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Harel N, Meir M, Gophna U, Stern A. Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations. Nucleic Acids Res 2019; 47:e148. [PMID: 31665473 PMCID: PMC7107797 DOI: 10.1093/nar/gkz907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/05/2019] [Accepted: 10/03/2019] [Indexed: 01/23/2023] Open
Abstract
One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms.
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Affiliation(s)
- Noam Harel
- School of Molecular Cell Biology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Moran Meir
- School of Molecular Cell Biology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Adi Stern
- School of Molecular Cell Biology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
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Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Res 2016; 239:106-114. [PMID: 28039047 DOI: 10.1016/j.virusres.2016.12.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/25/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
Abstract
Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. For this reason, the number of studies using whole genome deep sequencing to characterize viral quasi-species in clinical samples is still limited. We have previously undertaken a large scale whole genome deep sequencing study of HIV-1 populations. Here we discuss the challenges, error profiles, control experiments, and computational test we developed to quantify the accuracy of variant frequency estimation.
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Lin N, Gonzalez OA, Registre L, Becerril C, Etemad B, Lu H, Wu X, Lockman S, Essex M, Moyo S, Kuritzkes DR, Sagar M. Humoral Immune Pressure Selects for HIV-1 CXC-chemokine Receptor 4-using Variants. EBioMedicine 2016; 8:237-247. [PMID: 27428434 PMCID: PMC4919596 DOI: 10.1016/j.ebiom.2016.04.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/26/2022] Open
Abstract
Although both C-C chemokine receptor 5 (CCR5)- and CXC chemokine receptor 4 (CXCR4)-using HIV-1 strains cause AIDS, the emergence of CXCR4-utilizing variants is associated with an accelerated decline in CD4+ T cells. It remains uncertain if CXCR4-using viruses hasten disease or if these variants only emerge after profound immunological damage. We show that exclusively CXCR4- as compared to cocirculating CCR5-utilizing variants are less sensitive to neutralization by both contemporaneous autologous plasma and plasma pools from individuals that harbor only CCR5-using HIV-1. The CXCR4-utilizing variants, however, do not have a global antigenic change because they remain equivalently susceptible to antibodies that do not target coreceptor binding domains. Studies with envelope V3 loop directed antibodies and chimeric envelopes suggest that the neutralization susceptibility differences are potentially influenced by the V3 loop. In vitro passage of a neutralization sensitive CCR5-using virus in the presence of autologous plasma and activated CD4+ T cells led to the emergence of a CXCR4-utilizing virus in 1 of 3 cases. These results suggest that in some but not necessarily all HIV-1 infected individuals humoral immune pressure against the autologous virus selects for CXCR4-using variants, which potentially accelerates disease progression. Our observations have implications for using antibodies for HIV-1 immune therapy.
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Affiliation(s)
- Nina Lin
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Oscar A Gonzalez
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ludy Registre
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Carlos Becerril
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States
| | - Behzad Etemad
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Hong Lu
- Aaron Diamond AIDS Research Center, New York, NY, United States
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, New York, NY, United States
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States; Harvard School of Public Health, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Myron Essex
- Harvard School of Public Health, Boston, MA, United States; Botswana Harvard AIDS Institute, Gaborone, Botswana
| | | | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Manish Sagar
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, United States.
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Liu J, Song H, Liu D, Zuo T, Lu F, Zhuang H, Gao F. Extensive recombination due to heteroduplexes generates large amounts of artificial gene fragments during PCR. PLoS One 2014; 9:e106658. [PMID: 25211143 PMCID: PMC4161356 DOI: 10.1371/journal.pone.0106658] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Artificial recombinants can be generated during PCR when more than two genetically distinct templates coexist in a single PCR reaction. These recombinant amplicons can lead to the false interpretation of genetic diversity and incorrect identification of biological phenotypes that do not exist in vivo. We investigated how recombination between 2 or 35 genetically distinct HIV-1 genomes was affected by different PCR conditions using the parallel allele-specific sequencing (PASS) assay and the next generation sequencing method. In a standard PCR condition, about 40% of amplicons in a PCR reaction were recombinants. The high recombination frequency could be significantly reduced if the number of amplicons in a PCR reaction was below a threshold of 1013–1014 using low thermal cycles, fewer input templates, and longer extension time. Heteroduplexes (each DNA strand from a distinct template) were present at a large proportion in the PCR products when more thermal cycles, more templates, and shorter extension time were used. Importantly, the majority of recombinants were identified in heteroduplexes, indicating that the recombinants were mainly generated through heteroduplexes. Since prematurely terminated extension fragments can form heteroduplexes by annealing to different templates during PCR amplification, recombination has a better chance to occur with samples containing different genomes when the number of amplicons accumulate over the threshold. New technologies are warranted to accurately characterize complex quasispecies gene populations.
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Affiliation(s)
- Jia Liu
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Hongshuo Song
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United State of America
| | - Donglai Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United State of America
- National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, China
| | - Tao Zuo
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United State of America
- National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, China
| | - Fengmin Lu
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Hui Zhuang
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United State of America
- National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, China
- * E-mail:
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Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ. Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. PLoS One 2013; 8:e74249. [PMID: 24058534 PMCID: PMC3776835 DOI: 10.1371/journal.pone.0074249] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/31/2013] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04-0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9-2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification.
