1
|
Ji H, Sandstrom P, Paredes R, Harrigan PR, Brumme CJ, Avila Rios S, Noguera-Julian M, Parkin N, Kantor R. Are We Ready for NGS HIV Drug Resistance Testing? The Second "Winnipeg Consensus" Symposium. Viruses 2020; 12:E586. [PMID: 32471096 PMCID: PMC7354487 DOI: 10.3390/v12060586] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21-22 February, 2018), a second "Winnipeg Consensus" symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium's goals and highlights.
Collapse
Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Infectious Diseases Department, Hospital Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
| | - P. Richard Harrigan
- Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada;
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Santiago Avila Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City 14080, Mexico;
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic–Central University of Catalonia (UVic–UCC), Can Baumann, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA 95472, USA;
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA;
| |
Collapse
|
2
|
Vazquez-Guillen JM, Palacios-Saucedo GC, Rivera-Morales LG, Garcia-Campos J, Ortiz-Lopez R, Noguera-Julian M, Paredes R, Vielma-Ramirez HJ, Ramirez TJ, Chavez-Garcia M, Lopez-Guillen P, Briones-Lara E, Sanchez-Sanchez LM, Vazquez-Martinez CA, Rodriguez-Padilla C. Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART. PLoS One 2016; 11:e0147591. [PMID: 26807922 PMCID: PMC4725846 DOI: 10.1371/journal.pone.0147591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Although Structured Treatment Interruptions (STI) are currently not considered an alternative strategy for antiretroviral treatment, their true benefits and limitations have not been fully established. Some studies suggest the possibility of improving the quality of life of patients with this strategy; however, the information that has been obtained corresponds mostly to studies conducted in adults, with a lack of knowledge about its impact on children. Furthermore, mutations associated with antiretroviral resistance could be selected due to sub-therapeutic levels of HAART at each interruption period. Genotyping methods to determine the resistance profiles of the infecting viruses have become increasingly important for the management of patients under STI, thus low-abundance antiretroviral drug-resistant mutations (DRM’s) at levels under limit of detection of conventional genotyping (<20% of quasispecies) could increase the risk of virologic failure. In this work, we analyzed the protease and reverse transcriptase regions of the pol gene by ultra-deep sequencing in pediatric patients under STI with the aim of determining the presence of high- and low-abundance DRM’s in the viral rebounds generated by the STI. High-abundance mutations in protease and high- and low-abundance mutations in reverse transcriptase were detected but no one of these are directly associated with resistance to antiretroviral drugs. The results could suggest that the evaluated STI program is virologically safe, but strict and carefully planned studies, with greater numbers of patients and interruption/restart cycles, are still needed to evaluate the selection of DRM’s during STI.
Collapse
Affiliation(s)
- Jose Manuel Vazquez-Guillen
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Gerardo C. Palacios-Saucedo
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
- * E-mail:
| | - Lydia G. Rivera-Morales
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Jorge Garcia-Campos
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Rocio Ortiz-Lopez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA, IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, España and Cátedra de la SIDA, Universitat de Vic, Vic, España
| | - Roger Paredes
- Institut de Recerca de la SIDA, IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, España and Cátedra de la SIDA, Universitat de Vic, Vic, España
| | - Herlinda J. Vielma-Ramirez
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Teresa J. Ramirez
- Laboratorio Estatal de Salud Pública del Estado de Nuevo León, Secretaría de Salud, Nuevo León, México
| | - Marcelino Chavez-Garcia
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Paulo Lopez-Guillen
- Unidad de Infectología “Dr. Juan I. Menchaca”, Hospital General Regional No. 45, Instituto Mexicano del Seguro Social, Jalisco, México
| | - Evangelina Briones-Lara
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Luz M. Sanchez-Sanchez
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Carlos A. Vazquez-Martinez
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Cristina Rodriguez-Padilla
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| |
Collapse
|
3
|
