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Pröll J, Paar C, Taylor N, Skocic M, Freystetter A, Blaimschein A, Mayr R, Niklas N, Atzmüller S, Raml E, Wechselberger C. New aspects of the Virus Life Cycle and Clinical Utility of Next Generation Sequencing based HIV-1 Resistance Testing in the Genomic, the Proviral and the Viral Reservoir of Peripheral Blood Mononuclear Cells. Curr HIV Res 2022; 20:213-221. [PMID: 35331114 DOI: 10.2174/1570162x20666220324111418] [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: 09/04/2021] [Revised: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Typically, genotypic resistance testing is recommended at the start of antiretroviral therapy and is even mandatory in cases of virologic failure. The material of choice is plasma viral RNA. However, in patients with low viremia (viral load < 500 copies/ml), resistance testing by population-based sequencing is very difficult. OBJECTIVE Therefore, we aimed to investigate whether next generation sequencing (NGS) from proviral DNA and RNA could be an alternative. MATERIAL AND METHODS EDTA blood samples (n = 36) from routine clinical viral load testing were used for the study. Viral loads ranged from 96 to 390,000 copies/mL, with 100% of samples having low viremia. Distribution of subtypes A (n = 2), B (n = 16), C (n = 4), D (n = 2), G (1), CRF02 AG (n = 5), CRF01 AE (n = 5), undefined/mixed (n = 4). The extracted consensus sequences were uploaded to the Stanford HIV Drug Resistance Data Base and Geno2pheno for online analysis of drug resistance mutations and resistance factors. RESULTS A total of 2476 variants or drug resistance mutations (DRMs) were detected with Sanger sequencing, compared with 2892 variants with NGS. An average of 822/1008 variants were identified in plasma viral RNA by Sanger or NGS sequencing, 834/956 in cellular viral RNA, and 820/928 in cellular viral DNA. CONCLUSIONS Both methods are well suited for the detection of HIV substitutions or drug resistance mutations. Our results suggest that cellular RNA or cellular viral DNA is an informative alternative to plasma viral RNA for variant detection in patients with low viremia, as shown by the high correlation of variants in the different viral pools. And we show that by using UDS, a plus of two DRMs per patient becomes visible and that can make a big difference in the assessment of the expected resistance behavior of the virus.
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Affiliation(s)
- Johannes Pröll
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Christian Paar
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Ninon Taylor
- Department of Dermatology, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Matthias Skocic
- Department of Dermatology, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Andrea Freystetter
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Anna Blaimschein
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Roland Mayr
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Norbert Niklas
- Red Cross Transfusion Center for Upper Austria, Krankenhausstraße 7, A-4020, Austria
| | - Sabine Atzmüller
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Edeltraud Raml
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Christian Wechselberger
- Division of Pathophysiology, Institute for Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University, ADM Building, Krankenhausstraße 5, A-4020 Linz, Austria
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Chehadeh W, Albaksami O, Al-Shammari S. Virologic failure after 48 weeks of raltegravir-based regimen in low HIV-1 incidence setting. Antivir Chem Chemother 2021; 28:2040206620927908. [PMID: 32434393 PMCID: PMC7241205 DOI: 10.1177/2040206620927908] [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] [Indexed: 11/24/2022] Open
Abstract
Background With the advent of next generation integrase strand transfer inhibitors, the rates of virologic failure in treated subjects are expected to decrease. In this study, we analyzed the mutation patterns leading to virologic failure before and after starting integrase strand transfer inhibitor-based regimen as first-line or salvage therapy. Methods Between 2016 and 2019, blood samples were received from 258 patients with HIV-1 infection. Plasma HIV-1 RNA concentrations, and pol gene sequences were determined at baseline, and 16–48 weeks of treatment with integrase strand transfer inhibitor-based regimen. Only patients who did not achieve viral suppression at 48 weeks of integrase strand transfer inhibitor-based treatment were eligible for the current study. Results Virologic failure was observed in seven patients on raltegravir-based regimen. All patients with virologic failure but one were infected with CRF01_AE virus subtype. Raltegravir based-regimen was offered as first-line therapy for four patients, and as salvage therapy for three patients. M184V mutation associated with high level resistance to lamivudine and emtricitabine was detected in six out of seven patients. Primary mutations (Y143C, N155H, T66I, G118R, E138K) conferring high level resistance to raltegravir were detected in only three patients. Pre-existing polymorphic integrase mutation (T97A) was detected in two patients. Furthermore, two patients reported low adherence to treatment. Conclusions Emergence of primary mutations in the integrase gene can account for virologic failure in less than half of patients on raltegravir-based regimen. Low adherence to treatment, pre-existing accessory mutations, and resistance to reverse transcriptase inhibitors may have some role in virologic outcome.