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Affiliation(s)
- Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Osvaldo Zagordi
- Department of Biosystems Sciences and Engineering, ETH Zurich, Basel, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Yannick Duport
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Beda Joos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Rémy Bruggmann
- Functional Genomics Center Zurich (FGCZ), University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Sciences and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- * E-mail:
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7
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Kemal KS, Anastos K, Weiser B, Ramirez CM, Shi Q, Burger H. Molecular epidemiology of HIV type 1 subtypes in Rwanda. AIDS Res Hum Retroviruses 2013; 29:957-62. [PMID: 23458210 DOI: 10.1089/aid.2012.0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 infection is characterized by genetic diversity, with multiple subtypes and recombinant variants circulating, particularly in sub-Saharan Africa. During the Rwandan genocide, many women experienced multiple rapes and some became HIV-1 infected. We studied plasma and peripheral blood mononuclear cells (PBMCs) from 30 infected women comprising two exposure groups: those with numerous contacts, raped multiple times, and women with one lifetime sexual partner and no history of rape. Population-based sequences from gag, pol, and env genes were analyzed to determine HIV-1 subtypes and intersubtype recombination. Individual plasma-derived variants from 12 women were also analyzed. Subtype A was found in 24/30 (80%), intersubtype recombination (AC and AD) in 4/30 (13%), and subtypes C and D in 1/30 each. In two subjects, the pattern of HIV-1 recombination differed between plasma and PBMC-derived sequences. Intersubtype recombination was common, although there were no significant differences in subtype or recombination rates between exposure groups.
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Affiliation(s)
- Kimdar S. Kemal
- Wadsworth Center, New York State Department of Health, Albany, New York
| | | | - Barbara Weiser
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Medicine, Albany Medical College, Albany, New York
| | | | - Qiuhu Shi
- Epidemiology and Community Health, School of Health Sciences and Practice, New York Medical College, Valhalla, New York
| | - Harold Burger
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Medicine, Albany Medical College, Albany, New York
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Kemal KS, Ramirez CM, Burger H, Foley B, Mayers D, Klimkait T, Hamy F, Anastos K, Petrovic K, Minin VN, Suchard MA, Weiser B. Recombination between variants from genital tract and plasma: evolution of multidrug-resistant HIV type 1. AIDS Res Hum Retroviruses 2012; 28:1766-74. [PMID: 22364185 DOI: 10.1089/aid.2011.0383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Multidrug-resistant (MDR) HIV-1 presents a challenge to the efficacy of antiretroviral therapy (ART). To examine mechanisms leading to MDR variants in infected individuals, we studied recombination between single viral genomes from the genital tract and plasma of a woman initiating ART. We determined HIV-1 RNA sequences and drug resistance profiles of 159 unique viral variants obtained before ART and semiannually for 4 years thereafter. Soon after initiating zidovudine, lamivudine, and nevirapine, resistant variants and intrapatient HIV-1 recombinants were detected in both compartments; the recombinants had inherited genetic material from both genital and plasma-derived viruses. Twenty-three unique recombinants were documented during 4 years of therapy, comprising ~22% of variants. Most recombinant genomes displayed similar breakpoints and clustered phylogenetically, suggesting evolution from common ancestors. Longitudinal analysis demonstrated that MDR recombinants were common and persistent, demonstrating that recombination, in addition to point mutation, can contribute to the evolution of MDR HIV-1 in viremic individuals.
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Affiliation(s)
- Kimdar S. Kemal
- Wadsworth Center, New York State Department of Health, Albany, New York
| | | | - Harold Burger
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Medicine, Albany Medical College, Albany, New York
| | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - Thomas Klimkait
- Institute of Medical Microbiology, Basel, Switzerland
- InPheno AG, Basel, Switzerland
| | - François Hamy
- Institute of Medical Microbiology, Basel, Switzerland
- InPheno AG, Basel, Switzerland
| | | | | | - Vladimir N. Minin
- Department of Statistics, University of Washington, Seattle, Washington
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, California
- Department of Biomathematics, University of California, Los Angeles, California
- Department of Human Genetics, University of California, Los Angeles, California
| | - Barbara Weiser
- Wadsworth Center, New York State Department of Health, Albany, New York
- Department of Medicine, Albany Medical College, Albany, New York
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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: 163] [Impact Index Per Article: 13.6] [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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Lin NH, Becerril C, Giguel F, Novitsky V, Moyo S, Makhema J, Essex M, Lockman S, Kuritzkes DR, Sagar M. Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C. Virology 2012; 433:296-307. [PMID: 22954962 DOI: 10.1016/j.virol.2012.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/12/2012] [Accepted: 08/01/2012] [Indexed: 02/09/2023]
Abstract
HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C.
