretroviral therapy (ART) in determining virological outcome. This case-control study compared virologic nonresponder children (two viral loads [VLs] ≥ 200 copies/mL within 2 years of ART) and responder children (two VLs < 200 copies/mL after six months of ART) infected with HIV-1 initiated on nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based ART. The partial reverse-transcriptase gene of HIV-1 in cell-associated DNA was genotyped using next-generation sequencing (NGS; Illumina; threshold 0.5%; at baseline and month six of ART) and in cell-free RNA (concurrently and at virological failure; VL > 1000 copies/mL at ≥ 12 months of ART) using the Sanger method. Among 30 nonresponders and 37 responders, baseline differences were insignificant while adherence, VL, and drug resistance mutations (DRMs) observed at month six differed significantly ( P ≥ 0.05). At month six, NGS estimated a higher number of DRMs compared with Sanger (50% vs 33%; P = 0.001). Among the nonresponders carrying a resistant virus (86.6%) at virological failure, 26% harbored clinically relevant low-frequency DRMs in the cell-associated DNA at month six (0.5%-20%; K103N, G190A, Y181C, and M184I). Plasma VL of > 3 log 10 copies/mL (AOR, 30.4; 95% CI, 3.3-281; P = 0.003) and treatment-relevant DRMs detected in the cell-associated DNA at month six (AOR, 24.2; 95% CI, 2.6-221; P = 0.005) were independently associated with increased risk for early virological failure. Our findings suggest that treatment-relevant DRMs acquired in cell-associated DNA during the first six months of ART can predict virological failure in children initiated on NNRTI-based ART.
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Affiliation(s)
- Bindu Parachalil Gopalan
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,School of Integrative Health Sciences, University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Reena R D'Souza
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Niharika Rajnala
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Karthika Arumugam
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV/AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anita Shet
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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12
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Nicot F, Jeanne N, Raymond S, Delfour O, Carcenac R, Lefebvre C, Sauné K, Delobel P, Izopet J. Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene. J Med Virol 2018; 90:1486-1492. [PMID: 29750364 DOI: 10.1002/jmv.25224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 01/08/2023]
Abstract
The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson's analysis showed good concordance between the percentage of drug-resistant variants determined by MiSeq and 454 GS-FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS-FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.
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Affiliation(s)
- Florence Nicot
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Stéphanie Raymond
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Olivier Delfour
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Romain Carcenac
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Caroline Lefebvre
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Karine Sauné
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
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13
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Jagjit Singh GK, Kaye S, Abbott JC, Boesecke C, Rockstroh J, McClure MO, Nelson M. Use of next-generation sequencing in the CHAT study (acute HCV in HIV): effect of baseline resistance-associated NS3 variants on treatment failure. HIV CLINICAL TRIALS 2018; 19:46-51. [PMID: 29493385 DOI: 10.1080/15284336.2018.1439714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background The epidemic of acute HCV infection among HIV-infected men who have sex with men (MSM) is ongoing. Transmission of drug-resistant variants (DRVs) after HCV treatment failure could pose a major threat to the effectiveness of future therapies. We determined the baseline prevalence of pre-existing DRVs in the HCV NS3 protease gene and their effects on the addition of telaprevir (TVR) to standard pegylated interferon and ribavirin (PEG-IFN/RBV) for acute HCV infection in individuals enrolled in a multicentre randomized controlled trial (2013 and 2014). Methods The HCV NS3 viral protease was analyzed using Sanger and next-generation sequencing (NGS) for DRVs at baseline (n = 31), and at viral breakthrough following TVR-based treatment (n = 3) or PEG-IFN/RBV alone (n = 2). Results Sequence analysis indicated that all individuals were infected with HCV genotype 1a. Complete (100%) concordance was seen between Sanger and NGS for high levels of mutant viral populations. The simeprevir-associated Q80K variant was present at high frequency in the German samples (7/11-64%) and infrequently in the UK samples (1/20-5%). In the three TVR-based treatment failures, V36M/l and R155K/T emerged, but not R155G which was detectable at low levels in two individuals at baseline. Failure rate at week 24 was 26.7% (with baseline DRVs) vs. 6.3% (without baseline DRVs), p = 0.17). Comparison of sequences pre- and post-therapy in 5 who failed therapy revealed the emergence of not previously described variants V193G, E176K, P189S (on TVR), and V181S in one instance each. Conclusion The presence of baseline DRVs for the NS3 protease gene of HCV genotype 1a did not appear to predict treatment failure in our patient cohort. Where detected, Q80K was present at high levels (>98%), but had no effect on outcomes and remained high after failure.