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Affiliation(s)
- Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Osama Albaksami
- Infectious Diseases Hospital, Ministry of Health, Safat, Kuwait
| | - Shaikhah Al-Shammari
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
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Li M, Liang S, Zhou C, Chen M, Liang S, Liu C, Zuo Z, Liu L, Feng Y, Song C, Xing H, Ruan Y, Shao Y, Liao L. HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China. Pathogens 2021; 10:pathogens10030264. [PMID: 33668946 PMCID: PMC7996606 DOI: 10.3390/pathogens10030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 11/24/2022] Open
Abstract
Patients with antiretroviral therapy interruption have a high risk of virological failure when re-initiating antiretroviral therapy (ART), especially those with HIV drug resistance. Next-generation sequencing may provide close scrutiny on their minority drug resistance variant. A cross-sectional study was conducted in patients with ART interruption in five regions in China in 2016. Through Sanger and next-generation sequencing in parallel, HIV drug resistance was genotyped on their plasma samples. Rates of HIV drug resistance were compared by the McNemar tests. In total, 174 patients were included in this study, with a median 12 (interquartile range (IQR), 6–24) months of ART interruption. Most (86.2%) of them had received efavirenz (EFV)/nevirapine (NVP)-based first-line therapy for a median 16 (IQR, 7–26) months before ART interruption. Sixty-one (35.1%) patients had CRF07_BC HIV-1 strains, 58 (33.3%) CRF08_BC and 35 (20.1%) CRF01_AE. Thirty-four (19.5%) of the 174 patients were detected to harbor HIV drug-resistant variants on Sanger sequencing. Thirty-six (20.7%), 37 (21.3%), 42 (24.1%), 79 (45.4%) and 139 (79.9) patients were identified to have HIV drug resistance by next-generation sequencing at 20% (v.s. Sanger, p = 0.317), 10% (v.s. Sanger, p = 0.180), 5% (v.s. Sanger, p = 0.011), 2% (v.s. Sanger, p < 0.001) and 1% (v.s. Sanger, p < 0.001) of detection thresholds, respectively. K65R was the most common minority mutation, of 95.1% (58/61) and 93.1% (54/58) in CRF07_BC and CRF08_BC, respectively, when compared with 5.7% (2/35) in CRF01_AE (p < 0.001). In 49 patients that followed-up a median 10 months later, HIV drug resistance mutations at >20% frequency such as K103N, M184VI and P225H still existed, but with decreased frequencies. The prevalence of HIV drug resistance in ART interruption was higher than 15% in the survey. Next-generation sequencing was able to detect more minority drug resistance variants than Sanger. There was a sharp increase in minority drug resistance variants when the detection threshold was below 5%.