Cheriro W, Kiptoo M, Kikuvi G, Mining S, Emonyi W, Songok E. High Prevalence of HIV Low Abundance Drug-Resistant Variants in a Treatment-Naive Population in North Rift Kenya. AIDS Res Hum Retroviruses 2015; 31:1274-7. [PMID: 26414430 DOI: 10.1089/aid.2015.0039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The advent of antiretroviral treatment (ART) has resulted in a dramatic reduction in AIDS-related morbidity and mortality. However, the emergence and spread of antiretroviral drug resistance (DR) threaten to negatively impact treatment regimens and compromise efforts to control the epidemic. It is recommended that surveillance of drug resistance occur in conjunction with scale-up efforts to ensure that appropriate first-line therapy is offered relative to the resistance that exists. However, standard resistance testing methods used in Sub-Saharan Africa rely on techniques that do not include low abundance DR variants (LADRVs) that have been documented to contribute to treatment failure. The use of next generation sequencing (NGS) has been shown to be more sensitive to LADRVS. We have carried out a preliminary investigation using NGS to determine the prevalence of LDRVS among a drug-naive population in North Rift Kenya. Antiretroviral-naive patients attending a care clinic in North Rift Kenya were requested to provide and with consent provided blood samples for DR analysis. DNA was extracted and amplified and nested PCR was conducted on the pol RT region using primers tagged with multiplex identifiers (MID). Resulting PCR amplicons were purified, quantified, and pyrosequenced using a GS FLX Titanium PicoTiterPlate (Roche). Valid pyrosequencing reads were aligned with HXB-2 and the frequency and distribution of nucleotide and amino acid changes were determined using an in-house Perl script. DR mutations were identified using the IAS-USA HIV DR mutation database. Sixty samples were successfully sequenced of which 26 were subtype A, 9 were subtype D, 2 were subtype C, and the remaining were recombinants. Forty-six (76.6%) had at least one drug resistance mutation, with 25 (41.6%) indicated as major and the remaining 21 (35%) indicated as minor. The most prevalent mutation was NRTI position K219Q/R (11/46, 24%) followed by NRTI M184V (5/46, 11%) and NNRTI K103N (4/46, 9%). Our use of NGS technology revealed a high prevalence of LADRVs among drug-naive populations in Kenya, a region with predominantly non-B subtypes. The impact of these mutations on the clinical outcome of ART can be ascertained only through long-term follow-up.
Collapse
Affiliation(s)
- Winfrida Cheriro
- 1 Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
- 2 Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Michael Kiptoo
- 1 Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
- 3 Kenya Medical Research Institute, Nairobi, Kenya
| | - Gideon Kikuvi
- 1 Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Simeon Mining
- 4 School of Medicine, Moi University, Eldoret, Kenya
| | | | - Elijah Songok
- 1 Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
- 3 Kenya Medical Research Institute, Nairobi, Kenya
- 5 Department of Medical Microbiology, University of Manitoba, Winnipeg, MN, Canada
| |
Collapse
|
4
|
Suez M, Behdenna A, Brouillet S, Graça P, Higuet D, Achaz G. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads. Mol Ecol Resour 2015; 16:524-33. [DOI: 10.1111/1755-0998.12467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Marie Suez
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
| | - Abdelkader Behdenna
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
- SMILE; CIRB (UMR 7241); Collège de France; 11, Place Marcelin Berthelot Paris Cedex 05 75231 Paris France
| | - Sophie Brouillet
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
| | - Paula Graça
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
| | - Dominique Higuet
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
| | - Guillaume Achaz
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
- SMILE; CIRB (UMR 7241); Collège de France; 11, Place Marcelin Berthelot Paris Cedex 05 75231 Paris France
| |
Collapse
|
5
|
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.
Collapse
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:
| |
Collapse
|
6
|
HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument. Antimicrob Agents Chemother 2015; 59:6824-33. [PMID: 26282425 DOI: 10.1128/aac.01490-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/10/2015] [Indexed: 11/20/2022] Open
Abstract
Limited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n = 759) and from a Ugandan study cohort (n = 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of <3.0 log10 HIV RNA copies/ml. Overall, 99.3% nucleotide concordance between methods was observed. MiSeq sequencing achieved 97.4% sensitivity and 99.3% specificity in detecting resistance mutations identified by Sanger sequencing. Findings suggest that the Illumina MiSeq platform can yield high-quality data with a high-multiplex "wide" sequencing approach. This strategy can be used for multiple HIV subtypes, demonstrating the potential for widespread individual testing and annual population surveillance in resource-limited settings.