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Affiliation(s)
- Gurmit Kaur Jagjit Singh
- a Department of HIV and Sexual Health , Chelsea and Westminster Hospital NHS Foundation Trust , London , UK
| | - Steve Kaye
- b Division of Infectious Diseases , Imperial College London , London , UK
| | - James C Abbott
- c Department of Surgery and Cancer , Imperial College London , London , UK
| | | | - Juergen Rockstroh
- d Department of Medicine , Bonn University Hospital , Bonn , Germany
| | - Myra O McClure
- b Division of Infectious Diseases , Imperial College London , London , UK
| | - Mark Nelson
- a Department of HIV and Sexual Health , Chelsea and Westminster Hospital NHS Foundation Trust , London , UK.,b Division of Infectious Diseases , Imperial College London , London , UK
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14
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Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW. Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing. J Infect Dis 2017; 216:387-391. [PMID: 28859436 DOI: 10.1093/infdis/jix338] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/17/2017] [Indexed: 11/14/2022] Open
Abstract
Minority variant human immunodeficiency virus type 1 (HIV-1) nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations are associated with an increased risk of virological failure during treatment with NNRTI-containing regimens. To determine whether individuals to whom variants with isolated NNRTI-associated drug resistance were transmitted are at increased risk of virological failure during treatment with a non-NNRTI-containing regimen, we identified minority variant resistance mutations in 33 individuals with isolated NNRTI-associated transmitted drug resistance and 49 matched controls. We found similar proportions of overall and nucleoside reverse transcriptase inhibitor-associated minority variant resistance mutations in both groups, suggesting that isolated NNRTI-associated transmitted drug resistance may not be a risk factor for virological failure during treatment with a non-NNRTI-containing regimen.
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Affiliation(s)
| | - Shuntai Zhou
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill
| | - Vici Varghese
- Division of Infectious Diseases and Geographic Medicine
| | - Soo-Yon Rhee
- Division of Infectious Diseases and Geographic Medicine
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine.,Department of Pathology, Stanford University School of Medicine
| | - W Jeffrey Fessel
- Department of Internal Medicine, San Francisco Medical Center, Kaiser Permanente Northern California,San Francisco
| | - Daniel B Klein
- Department of Infectious Diseases, San Leandro Medical Center, Kaiser Permanente Northern California,San Leandro
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill
| | | | - Leo B Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Michael J Silverberg
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill
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15
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Theotokis PI, Usher L, Kortschak CK, Schwalbe E, Moschos SA. Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:22-33. [PMID: 29246301 PMCID: PMC5602524 DOI: 10.1016/j.omtn.2017.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 01/08/2023]
Abstract
Low allelic and clonal variability among endogenous RNAi targets has focused mismatch tolerance studies to RNAi-active guide strands. However, the inherent genomic instability of RNA viruses such as hepatitis C virus (HCV) gives rise to quasi-species mutants within discrete clones: this facilitates mismatch tolerance studies from a target perspective. We recently quantified the slicing imprecision of Argonaute 2 using small interfering RNA (siRNA) analogs of the DNA-directed RNAi drug TT-034 and next-generation sequencing of 5' RNA ligase-mediated rapid amplification of cDNA ends (RACE-SEQ). Here, we present an open-source, customizable, and computationally light RACE-SEQ bioinformatic pipeline, describing adaptations that semiquantitatively report the impact of RNAi hybridization site mismatches from the target perspective. The analysis shows that Argonaute 2 has a substitution-specific, 3- to 5-log activity window between fully complementary targets and targets with mismatches across positions 10-11. It further focuses the endonucleotic Slicer imprecision around positions 13-17, demonstrating its dependence on guide strand central region complementarity, and potentiation by even a single mismatch. We further propose pharmacogenomics value in testing endogenous targets using recombinant replicon systems and RACE-SEQ to report the pharmacodynamics of sequence-specific oligonucleotide therapeutics against all possible polymorphisms in a population, in a minimally biased, patient-free manner.