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Affiliation(s)
- Miaomiao Li
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Shujia Liang
- Guangxi Center for Disease Control and Prevention, Nanning 530028, China;
| | - Chao Zhou
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China;
| | - Min Chen
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China;
| | - Shu Liang
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, China;
| | - Chunhua Liu
- Henan Center for Disease Control and Prevention, Zhengzhou 450016, China;
| | - Zhongbao Zuo
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lei Liu
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Chang Song
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
- Correspondence:
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Zuo L, Peng K, Hu Y, Xu Q. Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China. Curr HIV Res 2020; 17:225-239. [PMID: 31560290 DOI: 10.2174/1570162x17666190927154110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of "90-90-90" to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.
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Affiliation(s)
- Lulu Zuo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China.,Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yihong Hu
- Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Qinggang Xu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China
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Chen NY, Kao SW, Liu ZH, Wu TS, Tsai CL, Lin HH, Wong WW, Chang YY, Chen SS, Ku SWW. Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection. Int J Infect Dis 2020; 93:182-191. [PMID: 32061862 DOI: 10.1016/j.ijid.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. OBJECTIVES To compare deep sequencing performance to standard Sanger genotyping with clinical samples, in an effort to delineate the correlation between the results from the two methods and to find the optimal deep sequencing threshold for clinical utilisation. METHODS We conducted a retrospective study using stored plasma collected from August 2014 to March 2018 for HIV genotyping with the commercial Sanger genotyping kit. Samples with available Sanger genotyping reports were further deep sequenced. Drug resistance was interpreted according to the Stanford HIV drug resistance database algorithm. RESULTS At 15-25% minority detection thresholds, 9-15% cases had underestimated DRMs by Sanger sequencing. The concordance between the Sanger and deep sequencing reports was 68-82% in protease-reverse transcriptase region and 88-97% in integrase region at 5-25% thresholds. The undetected drug resistant minority variants by Sanger sequencing contributed to the lower negative predictive value of Sanger genotyping in cases harbouring DRMs. CONCLUSIONS Use of deep sequencing improved detection of antiretroviral resistance mutations especially in cases with virological failure or previous treatment interruption. Deep sequencing with 10-15% detection thresholds may be considered a suitable substitute for Sanger sequencing on antiretroviral DRM detection.
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Affiliation(s)
- Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Shu-Wei Kao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Zhuo-Hao Liu
- Department of Neurosurgery, Chang Gung Memorial Hospital Linkou Branch, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taiwan
| | - Hsi-Hsun Lin
- General Clinical Research Centre, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Public Health, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wing-Wai Wong
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yea-Yuan Chang
- Division of Infectious Diseases, Department of Internal Medicine, National Yang-Ming University Hospital, Yilan, Taiwan; Institute of Clinical Medicine and AIDS Prevention and Research Centre, National Yang-Ming University, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan
| | - Shu-Sheng Chen
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Stephane Wen-Wei Ku
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan.
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Rodriguez C, Nere ML, Demontant V, Charreau I, Mercier-Darty M, Delagreverie H, Salmona M, de Castro N, Chaix ML, Molina JM, Delaugerre C. Ultra-deep sequencing improves the detection of drug resistance in cellular DNA from HIV-infected patients on ART with suppressed viraemia. J Antimicrob Chemother 2019; 73:3122-3128. [PMID: 30137335 DOI: 10.1093/jac/dky315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
Background Standard genotypic tests performed on HIV DNA from patients on suppressive ART, with previous resistance-associated mutations (RAMs) detected in their plasma, underestimate resistance. We thus compared ultra-deep sequencing (UDS) with bulk sequencing of DNA to detect RAMs previously identified in plasma. Methods We sequenced the DNA of 169 highly treatment experienced patients with suppressed viraemia (ANRS 138-EASIER trial). Protease (PR) and reverse transcriptase (RT) genes from HIV DNA were sequenced by bulk sequencing and UDS, comparing 1% and 20% as thresholds of detection for UDS. Results Patients were highly treatment experienced (13.6 years). UDS of DNA was successful for the RT and PR genes in 133 (79%) and 137 (81%) patients, respectively. The detection of RAMs was similar by bulk sequencing and UDS with a 20% cut-off. However, the detection of RAMs by UDS with a 1% cut-off was significantly higher than that of bulk sequencing for RT codons D67N (65.4% versus 52.3%), M184V (66.2% versus 52.3%), L210W (48.9% versus 36.4%) and T215Y (57.9% versus 42.1%) and PR codons M46I (46% versus 26%), I54L (12.4% versus 3.9%), V82A (44.5% versus 29.9%) and L90M (57.7% versus 42.5%). Conclusions Genotypic resistance testing of cellular HIV DNA of well-controlled patients should use UDS technology with a sensitivity threshold of 1% to improve the detection of the resistant reservoir.