Collapse
|
7
|
Ji H, Kozak RA, Biondi MJ, Pilon R, Vallee D, Liang BB, La D, Kim J, Van Domselaar G, Leonard L, Sandstrom P, Brooks J. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. Virology 2015; 477:1-9. [PMID: 25600207 DOI: 10.1016/j.virol.2014.12.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/11/2014] [Accepted: 12/23/2014] [Indexed: 01/06/2023]
Abstract
Identifying HCV drug resistance mutations (DRMs) is increasingly important as new direct acting antiviral therapies (DAA) become available. Tagged pooled pyrosequencing (TPP) was originally developed as cost-effective approach for detecting low abundance HIV DRMs. Using 127 HCV-positive samples from a Canadian injection drug user cohort, we demonstrated the suitability and efficiency of TPP for evaluating DRMs in HCV NS5B gene. At a mutation identification threshold of 1%, no nucleoside inhibitor DRMs were detected among these DAA naïve subjects. Clinical NS5B resistance to non-nucleoside inhibitors and interferon/ribavirin was predicted to be low within this cohort. S282T mutation, the primary mutation selected by sofosbuvir in vitro, was not identified while S282G/C/R variants were detected in 9 subjects. Further characterization on these new S282 variants using in silico molecular modeling implied their potential association with resistance. Combining TPP with in silico analysis detects NS5B polymorphisms that may explain differences in treatment outcomes.
Collapse
Affiliation(s)
- Hezhao Ji
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Robert A Kozak
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Mia J Biondi
- Arthur Labatt Family School of Nursing, Western University, London, Canada
| | - Richard Pilon
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Dominic Vallee
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Ben Binhua Liang
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - David La
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - John Kim
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Gary Van Domselaar
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Lynne Leonard
- Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - James Brooks
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada.
| |
Collapse
|
8
|
Contribution of human immunodeficiency virus type 1 minority variants to reduced drug susceptibility in patients on an integrase strand transfer inhibitor-based therapy. PLoS One 2014; 9:e104512. [PMID: 25110880 PMCID: PMC4128663 DOI: 10.1371/journal.pone.0104512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
The role of HIV-1 minority variants on transmission, pathogenesis, and virologic failure to antiretroviral regimens has been explored; however, most studies of low-level HIV-1 drug-resistant variants have focused in single target regions. Here we used a novel HIV-1 genotypic assay based on deep sequencing, DEEPGEN (Gibson et al 2014 Antimicrob Agents Chemother 58∶2167) to simultaneously analyze the presence of minority variants carrying mutations associated with reduced susceptibility to protease (PR), reverse transcriptase (RT), and integrase strand transfer integrase inhibitors (INSTIs), as well as HIV-1 coreceptor tropism. gag-p2/NCp7/p1/p6/pol-PR/RT/INT and env/C2V3 PCR products were obtained from twelve heavily treatment-experienced patients experiencing virologic failure while participating in a 48-week dose-ranging study of elvitegravir (GS-US-183-0105). Deep sequencing results were compared with (i) virological response to treatment, (ii) genotyping based on population sequencing, (iii) phenotyping data using PhenoSense and VIRALARTS, and (iv) HIV-1 coreceptor tropism based on the phenotypic test VERITROP. Most patients failed the antiretroviral regimen with numerous pre-existing mutations in the PR and RT, and additionally newly acquired INSTI-resistance mutations as determined by population sequencing (mean 9.4, 5.3, and 1.4 PI- RTI-, and INSTI-resistance mutations, respectively). Interestingly, since DEEPGEN allows the accurate detection of amino acid substitutions at frequencies as low as 1% of the population, a series of additional drug resistance mutations were detected by deep sequencing (mean 2.5, 1.5, and 0.9, respectively). The presence of these low-abundance HIV-1 variants was associated with drug susceptibility, replicative fitness, and coreceptor tropism determined using sensitive phenotypic assays, enhancing the overall burden of resistance to all four antiretroviral drug classes. Further longitudinal studies based on deep sequencing tests will help to clarify (i) the potential impact of minority HIV-1 drug resistant variants in response to antiretroviral therapy and (ii) the importance of the detection of HIV minority variants in the clinical practice.