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Affiliation(s)
- Nina H Lin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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11
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Winters MA, Lloyd RM, Shafer RW, Kozal MJ, Miller MD, Holodniy M. Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations. PLoS One 2012; 7:e40514. [PMID: 22815755 PMCID: PMC3399858 DOI: 10.1371/journal.pone.0040514] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/12/2012] [Indexed: 12/04/2022] Open
Abstract
Failure of antiretroviral regimens containing elvitegravir (EVG) and raltegravir (RAL) can result in the appearance of integrase inhibitor (INI) drug-resistance mutations (DRMs). While several INI DRMs have been identified, the evolution of EVG DRMs and the linkage of these DRMs with protease inhibitor (PI) and reverse transcriptase inhibitor (RTI) DRMs have not been studied at the clonal level. We examined the development of INI DRMs in 10 patients failing EVG-containing regimens over time, and the linkage of INI DRMs with PI and RTI DRMs in these patients plus 6 RAL-treated patients. A one-step RT-nested PCR protocol was used to generate a 2.7 kB amplicon that included the PR, RT, and IN coding region, and standard cloning and sequencing techniques were used to determine DRMs in 1,277 clones (mean 21 clones per time point). Results showed all patients had multiple PI, NRTI, and/or NNRTI DRMs at baseline, but no primary INI DRM. EVG-treated patients developed from 2 to 6 strains with different primary INI DRMs as early as 2 weeks after initiation of treatment, predominantly as single mutations. The prevalence of these strains fluctuated and new strains, and/or strains with new combinations of INI DRMs, developed over time. Final failure samples (weeks 14 to 48) typically showed a dominant strain with multiple mutations or N155H alone. Single N155H or multiple mutations were also observed in RAL-treated patients at virologic failure. All patient strains showed evidence of INI DRM co-located with single or multiple PI and/or RTI DRMs on the same viral strand. Our study shows that EVG treatment can select for a number of distinct INI-resistant strains whose prevalence fluctuates over time. Continued appearance of new INI DRMs after initial INI failure suggests a potent, highly dynamic selection of INI resistant strains that is unaffected by co-location with PI and RTI DRMs.
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Affiliation(s)
- Mark A Winters
- AIDS Research Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America.
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Boulanger J, Muresan L, Tiemann-Boege I. Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules. PLoS One 2012; 7:e36064. [PMID: 22558329 PMCID: PMC3340404 DOI: 10.1371/journal.pone.0036064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/30/2012] [Indexed: 12/12/2022] Open
Abstract
In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.
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Affiliation(s)
- Jérôme Boulanger
- Cell and Tissue Imaging Core, Centre National de la Recherche Scientifique, Institut Curie, Paris, France
- Radon Institute for Computational and Applied Mathematics of the Austrian Academy of Sciences, Linz, Austria
| | - Leila Muresan
- Department of Knowledge-Based Mathematical Systems, Johannes Kepler University, Linz, Austria
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Absence of HIV-1 evolution in the gut-associated lymphoid tissue from patients on combination antiviral therapy initiated during primary infection. PLoS Pathog 2012; 8:e1002506. [PMID: 22319447 PMCID: PMC3271083 DOI: 10.1371/journal.ppat.1002506] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 12/13/2011] [Indexed: 12/15/2022] Open
Abstract
Mucosal mononuclear (MMC) CCR5+CD4+ T cells of the gastrointestinal (GI) tract are selectively infected and depleted during acute HIV-1 infection. Despite early initiation of combination antiretroviral therapy (cART), gut-associated lymphoid tissue (GALT) CD4+ T cell depletion and activation persist in the majority of HIV-1 positive individuals studied. This may result from ongoing HIV-1 replication and T-cell activation despite effective cART. We hypothesized that ongoing viral replication in the GI tract during cART would result in measurable viral evolution, with divergent populations emerging over time. Subjects treated during early HIV-1 infection underwent phlebotomy and flexible sigmoidoscopy with biopsies prior to and 15–24 months post initiation of cART. At the 2nd biopsy, three GALT phenotypes were noted, characterized by high, intermediate and low levels of immune activation. A representative case from each phenotype was analyzed. Each subject had plasma HIV-1 RNA levels <50 copies/ml at 2nd GI biopsy and CD4+ T cell reconstitution in the peripheral blood. Single genome amplification of full-length HIV-1 envelope was performed for each subject pre- and post-initiation of cART in GALT and PBMC. A total of 280 confirmed single genome sequences (SGS) were analyzed for experimental cases. For each subject, maximum likelihood phylogenetic trees derived from molecular sequence data showed no evidence of evolved forms in the GALT over the study period. During treatment, HIV-1 envelope diversity in GALT-derived SGS did not increase and post-treatment GALT-derived SGS showed no substantial genetic divergence from pre-treatment sequences within transmitted groups. Similar results were obtained from PBMC-derived SGS. Our results reveal that initiation of cART during acute/early HIV-1 infection can result in the interruption of measurable viral evolution in the GALT, suggesting the absence of de-novo rounds of HIV-1 replication in this compartment during suppressive cART. This study was undertaken to determine if the gastrointestinal tract is a site of ongoing viral replication during suppressive combination antiretroviral therapy (cART) (defined by plasma HIV-1 RNA levels below 50 copies/ml). We found no evidence of substantial viral evolution in HIV-1 envelope sequences derived from peripheral blood mononuclear cells or cells of the gastrointestinal tract lymphoid tissue in participants initiating cART during early HIV-1 infection. To our knowledge, this is the first application of the single genome amplification technique to the comparative analysis of HIV-1 quasi-species derived from the gastrointestinal tract, demonstrating that in these individuals, cART has the ability to halt measurable evolution of HIV-1 envelope in this compartment. These findings suggest the absence of de-novo rounds of HIV-1 replication during suppressive cART and by extension, that experimentally observed, persistently elevated levels of immune activation in the gastrointestinal lymphoid tissue seen after the early initiation and uninterrupted use of cART (despite relative immune reconstitution in the blood) is likely due to factors other than ongoing viral replication. This implies that in this virally suppressed population, cART intensification is unlikely to significantly impact persistent CD4+ T cell depletion or increased levels of immune activation in the gastrointestinal tract.