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Affiliation(s)
- Christophe Rodriguez
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | - Marie Laure Nere
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Vanessa Demontant
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | | | - Mélanie Mercier-Darty
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | - Héloïse Delagreverie
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Maud Salmona
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | | | - Marie Laure Chaix
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Jean Michel Molina
- Université Paris Diderot, Inserm U941, Paris, France
- Maladies infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Constance Delaugerre
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
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Nucleic acid testing and molecular characterization of HIV infections. Eur J Clin Microbiol Infect Dis 2019; 38:829-842. [PMID: 30798399 DOI: 10.1007/s10096-019-03515-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/14/2019] [Indexed: 01/21/2023]
Abstract
Significant advances have been made in the molecular assays used for the detection of human immunodeficiency virus (HIV), which are crucial in preventing HIV transmission and monitoring disease progression. Molecular assays for HIV diagnosis have now reached a high degree of specificity, sensitivity and reproducibility, and have less operator involvement to minimize risk of contamination. Furthermore, analyses have been developed for the characterization of host gene polymorphisms and host responses to better identify and monitor HIV-1 infections in the clinic. Currently, molecular technologies including HIV quantitative and qualitative assays are mainly based on the polymerase chain reaction (PCR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and branched chain (b) DNA methods and widely used for HIV detection and characterization, such as blood screening, point-of-care testing (POCT), pediatric diagnosis, acute HIV infection (AHI), HIV drug resistance testing, antiretroviral (AR) susceptibility testing, host genome polymorphism testing, and host response analysis. This review summarizes the development and the potential utility of molecular assays used to detect and characterize HIV infections.
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Epaulard O, Signori-Schmuck A, Larrat S, Kulkarni O, Blum MG, Fusillier K, Blanc M, Leclercq P, François O, Morand P. Ultradeep sequencing of B and non-B HIV-1 subtypes: Viral diversity and drug resistance mutations before and after one month of antiretroviral therapy in naive patients. J Clin Virol 2017; 95:13-19. [PMID: 28830014 DOI: 10.1016/j.jcv.2017.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 04/06/2017] [Accepted: 07/21/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ultradeep pyrosequencing technologies permit an assessment of the genetic diversity and the presence and frequency of minority variants in a viral population. The effect of these parameters on the outcome of highly active antiretroviral therapy (HAART) in HIV-infected patients is poorly understood. OBJECTIVES The present study used the pyrosequencing Roche 454 prototype assay to determine whether antiretroviral efficacy is correlated with viral diversity and minority drug resistance mutations in HIV-infected treatment-naive patients and to compare assay performance in B and non-B subtypes. STUDY DESIGN The study included 30 HIV-1 infected naive patients (20 with subtype non-B and 10 with subtype B). Ultradeep pyrosequencing of protease and reverse transcriptase genes was performed at baseline and 1 month after HAART initiation. Plasma HIV VL was measured at 0 and after 1, 3, and 6 months of HAART. RESULTS Pre-HAART minority drug resistance mutations were observed to NRTI in 4 patients, to NNRTI in 6 patients, and to PI in 1 patient; there was no difference in HAART-induced VL decay between patients. Pre-HAART diversity was significantly correlated with the time elapsed since HIV-1 infection diagnosis, but not with the subtype, VL, or CD4 count. Patients with an undetectable VL after 3 months of HAART had a higher pre-HAART diversity. Pre- and post-HAART diversities were not statistically different. There was no difference in assay performance between subtype B and non-B. CONCLUSIONS A high pre-HAART viral diversity might have a positive effect on the outcome of HAART. Pre-therapeutic minority drug resistance mutations are uncommon in naive patients.