Collapse
|
9
|
Hunt GM, Morris L, Moorthy A, Coovadia A, Abrams EJ, Strehlau R, Kuhn L, Persaud D. Concordance between allele-specific PCR and ultra-deep pyrosequencing for the detection of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. J Virol Methods 2014; 207:182-7. [PMID: 25034127 DOI: 10.1016/j.jviromet.2014.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/01/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022]
Abstract
Recent advances in genotyping technologies have allowed for detection of HIV-1 drug resistance mutations present at low levels. The presence and percentage of Y181C and K103N drug-resistant variants in the blood of 105 subtype C HIV-infected infants who failed single-dose nevirapine prophylaxis for HIV transmission were compared using two highly sensitive genotyping methods, allele-specific PCR (AS-PCR) and ultra-deep pyrosequencing. Significant correlations in detection between both methods were found for both Y181C (correlation coefficients of 0.94 [95% CI 0.91-0.96]) and K103N (0.89 [95% CI 0.84-0.92]) mutations. The majority of discordant specimens (3/5 Y181C and 8/11 K103N) had wild-type variants when population sequencing was used, but mutant variants were detectable at very low levels (≤5%) with either assay. This difference is most likely due to stochastic variations in the appearance of mutant variants. Overall, both AS-PCR and ultra-deep pyrosequencing methods have proven to be sensitive and accurate, and may confidently be used where feasible.
Collapse
Affiliation(s)
- Gillian M Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anitha Moorthy
- Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| | - Ashraf Coovadia
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Elaine J Abrams
- ICAP, Columbia University Mailman School of Public Health, New York, NY, United States.
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States.
| | - Deborah Persaud
- Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
10
|
Rodriguez-Frias F, Buti M, Tabernero D, Homs M. Quasispecies structure, cornerstone of hepatitis B virus infection: Mass sequencing approach. World J Gastroenterol 2013; 19:6995-7023. [PMID: 24222943 PMCID: PMC3819535 DOI: 10.3748/wjg.v19.i41.6995] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/23/2013] [Accepted: 09/17/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is a DNA virus with complex replication, and high replication and mutation rates, leading to a heterogeneous viral population. The population is comprised of genomes that are closely related, but not identical; hence, HBV is considered a viral quasispecies. Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions, which is especially important in the P and S gene overlapping regions, but is less significant in the X and preCore/Core genes. Despite this restriction, several clinically and pathologically relevant variants have been characterized along the viral genome. Next-generation sequencing (NGS) approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains. In the present review, we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus. In addition, we provide an analysis of the clinical implications of HBV variants and their study by NGS.
Collapse
|
11
|
Paydary K, Khaghani P, Emamzadeh-Fard S, Alinaghi SAS, Baesi K. The emergence of drug resistant HIV variants and novel anti-retroviral therapy. Asian Pac J Trop Biomed 2013; 3:515-22. [PMID: 23835806 PMCID: PMC3695575 DOI: 10.1016/s2221-1691(13)60106-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/21/2013] [Indexed: 02/08/2023] Open
Abstract
After its identification in 1980s, HIV has infected more than 30 million people worldwide. In the era of highly active anti-retroviral therapy, anti-retroviral drug resistance results from insufficient anti-retroviral pressure, which may lead to treatment failure. Preliminary studies support the idea that anti-retroviral drug resistance has evolved largely as a result of low-adherence of patients to therapy and extensive use of anti-retroviral drugs in the developed world; however, a highly heterogeneous horde of viral quasi-species are currently circulating in developing nations. Thus, the prioritizing of strategies adopted in such two worlds should be quite different considering the varying anti-retroviral drug resistance prevalence. In this article, we explore differences in anti-retroviral drug resistance patterns between developed and developing countries, as they represent two distinct ecological niches of HIV from an evolutionary standpoint.