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14
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[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.
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Combined antiretroviral therapy and immune pressure lead to in vivo HIV-1 recombination with ancestral viral genomes. J Acquir Immune Defic Syndr 2011; 57:109-17. [PMID: 21372727 DOI: 10.1097/qai.0b013e318215ab0a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Studies on drug interruption have provided new insights on the adaptive evolution of rebounding HIV-1 during antiretroviral pressure. We investigated the origin of new viral variants after discontinuation of protease (PR) inhibitors as a treatment remained exclusively based on reverse transcriptase inhibitors, and whether drug susceptibility, viral fitness, and neutralizing antibodies could be major driving forces for the evolution of virus populations. METHODS The study comprised 3 treatment-experienced subjects. Phylogenetic analysis of the PR, reverse transcriptase, and the viral envelope were carried out to ascertain the origin of the new viral variants with samples obtained over a 10-year period before and after a PR inhibitor withdrawal. In addition, drug susceptibility, replication capacity, and neutralization assays were performed. RESULTS New viral variants from all 3 subjects were derived through recombination with ancestral quasispecies. Computerized recombination models confirmed these results. Recombination was demonstrated by increased replication capacity, decreased drug susceptibility, and neutralization of ancestral virus envelope by contemporaneous plasma samples. CONCLUSIONS These findings demonstrate the relevance of HIV-1 reservoirs in adaptive evolution throughout recombination in response to selective pressure, such as antiretroviral therapy and immune responses. This result might assist in the design of new treatment strategies for patients experiencing treatment failure.
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16
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Abstract
Throughout the living world, genetic recombination and nucleotide substitution are the primary processes that create the genetic variation upon which natural selection acts. Just as analyses of substitution patterns can reveal a great deal about evolution, so too can analyses of recombination. Evidence of genetic recombination within the genomes of apparently asexual species can equate with evidence of cryptic sexuality. In sexually reproducing species, nonrandom patterns of sequence exchange can provide direct evidence of population subdivisions that prevent certain individuals from mating. Although an interesting topic in its own right, an important reason for analysing recombination is to account for its potentially disruptive influences on various phylogenetic-based molecular evolution analyses. Specifically, the evolutionary histories of recombinant sequences cannot be accurately described by standard bifurcating phylogenetic trees. Taking recombination into account can therefore be pivotal to the success of selection, molecular clock and various other analyses that require adequate modelling of shared ancestry and draw increased power from accurately inferred phylogenetic trees. Here, we review various computational approaches to studying recombination and provide guidelines both on how to gain insights into this important evolutionary process and on how it can be properly accounted for during molecular evolution studies.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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17
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Kirchherr JL, Hamilton J, Lu X, Gnanakaran S, Muldoon M, Daniels M, Kasongo W, Chalwe V, Mulenga C, Mwananyanda L, Musonda RM, Yuan X, Montefiori DC, Korber BT, Haynes BF, Gao F. Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology 2010; 409:163-74. [PMID: 21036380 DOI: 10.1016/j.virol.2010.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/22/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
Neutralizing antibodies (Nabs) are thought to play an important role in prevention and control of HIV-1 infection and should be targeted by an AIDS vaccine. It is critical to understand how HIV-1 induces Nabs by analyzing viral sequences in both tested viruses and sera. Neutralization susceptibility to antibodies in autologous and heterologous plasma was determined for multiple Envs (3-6) from each of 15 subtype-C-infected individuals. Heterologous neutralization was divided into two distinct groups: plasma with strong, cross-reactive neutralization (n=9) and plasma with weak neutralization (n=6). Plasma with cross-reactive heterologous Nabs also more potently neutralized contemporaneous autologous viruses. Analysis of Env sequences in plasma from both groups revealed a three-amino-acid substitution pattern in the V4 region that was associated with greater neutralization potency and breadth. Identification of such potential neutralization signatures may have important implications for the development of HIV-1 vaccines capable of inducing Nabs to subtype C HIV-1.