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Affiliation(s)
- Pantazis I Theotokis
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - Louise Usher
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK; Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - Christopher K Kortschak
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - Ed Schwalbe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear NE1 8ST, UK
| | - Sterghios A Moschos
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK; Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK; Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear NE1 8ST, UK.
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16
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Vijgen L, Thys K, Vandebosch A, Van Remoortere P, Verloes R, De Meyer S. Virology analysis in HCV genotype 1-infected patients treated with the combination of simeprevir and TMC647055/ritonavir, with and without ribavirin, and JNJ-56914845. Virol J 2017; 14:101. [PMID: 28569206 PMCID: PMC5452362 DOI: 10.1186/s12985-017-0760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/01/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In study TMC647055HPC2001, a 3-direct-acting-antiviral (DAA) regimen combining NS3/4A protease inhibitor simeprevir (SMV), non-nucleoside NS5B inhibitor TMC647055/ritonavir (RTV) and NS5A inhibitor JNJ-56914845 resulted in high sustained virologic response 12 weeks after actual end of treatment (SVR12) in chronic hepatitis C virus (HCV) genotype 1-infected patients. SVR12 rates were generally lower in the 2-DAA regimen SMV + TMC647055/RTV with or without ribavirin. The objective of this study was to identify and characterise pre-existing and emerging resistance-associated variants (RAVs) in patients enrolled in study TMC647055HPC2001. METHODS HCV population sequencing analyses were performed on baseline isolates from all patients (n = 90) and post-baseline isolates from patients with virologic failure (n = 22). In addition, deep sequencing and phenotypic analyses were performed on selected baseline and post-baseline isolates. RESULTS The majority of patients with virologic failure had emerging RAVs to all study drugs at the time of failure: in all 22 patients SMV RAVs emerged at NS3 positions 80, 155, 156 and/or 168, consistent with the known SMV resistance profile. Emerging TMC647055 RAVs at NS5B position 495 were detected in the majority of patients (16/22), and all 5 patients who failed the 3-DAA regimen had emerging JNJ-56914845 RAVs at NS5A positions 30 and/or 31. While at the end of study emerging SMV and TMC647055 RAVs were no longer observed by population sequencing in 40% (8/20) and 62.5% (10/16) of patients with follow-up data available, respectively, emerging JNJ-56914845 RAVs were still detected in all (5/5) patients. CONCLUSIONS Virologic failure in the 2- and 3-DAA combinations was, in the majority of patients, associated with the emergence of RAVs to all study drugs. While emerging SMV and TMC647055 RAVs became undetectable during follow-up, JNJ-56914845 RAVs in NS5A were still observed at end of study. TRIAL REGISTRATION NUMBER NCT01724086 (date of registration: September 26, 2012).