Collapse
Affiliation(s)
- Koosha Paydary
- Iranian Research Center for HIV/AIDS, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Khaghani
- Iranian Research Center for HIV/AIDS, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sahra Emamzadeh-Fard
- Iranian Research Center for HIV/AIDS, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kazem Baesi
- Iranian Research Center for HIV/AIDS, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
12
|
Ji H, Li Y, Liang B, Pilon R, MacPherson P, Bergeron M, Kim J, Graham M, Van Domselaar G, Sandstrom P, Brooks J. Pyrosequencing dried blood spots reveals differences in HIV drug resistance between treatment naïve and experienced patients. PLoS One 2013; 8:e56170. [PMID: 23409150 PMCID: PMC3567018 DOI: 10.1371/journal.pone.0056170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/07/2013] [Indexed: 11/18/2022] Open
Abstract
Dried blood spots (DBS) are an alternative specimen collection format for HIV-1 genotyping. DBS produce HIV genotyping results that are robust and equivalent to plasma when using conventional sequencing methods. However, using tagged, pooled pyrosequencing, we demonstrate that concordance between plasma and DBS is not absolute and varies according to viral load (VL), duration of HIV infection and antiretroviral therapy (ART) status. The plasma/DBS concordance is the highest when VL is ≥5,000 copies/ml and/or the patient has no ART exposure and/or when the duration of HIV infection is ≤2 years. Stepwise regression analysis revealed that VL is most important independent predictor for concordance of DBS with plasma genotypes. This is the first study to use next generation sequencing to identify discordance between DBS and plasma genotypes. Consideration should be given to VL, duration of infection, and ART exposure when interpreting DBS genotypes produced using next generation sequencing. These findings are of particular significance when DBS are to be used for clinical monitoring purposes.
Collapse
Affiliation(s)
- Hezhao Ji
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Ji H, Liang B, Li Y, Van Domselaar G, Graham M, Tyler S, Merks H, Sandstrom P, Brooks J. Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing. J Virol Methods 2013; 187:314-20. [DOI: 10.1016/j.jviromet.2012.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 10/10/2012] [Accepted: 10/22/2012] [Indexed: 01/23/2023]
|
14
|
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: 169] [Impact Index Per Article: 14.1] [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.
Collapse
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
| |
Collapse
|
15
|
Singh DD, Jain A. Multipurpose instantaneous microarray detection of acute encephalitis causing viruses and their expression profiles. Curr Microbiol 2012; 65:290-303. [PMID: 22674173 PMCID: PMC7080014 DOI: 10.1007/s00284-012-0154-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/14/2012] [Indexed: 01/15/2023]
Abstract
Detection of multiple viruses is important for global analysis of gene or protein content and expression, opening up new prospects in terms of molecular and physiological systems for pathogenic diagnosis. Early diagnosis is crucial for disease treatment and control as it reduces inappropriate use of antiviral therapy and focuses surveillance activity. This requires the ability to detect and accurately diagnose infection at or close to the source/outbreak with minimum delay and the need for specific, accessible point-of-care diagnosis able to distinguish causative viruses and their subtypes. None of the available viral diagnostic assays combine a point-of-care format with the complex capability to identify a large range of human and animal viruses. Microarray detection provides a useful, labor-saving tool for detection of multiple viruses with several advantages, such as convenience and prevention of cross-contamination of polymerase chain reaction (PCR) products, which is of foremost importance in such applications. Recently, real-time PCR assays with the ability to confirm the amplification product and quantitate the target concentration have been developed. Furthermore, nucleotide sequence analysis of amplification products has facilitated epidemiological studies of infectious disease outbreaks and monitoring of treatment outcomes for infections, in particular for viruses that mutate at high frequency. This review discusses applications of microarray technology as a potential new tool for detection and identification of acute encephalitis-causing viruses in human serum, plasma, and cell cultures.