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Affiliation(s)
- Jennifer L Kirchherr
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
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18
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Lin NH, Negusse DM, Beroukhim R, Giguel F, Lockman S, Essex M, Kuritzkes DR. The design and validation of a novel phenotypic assay to determine HIV-1 coreceptor usage of clinical isolates. J Virol Methods 2010; 169:39-46. [PMID: 20599562 PMCID: PMC2930119 DOI: 10.1016/j.jviromet.2010.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/08/2010] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
Abstract
A phenotypic assay to determine coreceptor usage of HIV-1 has been developed for rapid testing of clinical samples. The assay is based on the synthesis of viral stock from full-length env amplicons isolated from patient's plasma. Pseudoviral stock is generated rapidly by using an overlapping PCR method to assemble a CMV promoter to env, followed by co-transfection into producer cells with a HIV plasmid (pNL4-3.Luc.R(-)E(-)) containing a non-functional env. The coreceptor used by the viral quasispecies is tested by infection into U87.CD4.CCR5 and U87.CD4.CXCR4 cells. Viral entry is indicated by the expression of the luciferase gene in relative light units (RLU). The use of CXCR4 coreceptor by minor variants is confirmed with sufficient suppression of RLU by a CXCR4 inhibitor. Two statistical tests are employed to confirm viral entry. This assay accurately assigned coreceptor usage of isolates of various subtypes and in the majority of samples of various viral loads. The sensitivity to detect minor species of CXCR4-using env is 1% at higher viral loads and 5% at less than 1,000 copies/ml. This assay provides a sensitive, efficient and relatively low-cost approach suitable for use by research laboratories for assessing HIV-1 coreceptor usage of plasma samples.
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Affiliation(s)
- Nina H. Lin
- Infectious Diseases Unit, Massachusetts General Hospital, 55 Fruit Street, Jackson 504, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
| | - Daniel M. Negusse
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02215, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Francoise Giguel
- Infectious Diseases Unit, Massachusetts General Hospital, 55 Fruit Street, Jackson 504, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
| | - Shahin Lockman
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Myron Essex
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, FXB 402, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Daniel R. Kuritzkes
- Harvard Medical School, Boston, MA, 02115 USA
- Section of Retroviral Therapeutics and Division of Infectious Diseases, Brigham and Women’s Hospital, 65 Landsdowne Street Rm 449, Cambridge, MA 02139, USA
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Shi B, Kitchen C, Weiser B, Mayers D, Foley B, Kemal K, Anastos K, Suchard M, Parker M, Brunner C, Burger H. Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy. Virology 2010; 404:5-20. [PMID: 20451945 DOI: 10.1016/j.virol.2010.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/15/2010] [Accepted: 04/12/2010] [Indexed: 02/04/2023]
Abstract
Characterization of residual plasma virus during antiretroviral therapy (ART) is a high priority to improve understanding of HIV-1 pathogenesis and therapy. To understand the evolution of HIV-1 pol and env genes in viremic patients under selective pressure of ART, we performed longitudinal analyses of plasma-derived pol and env sequences from single HIV-1 genomes. We tested the hypotheses that drug resistance in pol was unrelated to changes in coreceptor usage (tropism), and that recombination played a role in evolution of viral strains. Recombinants were identified by using Bayesian and other computational methods. High-level genotypic resistance was seen in approximately 70% of X4 and R5 strains during ART. There was no significant association between resistance and tropism. Each patient displayed at least one recombinant encompassing env and representing a change in predicted tropism. These data suggest that, in addition to mutation, recombination can play a significant role in shaping HIV-1 evolution.
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Affiliation(s)
- Binshan Shi
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
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20
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Powell RL, Lezeau L, Kinge T, Nyambi PN. Longitudinal quasispecies analysis of viral variants in HIV type 1 dually infected individuals highlights the importance of sequence identity in viral recombination. AIDS Res Hum Retroviruses 2010; 26:253-64. [PMID: 20334562 DOI: 10.1089/aid.2009.0174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Little is known regarding the likelihood of recombination between any given pair of nonidentical HIV-1 viruses in vivo. The present study analyzes the HIV-1 quasispecies in the C1C2 region of env, the vif-vpr-vpu accessory gene region, and the reverse transcriptase region of pol. These sequences were amplified from samples obtained sequentially over a 12- to 33-month period from five dually HIV-1-infected subjects. Analysis of an average of 248 clones amplified from each subject revealed no recombinants within the three loci studied of the subtype-discordant infecting strains, whose genetic diversity was >11% in env. In contrast, two subjects who were initially coinfected by two subtype-concordant variants with genetic diversity of 7.4% in env were found to harbor 10 unique recombinants of these strains, as exhibited by analysis of the env gene. The frequent recombination observed among the subtype-concordant strains studied herein correlates with prior sequence analyses that have commonly found higher rates of recombination at loci bearing the most conserved sequences, demonstrating an important role for sequence identity in HIV-1 recombination. Viral load analysis revealed that the samples studied contained an average of 8125 virus copies/ml (range, 882-31,626 copies/ml), signifying that the amount of viral RNA in the samples was not limiting for studying virus diversity. These data reveal that recombination between genetically distant strains may not be an immediate or common outcome to dual infection in vivo and suggest critical roles for viral and host factors such as viral fitness, virus diversity, and host immune responses that may contribute to limiting the frequency of intersubtype recombination during in vivo dual infection.