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Affiliation(s)
- Leen Vijgen
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Kim Thys
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - An Vandebosch
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pieter Van Remoortere
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - René Verloes
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Sandra De Meyer
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
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17
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High levels of local inter- and intra-host genetic variation of West Nile virus and evidence of fine-scale evolutionary pressures. INFECTION GENETICS AND EVOLUTION 2017; 51:219-226. [PMID: 28411164 DOI: 10.1016/j.meegid.2017.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/07/2017] [Accepted: 04/10/2017] [Indexed: 01/21/2023]
Abstract
West Nile virus (WNV; Flaviviridae, Flavivirus) has been endemic in New York State (NYS) since its 1999 introduction, yet prevalence in Culex mosquitoes varies substantially over small spatial and temporal scales. It is unclear if viral genetics plays a role in this variability, as genetic and phenotypic characterization on local scales has generally been lacking. In addition, intrahost diversity of circulating strains have not been fully characterized despite the documented role of minority variants in viral fitness and virulence. In an effort to characterize WNV variability within epidemiologically relevant scales, we performed phylogenetic analyses on NYS isolates from 1999 to 2012. In addition, we performed full-genome, deep-sequencing and genetic analyses on 15 WNV strains isolated in 2012 from Cx. pipiens in an endemic focus of Suffolk County, NY. Our results indicate continued evolution and seasonal maintenance in NYS, yet also widespread mixing and high levels of genetic diversity within geographic foci and individual seasons. Well supported local clusters with shared amino acid differences were identified and suggest local evolutionary pressures and the potential for phenotypic variability. Intrahost diversity of focal isolates was also high, with polymorphism at levels >1.0% identified in approximately 10% of the WNV genome. Although most minority mutations were unique, mutational hotspots shared among local isolates were identified, particularly in C, NS1 and NS2A genes. The most polymorphic region, positions 3198-3388 of the NS1 gene, was comprised predominately of non-synonymous mutations, suggesting a selective advantage for amino acid diversity in this region.
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Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use. Sci Rep 2017; 7:42215. [PMID: 28186189 PMCID: PMC5301480 DOI: 10.1038/srep42215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/06/2017] [Indexed: 01/31/2023] Open
Abstract
The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis. The genotypic prediction of HIV-1 tropism is based on sequencing the V3 region and interpreting the results with an appropriate algorithm. We compared the performances of the MiSeq (Illumina) and 454 GS-Junior (Roche) systems with a reference phenotypic assay. We used clinical samples for the NGS tropism predictions and assessed their ability to quantify CXCR4-using variants. The data show that the Illumina platform can be used to detect minor CXCR4-using variants in clinical practice but technical optimization are needed to improve quantification.
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MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing. J Virol Methods 2016; 240:7-13. [PMID: 27867045 DOI: 10.1016/j.jviromet.2016.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/17/2016] [Accepted: 11/11/2016] [Indexed: 02/08/2023]
Abstract
Genotypic monitoring of drug-resistance mutations (DRMs) in HIV-1 infected individuals is strongly recommended to guide selection of the initial antiretroviral therapy (ART) and changes of drug regimens. Traditionally, mutations conferring drug resistance are detected by population sequencing of the reverse transcribed viral RNA encoding the HIV-1 enzymes target by ART, followed by manual analysis and interpretation of Sanger sequencing traces. This process is labor intensive, relies on subjective interpretation from the operator, and offers limited sensitivity as only mutations above 20% frequency can be reliably detected. Here we present MinVar, a pipeline for the analysis of deep sequencing data, which allows reliable and automated detection of DRMs down to 5%. We evaluated MinVar with data from amplicon sequencing of defined mixtures of molecular virus clones with known DRM and plasma samples of viremic HIV-1 infected individuals and we compared it to VirVarSeq, another virus variant detection tool exclusively working on Illumina deep sequencing data. MinVar was designed to be compatible with a diverse range of sequencing platforms and allows the detection of DRMs and insertions/deletions from deep sequencing data without the need to perform additional bioinformatics analysis, a prerequisite to a widespread implementation of HIV-1 genotyping using deep sequencing in routine diagnostic settings.