Collapse
Affiliation(s)
- Desh Deepak Singh
- Virology Laboratory, Department of Microbiology, C S M Medical University, Lucknow, UP 226003, India.
| | | |
Collapse
|
16
|
Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. Application of next-generation sequencing technologies in virology. J Gen Virol 2012; 93:1853-1868. [PMID: 22647373 PMCID: PMC3709572 DOI: 10.1099/vir.0.043182-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.
Collapse
Affiliation(s)
- Alan D Radford
- University of Liverpool, Institute of Infection and Global Health, Leahurst Campus, Chester High Road, Neston, South Wirral CH64 7TE, UK
| | - David Chapman
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Linda Dixon
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Julian Chantrey
- University of Liverpool, School of Veterinary Science, Leahurst Campus, Chester High Road, Neston, South Wirral CH64 7TE, UK
| | - Alistair C Darby
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
| | - Neil Hall
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
17
|
Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 2012; 7:e36494. [PMID: 22574170 PMCID: PMC3344889 DOI: 10.1371/journal.pone.0036494] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/03/2012] [Indexed: 11/24/2022] Open
Abstract
Background Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. Methods/Results We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. Conclusion The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3–5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.
Collapse
|
18
|
Liang B, Luo M, Scott-Herridge J, Semeniuk C, Mendoza M, Capina R, Sheardown B, Ji H, Kimani J, Ball BT, Van Domselaar G, Graham M, Tyler S, Jones SJM, Plummer FA. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS One 2011; 6:e26745. [PMID: 22039546 PMCID: PMC3198814 DOI: 10.1371/journal.pone.0026745] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/03/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB) sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL) and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.
Collapse
Affiliation(s)
- Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
[Bioinformatics studies on drug resistance against anti-HIV-1 drugs]. Uirusu 2011; 61:35-47. [PMID: 21972554 DOI: 10.2222/jsv.61.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
More than 20 drugs have been available for anti-HIV-1 treatment in Japan. Combination therapy with these drugs dramatically decreases in morbidity and mortality of AIDS. However, due to high mutation rate of HIV-1, treatment with ineffective drugs toward patients infected with HIV-1 causes accumulation of mutations in the virus, and emergence of drug resistant viruses. Thus, to achieve appropriate application of the drugs toward the respective patients living with HIV-1, methods for predicting the level of drug-resistance using viral sequence information has been developed on the basis of bioinformatics. Furthermore, ultra-deep sequencing by next-generation sequencer whose data analysis is also based on bioinformatics, or in silico structural modeling have been achieved to understand drug resistant mechanisms. In this review, I overview the bioinformatics studies about drug resistance against anti-HIV-1 drugs.
Collapse
|
20
|
Lancaster KZ, Pfeiffer JK. Mechanisms controlling virulence thresholds of mixed viral populations. J Virol 2011; 85:9778-88. [PMID: 21795346 PMCID: PMC3196390 DOI: 10.1128/jvi.00355-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 07/16/2011] [Indexed: 02/05/2023] Open
Abstract
The propensity of RNA viruses to revert attenuating mutations contributes to disease and complicates vaccine development. Despite the presence of virulent revertant viruses in some live-attenuated vaccines, disease from vaccination is rare. This suggests that in mixed viral populations, attenuated viruses may limit the pathogenesis of virulent viruses, thus establishing a virulence threshold. Here we examined virulence thresholds using mixtures of virulent and attenuated viruses in a transgenic mouse model of poliovirus infection. We determined that a 1,000-fold excess of the attenuated Sabin strain of poliovirus was protective against disease induced by the virulent Mahoney strain. Protection was induced locally, and inactivated virus conferred protection. Treatment with a poliovirus receptor-blocking antibody phenocopied the protective effect of inactivated viruses in vitro and in vivo, suggesting that one mechanism controlling virulence thresholds may be competition for a viral receptor. Additionally, the type I interferon response reduces poliovirus pathogenesis; therefore, we examined virulence thresholds in mice lacking the alpha/beta interferon receptor. We found that the attenuated virus was virulent in immunodeficient mice due to the enhanced replication and reversion of attenuating mutations. Therefore, while the type I interferon response limits the virulence of the attenuated strain by reducing replication, protection from disease conferred by the attenuated strain in immunocompetent mice can occur independently of replication. Our results identified mechanisms controlling the virulence of mixed viral populations and indicate that live-attenuated vaccines containing virulent virus may be safe, as long as virulent viruses are present at levels below a critical threshold.