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Affiliation(s)
- Rebecca L.R. Powell
- Department of Microbiology, New York University School of Medicine, New York, New York
| | - Lynchy Lezeau
- Brooklyn College, The City University of New York, Brooklyn, New York
| | | | - Phillipe N. Nyambi
- Department of Pathology, New York University School of Medicine, New York, New York
- Veterans Affairs New York Harbor Healthcare Systems, New York, New York
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21
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Treurnicht FK, Seoighe C, Martin DP, Wood N, Abrahams MR, Rosa DDA, Bredell H, Woodman Z, Hide W, Mlisana K, Karim SA, Gray CM, Williamson C. Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure. Virology 2009; 396:213-25. [PMID: 19913270 DOI: 10.1016/j.virol.2009.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 07/21/2009] [Accepted: 10/04/2009] [Indexed: 01/12/2023]
Abstract
It is unresolved whether recently transmitted human immunodeficiency viruses (HIV) have genetic features that specifically favour their transmissibility. To identify potential "transmission signatures", we compared 20 full-length HIV-1 subtype C genomes from primary infections, with 66 sampled from ethnically and geographically matched individuals with chronic infections. Controlling for recombination and phylogenetic relatedness, we identified 39 sites at which amino acid frequency spectra differed significantly between groups. These sites were predominantly located within Env, Pol and Gag (14/39, 9/39 and 6/39 respectively) and were significantly clustered (33/39) within known immunoreactive peptides. Within 6 months of infection, we detected reversion-to-consensus mutations at 14 sites and potential CTL escape mutations at seven. Here we provide evidence that frequent reversion mutations probably allows the virus to recover replicative fitness which, together with immune escape driven by the HLA alleles of the new hosts, differentiate sequences from chronic infections from those sampled shortly after transmission.
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Affiliation(s)
- F K Treurnicht
- Institute of Infectious Diseases and Molecular Medicine (IIDMM), Division of Medical Virology, University of Cape Town, South Africa
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22
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Reichert AI, He XZ, Dixon RA. Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes. Biochem J 2009; 424:233-42. [PMID: 19725811 DOI: 10.1042/bj20090620] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PAL (L-phenylalanine ammonia-lyase), the first enzyme of phenylpropanoid biosynthesis, is often encoded by multigene families in plants. A PCR-based approach was used to isolate cDNA clones corresponding to the four PAL genes of tobacco (Nicotiana tabacum). By careful comparison of cDNA and genomic clones, a new PAL gene (PAL4) was defined. PCR amplification of PAL sequences from cDNA led to the generation of chimaeric clones between PAL1 and PAL4, and incorrect annotation of PAL4 ESTs (expressed sequence tags) as PAL1 in the EST database has given rise to a randomly shuffled tentative consensus sequence. The PAL2 previously described in the literature was shown, by domain swapping experiments with PAL1, to possess a single nucleotide substitution leading to an inactive enzyme. The altered amino acid resulting from this substitution maps to the base of the active site pocket in the three-dimensional structure of PAL. The inactive PAL2 allele could not be recovered from 13 different tobacco cultivars examined. PALs 1-4 were co-expressed in multiple plant organs, and were also co-induced following exposure of cell cultures to yeast elicitor or methyl jasmonate. All four tobacco PAL proteins expressed in Escherichia coli displayed normal Michaelis-Menten kinetics, with Km values between 36 and 60 muM. Co-expression of different PAL proteins in E. coli resulted in formation of heterotetramers, which possessed kinetic properties within the same range as those of the individual homotetramers. The potential physiological function of heterotetrameric PAL forms is discussed.
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Affiliation(s)
- Angelika I Reichert
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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23
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Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool. J Virol Methods 2009; 162:280-3. [PMID: 19698751 DOI: 10.1016/j.jviromet.2009.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 08/02/2009] [Accepted: 08/11/2009] [Indexed: 11/29/2022]
Abstract
Typically, population-based sequencing of HIV does not detect minority variants present at levels below 20-30%. Single genome amplification (SGA) and sequencing improves detection, but it requires many PCRs to find the optimal terminal dilution to use. A novel method for guiding the selection of a terminal dilution was developed and compared to standard methods. A quantitative real-time PCR (qRT-PCR) protocol was developed. HIV RNA was extracted, reverse transcribed, and quantitated. A bioinformatics web-based application was created for calculating the optimal concentration of cDNA to use based on results of a trial PCR using the dilution suggested by the qRT-PCR results. This method was compared to the standard. Using the standard protocol, the mean number of PCRs giving an average of 30 (26-34, SD=3) SGA per sample was 245 (218-266, SD=20) after an average of 8 trial dilutions. Using this method, 135 PCRs (135-135, SD=0) produced 30 (27-30, SD=1) SGA using exactly two dilutions. This new method reduced turnaround time from 8 to 2 days. Standard methods of SGA sequencing can be costly and both time- and labor-intensive. By choosing a terminal dilution concentration with the proposed method, the number of PCRs required is decreased and efficiency improved.