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Affiliation(s)
- Olivier Epaulard
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France.
| | - Anne Signori-Schmuck
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Sylvie Larrat
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Om Kulkarni
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Michael G Blum
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Katia Fusillier
- Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Myriam Blanc
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Pascale Leclercq
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Olivier François
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Patrice Morand
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
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Abstract
Diversity, evolution, and epidemiology of HIV are directly relevant to HIV transmission and pathogenesis; hence, they play a key role in antiretroviral treatment and vaccine design. Global HIV whole-genome sequencing would provide a treasure chest of data to answer many questions still open in these fields. An article by Berg et al. in this issue of theJournal of Clinical Microbiologydescribes a universal strategy to amplify and sequence heterogeneous HIV whole genomes (M. G. Berg, J. Yamaguchi, E. Alessandri-Gradt, R. W. Tell, J.-C. Plantier, and C. A. Brennan, J Clin Microbiol 54:868-882, 2016,http://dx.doi.org/10.1128/JCM.02479-15).
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St. John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP. A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PLoS One 2016; 11:e0146687. [PMID: 26756901 PMCID: PMC4710461 DOI: 10.1371/journal.pone.0146687] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. METHODS A multicenter study was conducted to validate an updated assay design for 454 Life Sciences' GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940-447,400 copies/mL, two dilution series (52,129-1,340 and 25,130-734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10-99, RT codons 1-251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. RESULTS The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592-3,488) and 2,410 for V3 (IQR 786-3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P<0.001). The triplicate samples of a plasmid mixture confirmed the high inter-laboratory consistency (mean% ± stdev: 4.6 ±0.5, 4.8 ±0.4, 4.9 ±0.3) and revealed good intra-laboratory consistency (mean% range ± stdev range: 4.2-5.2 ± 0.04-0.65). In the two dilutions series, no variants >20% were missed, variants 2-10% were detected at most sites (even at low VT), and variants 1-2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. CONCLUSIONS This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing.
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Affiliation(s)
| | - Birgitte B. Simen
- 454 Life Sciences, A Roche Company, Branford, CT, United States of America
| | | | | | - Isabella Abbate
- National Institute for Infectious Diseases “L. Spallanzani, Rome, Italy
| | - Jeroen Aerssens
- Janssen Infectious Diseases—Diagnostics bvba, Beerse, Belgium
| | - Olivier Bouchez
- Plateforme Génomique Toulouse/Laboratoire Génétique Cellulaire, Toulouse, France
| | | | | | | | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Roger Paredes
- Institut de Recerca de la SIDA–IrsiCaixa, Badalona, Spain
| | - James Sakwa
- Technology Innovation Agency-National Genomics Platform, Durban, South Africa
| | | | | | | | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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11
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Hauser A, Kuecherer C, Kunz A, Dabrowski PW, Radonić A, Nitsche A, Theuring S, Bannert N, Sewangi J, Mbezi P, Dugange F, Harms G, Meixenberger K. Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission. PLoS One 2015; 10:e0140809. [PMID: 26469189 PMCID: PMC4607442 DOI: 10.1371/journal.pone.0140809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/29/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS) and allele-specific real-time PCR (ASPCR) for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT). METHODS Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F). In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System. RESULTS Drug-resistant HIV-variants were identified in 69% (20/29) of women by UDS and in 45% (13/29) by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24). By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41). The proportions of variants quantified by UDS were approximately 2-3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml), resulting in missing or insufficient sequence coverage. CONCLUSIONS Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in the HIV-1 quasispecies.