Collapse
Affiliation(s)
| | - Julie K. Pfeiffer
- Corresponding author. Mailing address: Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9048. Phone: (214) 633-1377. Fax: (214) 648-5905. E-mail:
| |
Collapse
|
21
|
Lefebvre G, Desfarges S, Uyttebroeck F, Muñoz M, Beerenwinkel N, Rougemont J, Telenti A, Ciuffi A. Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell. J Virol 2011; 85:6205-11. [PMID: 21507965 PMCID: PMC3126515 DOI: 10.1128/jvi.00252-11] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 04/08/2011] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection.
Collapse
Affiliation(s)
- Gregory Lefebvre
- Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Evaluation of: Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV: Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS ONE 5(10), E13564 (2010). The recent commercialization of high-throughput sequencing technologies has brought about the possibility of characterizing complex viral populations at previously unattainable scales. An important consideration in designing experiments with these technologies is the need for large quantities of input DNA. To accommodate low-input samples, an amplification step is required, usually a PCR, which comes at the risk of introducing a bias that potentially distorts the view of the viral population composition. By implementing a new sample preprocessing protocol, Willerth et al. address these experimental limitations in the context of complete HIV genome sequencing. Moreover, to facilitate the assembly of short and potentially divergent HIV-derived reads, the authors construct a full-length data-specific consensus sequence using a novel bioinformatics approach that capitalizes on the available HIV complete genomes.
Collapse
Affiliation(s)
| | - Philippe Lemey
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| |
Collapse
|
23
|
HIV quasispecies dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs. PLoS One 2011; 6:e18204. [PMID: 21455303 PMCID: PMC3063788 DOI: 10.1371/journal.pone.0018204] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/27/2011] [Indexed: 12/02/2022] Open
Abstract
The human immunodeficiency virus (HIV) can be suppressed by highly active anti-retroviral therapy (HAART) in the majority of infected patients. Nevertheless, treatment interruptions inevitably result in viral rebounds from persistent, latently infected cells, necessitating lifelong treatment. Virological failure due to resistance development is a frequent event and the major threat to treatment success. Currently, it is recommended to change treatment after the confirmation of virological failure. However, at the moment virological failure is detected, drug resistant mutants already replicate in great numbers. They infect numerous cells, many of which will turn into latently infected cells. This pool of cells represents an archive of resistance, which has the potential of limiting future treatment options. The objective of this study was to design a treatment strategy for treatment-naive patients that decreases the likelihood of early treatment failure and preserves future treatment options. We propose to apply a single, pro-active treatment switch, following a period of treatment with an induction regimen. The main goal of the induction regimen is to decrease the abundance of randomly generated mutants that confer resistance to the maintenance regimen, thereby increasing subsequent treatment success. Treatment is switched before the overgrowth and archiving of mutant strains that carry resistance against the induction regimen and would limit its future re-use. In silico modelling shows that an optimal trade-off is achieved by switching treatment at days after the initiation of antiviral therapy. Evaluation of the proposed treatment strategy demonstrated significant improvements in terms of resistance archiving and virological response, as compared to conventional HAART. While continuous pro-active treatment alternation improved the clinical outcome in a randomized trial, our results indicate that a similar improvement might also be reached after a single pro-active treatment switch. The clinical validity of this finding, however, remains to be shown by a corresponding trial.
Collapse
|
24
|
Ji H, Li Y, Graham M, Liang BB, Pilon R, Tyson S, Peters G, Tyler S, Merks H, Bertagnolio S, Soto-Ramirez L, Sandstrom P, Brooks J. Next-generation sequencing of dried blood spot specimens: a novel approach to HIV drug-resistance surveillance. Antivir Ther 2011; 16:871-8. [DOI: 10.3851/imp1839] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|