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Affiliation(s)
- David M Butler
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, Mail Code 0679, La Jolla, CA 92039, USA.
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24
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Templeton AR, Kramer MG, Jarvis J, Kowalski J, Gange S, Schneider MF, Shao Q, Zhang GW, Yeh MF, Tsai HL, Zhang H, Markham RB. Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women. Retrovirology 2009; 6:54. [PMID: 19493346 PMCID: PMC2700066 DOI: 10.1186/1742-4690-6-54] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 06/03/2009] [Indexed: 11/29/2022] Open
Abstract
Background Recombination between strains of HIV-1 only occurs in individuals with multiple infections, and the incidence of recombinant forms implies that multiple infection is common. Most direct studies indicate that multiple infection is rare. We determined the rate of multiple infection in a longitudinal study of 58 HIV-1 positive participants from The Women's Interagency HIV Study with a richer sampling design than previous direct studies, and we investigated the role of recombination and sampling design on estimating the multiple infection rate. Results 40% of our sample had multiple HIV-1 infections. This rate of multiple infection is statistically consistent with previous studies once differences in sampling design are taken into account. Injection drug use significantly increased the incidence of multiple infections. In general there was rapid elimination of secondary strains to undetectable levels, but in 3 cases a superinfecting strain displaced the initial infecting strain and in two cases the strains coexisted throughout the study. All but one secondary strain was detected as an inter- and/or intra-genic recombinant. Injection drug use significantly increased the rate of observed recombinants. Conclusion Our multiple infection rate is consistent with rates estimated from the frequency of recombinant forms of HIV-1. The fact that our results are also consistent with previous direct studies that had reported a much lower rate illustrates the critical role of sampling design in estimating this rate. Multiple infection and recombination significantly add to the genetic diversity of HIV-1 and its evolutionary potential, and injection drug use significantly increases both.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St Louis, Missouri, USA.
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25
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Kemal KS, Reinis M, Weiser B, Burger H. Methods for viral RNA isolation and PCR amplification for sequencing of near full-length HIV-1 genomes. Methods Mol Biol 2009; 485:3-14. [PMID: 19020814 DOI: 10.1007/978-1-59745-170-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
HIV-1 in plasma represents the viral quasispecies replicating in the patient at any given time. Studies of HIV-1 viral RNA from plasma or other body fluids therefore reflect the virus present in real time. To obtain near full-length genomic sequences derived from virion RNA it is first necessary to carefully isolate and amplify the RNA.The procedure described below, involves viral RNA extraction, reverse transcription (RT) of the extracted RNA to produce cDNA copies, and PCR amplification of long HIV-1 gene fragments using site-specific, overlapping primers. The primers are based on subtype B HIV-1 strains, and plasma specimens are used in the procedures. However, the protocol can easily be adapted to other HIV-1 subtypes by modifying the primers to match the subtype of interest.
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26
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Powell RLR, Urbanski MM, Nyambi PN. A heteroduplex assay for the rapid detection of dual Human Immunodeficiency Virus Type 1 infections. J Virol Methods 2008; 149:20-7. [PMID: 18314205 DOI: 10.1016/j.jviromet.2008.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 12/16/2022]
Abstract
The predominance of circulating and unique recombinant forms (URFs) of Human Immunodeficiency Virus Type 1 (HIV-1) in Cameroon suggests that dual infection occurs frequently in this region. Despite the potential impact of these infections on the evolution of HIV diversity, relatively few have been detected. The failure to detect dual infections may be attributable to the laborious and costly sequence analysis involved in their identification. As such, there is a need for a cost-effective, more rapid method to efficiently distinguish this subset of HIV-positive individuals, particularly in regions where HIV diversity is broad. In the present study, the heteroduplex assay (HDA) was developed to detect dual HIV-1 infection. This assay was validated on sequential specimens obtained from 20 HIV+ study subjects, whose single or dual infection status was determined by standard sequence analysis. By mixing gag fragments amplified from the sequential specimens from each study subject in HDA reactions, it was shown that single and dual infection status correlated with the absence and presence, respectively, of heteroduplex bands upon gel electrophoresis. Therefore, this novel assay is capable of identifying dual infections with a sensitivity and specificity equivalent to that of sequence analysis. Given the impact of dual infection on viral recombination and diversity, this simple technique will be beneficial to understanding HIV-1 evolution within an individual, as well as at a population level, in West-Central Africa and globally.