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Affiliation(s)
- Andrea Hauser
- HIV and other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | | | - Andrea Kunz
- Institute of Tropical Medicine and International Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Piotr Wojtek Dabrowski
- Centre for Biological Threats and Special Pathogens 1, Highly Pathogenic Viruses, Robert Koch-Institute, Berlin, Germany
| | - Aleksandar Radonić
- Centre for Biological Threats and Special Pathogens 1, Highly Pathogenic Viruses, Robert Koch-Institute, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens 1, Highly Pathogenic Viruses, Robert Koch-Institute, Berlin, Germany
| | - Stefanie Theuring
- Institute of Tropical Medicine and International Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Norbert Bannert
- HIV and other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | - Julius Sewangi
- Regional AIDS Control Program Mbeya Region, Ministry of Health and Social Welfare, Dar es Salaam, Tanzania
| | - Paulina Mbezi
- PMTCT Service Mbeya Region, Ministry of Health and Social Welfare, Dar es Salaam, Tanzania
| | - Festo Dugange
- Kyela District Hospital, Ministry of Health and Social Welfare, Dar es Salaam, Tanzania
| | - Gundel Harms
- Institute of Tropical Medicine and International Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Nishizawa M, Matsuda M, Hattori J, Shiino T, Matano T, Heneine W, Johnson JA, Sugiura W. Longitudinal Detection and Persistence of Minority Drug-Resistant Populations and Their Effect on Salvage Therapy. PLoS One 2015; 10:e0135941. [PMID: 26360259 PMCID: PMC4567277 DOI: 10.1371/journal.pone.0135941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Drug-resistant HIV are more prevalent and persist longer than previously demonstrated by bulk sequencing due to the ability to detect low-frequency variants. To clarify a clinical benefit to monitoring minority-level drug resistance populations as a guide to select active drugs for salvage therapy, we retrospectively analyzed the dynamics of low-frequency drug-resistant population in antiretroviral (ARV)-exposed drug resistant individuals. MATERIALS AND METHODS Six HIV-infected individuals treated with ARV for more than five years were analyzed. These individuals had difficulty in controlling viremia, and treatment regimens were switched multiple times guided by standard drug resistance testing using bulk sequencing. To detect minority variant populations with drug resistance, we used a highly sensitive allele-specific PCR (AS-PCR) with detection thresholds of 0.3-2%. According to ARV used in these individuals, we focused on the following seven reverse transcriptase inhibitor-resistant mutations: M41L, K65R, K70R, K103N, Y181C, M184V, and T215F/Y. Results of AS-PCR were compared with bulk sequencing data for concordance and presence of additional mutations. To clarify the genetic relationship between low-frequency and high-frequency populations, AS-PCR amplicon sequences were compared with bulk sequences in phylogenetic analysis. RESULTS The use of AS-PCR enabled detection of the drug-resistant mutations, M41L, K103N, Y181C, M184V and T215Y, present as low-frequency populations in five of the six individuals. These drug resistant variants persisted for several years without ARV pressure. Phylogenetic analysis indicated that pre-existing K103N and T215I variants had close genetic relationships with high-frequency K103N and T215I observed during treatment. DISCUSSION AND CONCLUSION Our results demonstrate the long-term persistence of drug-resistant viruses in the absence of drug pressure. The rapid virologic failures with pre-existing mutant viruses detectable by AS-PCR highlight the clinical importance of low-frequency drug-resistant viruses. Thus, our results highlight the usefulness of AS-PCR and support its expanded evaluation in ART clinical management.