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Ma Y, Kuang JZ, Nie TG, Zhu W, Yang Z. Next generation sequencing: Improved resolution for paternal/maternal duos analysis. Forensic Sci Int Genet 2016; 24:83-85. [DOI: 10.1016/j.fsigen.2016.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 11/28/2022]
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Hasing ME, Hazes B, Lee BE, Preiksaitis JK, Pang XL. A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection. BMC Genomics 2016; 17:480. [PMID: 27363999 PMCID: PMC4929757 DOI: 10.1186/s12864-016-2831-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/12/2016] [Indexed: 12/12/2022] Open
Abstract
Background Immunocompromised individuals with chronic norovirus (NoV) infection and elderly patients are hypothesized to be reservoirs where NoV might accumulate mutations and evolve into pandemic strains. Next generation sequencing (NGS) methods can monitor the intra-host diversity of NoV and its evolution but low abundance of viral RNA results in sub-optimal efficiency. In this study, we: 1) established a next generation sequencing-based method for NoV using bacterial rRNA depletion as a viral RNA enrichment strategy, and 2) measured the intra-host genetic diversity of NoV in specimens of patients with acute NoV infection (n = 4) and in longitudinal specimens of an immunocompromised patient with chronic NoV infection (n = 2). Results A single Illumina MiSeq dataset resulted in near full-length genome sequences for 5 out of 6 multiplexed samples. Experimental depletion of bacterial rRNA in stool RNA provided up to 1.9 % of NoV reads. The intra-host viral population in patients with acute NoV infection was homogenous and no single nucleotide variants (SNVs) were detected. In contrast, the NoV population from the immunocompromised patient was highly diverse and accumulated SNVs over time (51 SNVs in the first sample and 122 SNVs in the second sample collected 4 months later). The percentages of SNVs causing non-synonymous mutations were 27.5 % and 20.5 % for the first and second samples, respectively. The majority of non-synonymous mutations occurred, in increasing order of frequency, in p22, the major capsid (VP1) and minor capsid (VP2) genes. Conclusions The results provide data useful for the selection and improvement of NoV RNA enrichment strategies for NGS. Whole genome analysis using next generation sequencing confirmed that the within-host population of NoV in an immunocompromised individual with chronic NoV infection was more diverse compared to that in individuals with acute infection. We also observed an accumulation of non-synonymous mutations at the minor capsid gene that has not been reported in previous studies and might have a role in NoV adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2831-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria E Hasing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Bart Hazes
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, AB, T6G 1C9, Canada
| | - Jutta K Preiksaitis
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Xiaoli L Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada. .,Provincial Laboratory for Public Health (ProvLab), Edmonton, AB, T6G 2 J2, Canada.
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Fevery B, Thys K, Van Eygen V, Verbinnen T, Van Rossem E, Buelens A, Aerssens J, Witek J, Picchio G, De Meyer S, Lenz O. Pre-existence and Persistence of Resistant Minority Hepatitis C Virus Variants in Genotype 1-Infected Patients Treated With Simeprevir/Peginterferon/Ribavirin. Open Forum Infect Dis 2016; 3:ofw052. [PMID: 27186579 PMCID: PMC4866569 DOI: 10.1093/ofid/ofw052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/04/2016] [Indexed: 01/27/2023] Open
Abstract
Deep sequencing analyses in HCV genotype 1-infected patients treated with simeprevir/peginterferon/ribavirin showed that pre-existing minority HCV variants did not impact treatment outcome and emerging resistant variants in patients failing treatment were not persisting at minority levels Background. The pre-existence of minority hepatitis C virus (HCV) variants and their impact on treatment outcome, as well as the persistence of emerging resistant variants posttreatment in patients failing treatment with simeprevir/peginterferon/ribavirin (SMV/PR), were assessed by deep sequencing (DS). Methods. Population sequencing (PS) and Illumina DS were performed on HCV genotype 1 isolates from patients treated with SMV/PR in Phase 2b (PILLAR [NCT00882908] and ASPIRE [NCT00980330]) and Phase 3 (QUEST-1 [NCT01289782], QUEST-2 [NCT01290679], and PROMISE [NCT01281839]) trials. Results. Minority polymorphisms (ie, detected pretreatment by DS only) reducing SMV activity in vitro were uncommon (3.6%, 19 of 534 patients). These SMV-resistant minority polymorphisms were detected in similar proportions of patients achieving (3.7%) and not achieving (3.3%) sustained virologic response with SMV/PR and generally did not emerge as major variants at time of failure. SMV-resistant variants emerging at time of failure were no longer detected at end of study in 69.3% and 52.0% of the patients by PS and DS, respectively. Conclusions. Minority polymorphisms did not impact outcome of SMV/PR treatment. The majority of emerging variants that became undetectable at end of study by PS were also undetectable by DS. These results suggest no added value of DS for clinical usage of SMV.
