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Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
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Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
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Ssekagiri A, Jjingo D, Lujumba I, Bbosa N, Bugembe DL, Kateete DP, Jordan IK, Kaleebu P, Ssemwanga D. QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data. BIOINFORMATICS ADVANCES 2022; 2:vbac089. [PMID: 36699347 PMCID: PMC9722223 DOI: 10.1093/bioadv/vbac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Summary Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%. Availability and implementation QuasiFlow and corresponding documentation are publicly available at https://github.com/AlfredUg/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Daudi Jjingo
- Department of Computer Science, Makerere University, Kampala 10207, Uganda,African Center of Excellence in Bioinformatics and Data Intensive Sciences, Makerere University, Kampala 10207, Uganda
| | - Ibra Lujumba
- Department of Immunology and Molecular Biology, Makerere University, Kampala 10206, Uganda
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
| | - Daniel L Bugembe
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Kampala 10206, Uganda
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pontiano Kaleebu
- Department of General Virology, Uganda Virus Research Institute, Entebbe 31405, Uganda,Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
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3
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Mbisa JL, Kirwan P, Tostevin A, Ledesma J, Bibby DF, Brown A, Myers R, Hassan AS, Murphy G, Asboe D, Pozniak A, Kirk S, Gill ON, Sabin C, Delpech V, Dunn DT. Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction. Clin Infect Dis 2020; 69:1136-1143. [PMID: 30534981 PMCID: PMC6743824 DOI: 10.1093/cid/ciy1048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. METHODS Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. RESULTS Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). CONCLUSIONS Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Peter Kirwan
- National Infection Service, Public Health England, London, United Kingdom
| | - Anna Tostevin
- Institute for Global Health, University College London, London, United Kingdom
| | - Juan Ledesma
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David F Bibby
- National Infection Service, Public Health England, London, United Kingdom
| | - Alison Brown
- National Infection Service, Public Health England, London, United Kingdom
| | - Richard Myers
- National Infection Service, Public Health England, London, United Kingdom
| | - Amin S Hassan
- HIV/STI Group, Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gary Murphy
- National Infection Service, Public Health England, London, United Kingdom
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Stuart Kirk
- University College London Hospital, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Caroline Sabin
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom.,Institute for Global Health, University College London, London, United Kingdom
| | - Valerie Delpech
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David T Dunn
- Institute for Global Health, University College London, London, United Kingdom
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Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors. J Clin Microbiol 2018; 56:JCM.01443-18. [PMID: 30305383 PMCID: PMC6258839 DOI: 10.1128/jcm.01443-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 02/02/2023] Open
Abstract
HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. However, the clinical value added from NGS approaches to antiviral resistance testing remains to be demonstrated. We compared the variant detection capacity of NGS versus Sanger sequencing methods for resistance genotyping in 144 drug resistance tests (105 protease-reverse transcriptase tests and 39 integrase tests) submitted to our clinical virology laboratory over a four-month period in 2016 for Sanger-based HIV drug resistance testing. NGS detected all true high-frequency drug resistance mutations (>20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers HyDRA and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low-frequency mutations (1 to 20% frequency) associated with higher levels of drug resistance in 30/105 (29%) protease-reverse transcriptase tests and 4/39 (10%) integrase tests. In clinical follow-up of 69 individuals for a median of 674 days, we did not find a difference in rates of virological failure between individuals with and without low-frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low-frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during the preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points, consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.
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Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. J Clin Microbiol 2018; 56:JCM.00105-18. [PMID: 29618499 DOI: 10.1128/jcm.00105-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an in vitro diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.
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L. Machado S, Gonçalves GS, Dudley D, O'Connor D, Keiko Toma H, Fernandes JCC, Tanuri A. Development of a Qualitative Quantitative Polymerase Chain Reaction Test to Identify Patients Failing First-Line Therapy to Non-Nucleotide Reverse Transcriptase Inhibitor. AIDS Res Hum Retroviruses 2017; 33:386-394. [PMID: 27819156 DOI: 10.1089/aid.2016.0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy (ART) can be compromised by selection of drug resistance strains, which can be promoted by lack of adherence during therapy and drug tolerance, and some of these drug-resistant strains can persist for years as minority populations. The K103N drug resistance mutation is selected by the use of non-nucleotide reverse transcriptase inhibitors, including nevirapine or efavirenz (EFV), used in low-income countries. Here we describe the use of a less expensive qualitative point mutation polymerase chain reaction (PMqPCRK103N) targeting K103N mutation. To validate the use of this methodology, we tested previously sequenced samples from patients treated with highly active ART with viral loads above 2,000 copies/ml and compared the results of our assay with Illumina deep sequencing. Due to its low cost and high specificity, this test is particularly suitable for low-income countries to screen for pretreatment resistance in patients either initiating ART or failing first-line regimens containing EFV.
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Affiliation(s)
- Sergio L. Machado
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriel S. Gonçalves
- Laboratório de Virologia Molecular, Instituto de Biologia, Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Dawn Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - David O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Helena Keiko Toma
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level. ACTA ACUST UNITED AC 2015; 7. [PMID: 26949565 PMCID: PMC4775093 DOI: 10.4172/2153-0602.1000182] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.
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Affiliation(s)
- Da Wei Huang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA; National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Castle Raley
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Min Kang Jiang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Xin Zheng
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Dun Liang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - M Tauseef Rehman
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Helene C Highbarger
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Xiaoli Jiao
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Brad Sherman
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Liang Ma
- Critical Care Medicine Department, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaofeng Chen
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Thomas Skelly
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Jennifer Troyer
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA; National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, USA
| | - Robert Stephens
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Tomozumi Imamichi
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Alice Pau
- Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA
| | - Richard A Lempicki
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Bao Tran
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Dwight Nissley
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - H Clifford Lane
- Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA
| | - Robin L Dewar
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
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Abstract
PURPOSE OF REVIEW The review discusses new technologies for the sensitive detection of HIV drug resistance, with a focus on applications in antiretroviral treatment (ART)-naïve populations. RECENT FINDINGS Conventional sequencing is well established for detecting HIV drug resistance in routine care and guides optimal treatment selection in patients starting ART. Access to conventional sequencing is nearly universal in Western countries, but remains limited in Asia, Latin America, and Africa. Technological advances now allow detection of resistance with greatly improved sensitivity compared with conventional sequencing, variably increasing the yield of resistance testing in ART-naïve populations. There is strong cumulative evidence from retrospective studies that sensitive detection of resistant mutants in baseline plasma samples lacking resistance by conventional sequencing more than doubles the risk of virological failure after starting efavirenz-based or nevirapine-based ART. SUMMARY Sensitive resistance testing methods are mainly confined to research applications and in this context have provided great insight into the dynamics of drug resistance development, persistence, and transmission. Adoption in care settings is becoming increasingly possible, although important challenges remain. Platforms for diagnostic use must undergo technical improvements to ensure good performance and ease of use, and clinical validation is required to ensure utility.
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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.
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