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Affiliation(s)
- Masako Nishizawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Teiichiro Shiino
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Walid Heneine
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jeffrey A. Johnson
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Wataru Sugiura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Department of AIDS Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- * E-mail:
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Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection. PLoS One 2015; 10:e0135903. [PMID: 26317928 PMCID: PMC4552882 DOI: 10.1371/journal.pone.0135903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 07/27/2015] [Indexed: 01/03/2023] Open
Abstract
Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects infected with single founders and 33% of subjects infected with multiple founder variants: among the subjects with disagreements, mismatches were found in less than 1% of the sites evaluated (of a total of nearly 117,000 sites across all subjects). The majority of the SNPs observed only in pyrosequences were present at less than 2% of the subject’s viral sequence population. These results demonstrate the utility of the Sanger approach for study of early HIV infection and provide guidance regarding the design, utility and limitations of population sequencing from variable template sources, and emphasize parameters for improving the interpretation of massively parallel sequencing data to address important questions regarding target sequence evolution.
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Affiliation(s)
- Shyamala Iyer
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Eleanor Casey
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Heather Bouzek
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Moon Kim
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Brendan B. Larsen
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Roger E. Bumgarner
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, WRAIR, Silver Spring, MD, 20910, United States of America
- Henry Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, 20817, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
- Department of Medicine, University of Washington, Seattle, WA, 98195, United States of America
- Department of Laboratory Medicine, Seattle, WA, 98195, United States of America
- * E-mail:
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14
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Ram D, Leshkowitz D, Gonzalez D, Forer R, Levy I, Chowers M, Lorber M, Hindiyeh M, Mendelson E, Mor O. Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory. J Virol Methods 2014; 212:12-6. [PMID: 25445792 DOI: 10.1016/j.jviromet.2014.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/02/2014] [Accepted: 11/04/2014] [Indexed: 01/20/2023]
Abstract
Population HIV-1 sequencing is currently the method of choice for the identification and follow-up of HIV-1 antiretroviral drug resistance. It has limited sensitivity and results in a consensus sequence showing the most prevalent nucleotide per position. Moreover concomitant sequencing and interpretation of the results for several samples together is laborious and time consuming. In this study, the practical use of GS Junior and MiSeq bench-top next generation sequencing (NGS) platforms as an alternative to Trugene Sanger-based population sequencing in the clinical HIV laboratory was assessed. DeepChek(®)-HIV TherapyEdge software was used for processing all the protease and reverse transcriptase sequences and for resistance interpretation. Plasma samples from nine HIV-1 carriers, representing the major HIV-1 subtypes in Israel, were compared. The total number of amino acid substitutions identified in the nine samples by GS Junior (232 substitutions) and MiSeq (243 substitutions) was similar and higher than Trugene (181 substitutions), emphasizing the advantage of deep sequencing on population sequencing. More than 80% of the identified substitutions were identical between the GS Junior and MiSeq platforms, most of which (184 of 199) at similar frequency. Low abundance substitutions accounted for 20.9% of the MiSeq and 21.9% of the GS Junior output, the majority of which were not detected by Trugene. More drug resistance mutations were identified by both the NGS platforms, primarily, but not only, at low abundance. In conclusion, in combination with DeepChek, both GS Junior and MiSeq were found to be more sensitive than Trugene and adequate for HIV-1 resistance analysis in the clinical HIV laboratory.
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Affiliation(s)
- Daniela Ram
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
| | - Dena Leshkowitz
- Bioinformatics Unit, The Nancy and Stephen Grand National Center for Personalized Medicine, Weizmann Institute, Rehovot, Israel.
| | | | | | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel.
| | - Michal Chowers
- Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel.
| | - Margalit Lorber
- Autoimmune Disease Unit, Rambam Medical Center, Haifa, Israel.
| | - Musa Hindiyeh
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Ella Mendelson
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Orna Mor
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
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15
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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.
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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
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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.