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Affiliation(s)
| | - Kim Thys
- Janssen Discovery Sciences, Beerse , Belgium
| | | | | | | | | | | | - James Witek
- Janssen Research & Development , LLC , Titusville, New Jersey
| | - Gaston Picchio
- Janssen Research & Development , LLC , Titusville, New Jersey
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Perales C, Quer J, Gregori J, Esteban JI, Domingo E. Resistance of Hepatitis C Virus to Inhibitors: Complexity and Clinical Implications. Viruses 2015; 7:5746-66. [PMID: 26561827 PMCID: PMC4664975 DOI: 10.3390/v7112902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Selection of inhibitor-resistant viral mutants is universal for viruses that display quasi-species dynamics, and hepatitis C virus (HCV) is no exception. Here we review recent results on drug resistance in HCV, with emphasis on resistance to the newly-developed, directly-acting antiviral agents, as they are increasingly employed in the clinic. We put the experimental observations in the context of quasi-species dynamics, in particular what the genetic and phenotypic barriers to resistance mean in terms of exploration of sequence space while HCV replicates in the liver of infected patients or in cell culture. Strategies to diminish the probability of viral breakthrough during treatment are briefly outlined.
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Affiliation(s)
- Celia Perales
- 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, 08035 Barcelona, Spain.
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
| | - Josep Quer
- 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, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Josep Gregori
- 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, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Roche Diagnostics SL, 08174 Sant Cugat del Vallès, Spain.
| | - Juan Ignacio Esteban
- 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, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
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Van Eygen V, Thys K, Van Hove C, Rimsky LT, De Meyer S, Aerssens J, Picchio G, Vingerhoets J. Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE. J Med Virol 2015; 88:798-806. [PMID: 26412111 DOI: 10.1002/jmv.24395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/10/2022]
Abstract
Minority variants (1.0-25.0%) were evaluated by deep sequencing (DS) at baseline and virological failure (VF) in a selection of antiretroviral treatment-naïve, HIV-1-infected patients from the rilpivirine ECHO/THRIVE phase III studies. Linkage between frequently emerging resistance-associated mutations (RAMs) was determined. DS (llIumina®) and population sequencing (PS) results were available at baseline for 47 VFs and time of failure for 48 VFs; and at baseline for 49 responders matched for baseline characteristics. Minority mutations were accurately detected at frequencies down to 1.2% of the HIV-1 quasispecies. No baseline minority rilpivirine RAMs were detected in VFs; one responder carried 1.9% F227C. Baseline minority mutations associated with resistance to other non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 8/47 VFs (17.0%) and 7/49 responders (14.3%). Baseline minority nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) RAMs M184V and L210W were each detected in one VF (none in responders). At failure, two patients without NNRTI RAMs by PS carried minority rilpivirine RAMs K101E and/or E138K; and five additional patients carried other minority NNRTI RAMs V90I, V106I, V179I, V189I, and Y188H. Overall at failure, minority NNRTI RAMs and NRTI RAMs were found in 29/48 (60.4%) and 16/48 VFs (33.3%), respectively. Linkage analysis showed that E138K and K101E were usually not observed on the same viral genome. In conclusion, baseline minority rilpivirine RAMs and other NNRTI/NRTI RAMs were uncommon in the rilpivirine arm of the ECHO and THRIVE studies. DS at failure showed emerging NNRTI resistant minority variants in seven rilpivirine VFs who had no detectable NNRTI RAMs by PS.
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Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases BVBA, Beerse, Belgium
| | | | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
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