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17
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Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP. An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. J Virol Methods 2014; 204:31-7. [PMID: 24731928 DOI: 10.1016/j.jviromet.2014.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 10/25/2022]
Abstract
The detection of mutant spectra within the viral quasispecies is critical for therapeutic management of HIV-1 infections. Routine clinical application of ultrasensitive genotyping requires reproducibility and concordance within and between laboratories. The goal of the study was to evaluate a new protocol on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing (454-UDS) in an international multicenter study. Sixteen blinded HIV-1 subtype B samples were provided for 454-UDS as both RNA and cDNA with viral titers of 88,600-573,000 HIV-1 RNA copies/ml. Eight overlapping amplicons spanning protease (PR) codons 10-99 and reverse transcriptase (RT) codons 1-251 were generated using molecular barcoded primers. 454-UDS was performed using the 454 Life Sciences/Roche GS FLX platform. PR and RT sequences were analyzed using 454 Life Sciences Amplicon Variant Analyzer (AVA) software. Quantified variation data were analyzed for intra-laboratory reproducibility and inter-laboratory concordance. Routine population sequencing was performed using the ViroSeq HIV-1 genotyping system. Eleven laboratories and the reference laboratory 454 Life Sciences sequenced the HIV-1 sample set. Data presented are derived from seven laboratories and the reference laboratory since severe study protocol execution errors occurred in four laboratories leading to exclusion. The median sequencing depth across all sites was 1364 reads per position (IQR=809-2065). 100% of the ViroSeq-reported mutations were also detected by 454-UDS. Minority HIV-1 drug resistance mutations, defined as HIV-1 drug resistance mutations identified at frequencies of 1-25%, were only detected by 454-UDS. Analysis of 10 preselected majority and minority mutations were consistently found across sites. The analysis of drug-resistance mutations detected between 1 and 10% demonstrated high intra- and inter-laboratory consistency in frequency estimates for both RNA and prepared cDNA samples, indicating robustness of the method. HIV-1 drug resistance testing using 454 ultra-deep pyrosequencing results in an accurate and highly reproducible, albeit complex, approach to the analysis of HIV-1 mutant spectra, even at frequencies well below those detected by routine population sequencing.
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Affiliation(s)
| | | | - Isabella Abbate
- National Institute for Infectious Diseases "L. Spallanzani, Rome, Italy
| | - Jeroen Aerssens
- Janssen Infectious Diseases - Diagnostics bvba, Beerse, Belgium
| | - Yannick Bidet
- Centre Jean Perrin/Clermont University, Clermont-Ferrand, France
| | | | | | - Jacques Izopet
- INSERM U1043 and Virology Laboratory, CHU Toulouse, Toulouse, France
| | | | | | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | | | | | | | - James Sakwa
- TIA-National Genomics Platform, Durban, South Africa
| | | | | | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Martin P Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
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18
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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]
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19
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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
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20
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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]
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Abstract
Technologic advances in human immunodeficiency virus type 1 (HIV-1) sequencing have revolutionized the study of antiretroviral drug resistance and are increasingly moving from the laboratory to clinical practice. These techniques are able to detect HIV-1 drug resistance mutations present at low frequencies not detectable by current HIV-1 genotyping assays. For a number of commonly used antiretroviral medications, such as nonnucleoside reverse transcriptase inhibitors, the detection of these drug-resistant minority variants significantly increases the risk of treatment failure. The level of evidence, however, is insufficient to determine the impact of HIV-1 minority variants for several other classes of antiretroviral medications. Clinicians should be aware of the novel technologies that are moving into routine clinical use and the clinical implications of HIV-1 minority variants. Additional studies are needed to determine the optimal platform for clinical application of these new technologies and to provide guidance to clinicians on the type and frequency of clinically important HIV-1 minority variants.
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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Beerenwinkel N, Günthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol 2012; 3:329. [PMID: 22973268 PMCID: PMC3438994 DOI: 10.3389/fmicb.2012.00329] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/24/2012] [Indexed: 12/17/2022] Open
Abstract
Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.
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Affiliation(s)
- Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH ZurichBasel, Switzerland
- Swiss Institute of BioinformaticsBasel, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of ZurichZurich, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of BaselBasel, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of ZurichZurich, Switzerland
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