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Affiliation(s)
- Rebecca L R Powell
- Department of Microbiology, New York University School of Medicine, New York, NY 10010, USA
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27
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Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 2008; 82:3952-70. [PMID: 18256145 DOI: 10.1128/jvi.02660-07] [Citation(s) in RCA: 495] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating the transmission of human immunodeficiency virus type 1 (HIV-1) and in developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach to analyze HIV-1 env genes as intact genetic units amplified from plasma virion RNA by single-genome amplification (SGA), followed by direct sequencing of uncloned DNA amplicons. We show that this strategy precludes in vitro artifacts caused by Taq-induced nucleotide substitutions and template switching, provides an accurate representation of the env quasispecies in vivo, and has an overall error rate (including nucleotide misincorporation, insertion, and deletion) of less than 8 x 10(-5). Applying this method to the analysis of virus in plasma from 12 Zambian subjects from whom samples were obtained within 3 months of seroconversion, we show that transmitted or early founder viruses can be identified and that molecular pathways and rates of early env diversification can be defined. Specifically, we show that 8 of the 12 subjects were each infected by a single virus, while 4 others acquired more than one virus; that the rate of virus evolution in one subject during an 80-day period spanning seroconversion was 1.7 x 10(-5) substitutions per site per day; and that evidence of strong immunologic selection can be seen in Env and overlapping Rev sequences based on nonrandom accumulation of nonsynonymous mutations. We also compared the results of the SGA approach with those of more-conventional bulk PCR amplification methods performed on the same patient samples and found that the latter is associated with excessive rates of Taq-induced recombination, nucleotide misincorporation, template resampling, and cloning bias. These findings indicate that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately.
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28
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Nadai Y, Eyzaguirre LM, Constantine NT, Sill AM, Cleghorn F, Blattner WA, Carr JK. Protocol for nearly full-length sequencing of HIV-1 RNA from plasma. PLoS One 2008; 3:e1420. [PMID: 18183300 PMCID: PMC2170516 DOI: 10.1371/journal.pone.0001420] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 12/07/2007] [Indexed: 11/18/2022] Open
Abstract
Nearly full-length genome sequencing of HIV-1 using peripheral blood mononuclear cells (PBMC) DNA as a template for PCR is now a relatively routine laboratory procedure. However, this has not been the case when using virion RNA as the template and this has made full genome analysis of circulating viruses difficult. Therefore, a well-developed procedure for sequencing of full-length HIV-1 RNA directly from plasma was needed. Plasma from U.S. donors representing a range of viral loads (VL) was used to develop the assay. RNA was extracted from plasma and reverse-transcribed. Two or three overlapping regions were PCR amplified to cover the entire viral genome and sequenced for verification. The success of the procedure was sensitive to VL but was routinely successful for VL greater than 105 and the rate declined in proportion to the VL. While the two-amplicon strategy had an advantage of increasing the possibility of amplifying a single species of HIV-1, the three-amplicon strategy was more successful in amplifying samples with low viral loads. This protocol provides a useful tool for molecular analysis to understand the HIV epidemic and pathogenesis, as well as diagnosis, therapy and future vaccine strategies.
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Affiliation(s)
- Yuka Nadai
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Lindsay M. Eyzaguirre
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Niel T. Constantine
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Anne M. Sill
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | | | - William A. Blattner
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Jean K. Carr
- Department of Epidemiology, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Kirchherr JL, Lu X, Kasongo W, Chalwe V, Mwananyanda L, Musonda RM, Xia SM, Scearce RM, Liao HX, Montefiori DC, Haynes BF, Gao F. High throughput functional analysis of HIV-1 env genes without cloning. J Virol Methods 2007; 143:104-11. [PMID: 17416428 PMCID: PMC1948023 DOI: 10.1016/j.jviromet.2007.02.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/23/2007] [Accepted: 02/27/2007] [Indexed: 11/16/2022]
Abstract
Functional human immunodeficiency virus type 1 (HIV-1) env genes have been widely used for vaccine design, neutralization assays, and pathogenesis studies. However, obtaining bona fide functional env clones is a time consuming and labor intensive process. A new high throughput method has been developed to characterize HIV-1 env genes. Multiple rev/env gene cassettes were obtained from each of seven HIV-1 strains using single genome amplification (SGA) PCR. The cytomegalovirus (CMV) promoter was amplified separately by PCR. A promoter PCR (pPCR) method was developed to link both PCR products using an overlapping PCR method. Pseudovirions were generated by cotransfection of pPCR products and pSG3 Delta env backbone into 293T cells. After infecting TZM-bl cells, 75 out of 87 (86%) of the rev/env gene cassettes were functional. Pseudoviruses generated with pPCR products or corresponding plasmid DNA showed similar sensitivity to six HIV-1 positive sera and three monoclonal antibodies, suggesting neutralization properties are not altered in pPCR pseudovirions. Furthermore, sufficient amounts of pseudovirions can be obtained for a large number of neutralization assays. The new pPCR method eliminates cloning, transformation, and plasmid DNA preparation steps in the generation of HIV-1 pseudovirions. This allows for quick analysis of multiple env genes from HIV-1 infected individuals.
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Affiliation(s)
- Jennifer L Kirchherr
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Webster Kasongo
- The Tropical Disease Research Centre, PO Box 71769 Ndola, Zambia
| | - Victor Chalwe
- The Tropical Disease Research Centre, PO Box 71769 Ndola, Zambia
| | | | | | - Shi-Mao Xia
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Richard M Scearce
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - David C Montefiori
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Barton F Haynes
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Feng Gao
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
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30
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Reinis M, Weiser B, Kuiken C, Dong T, Lang D, Nachman S, Zhang Y, Rowland-Jones S, Burger H. Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressors. AIDS Res Hum Retroviruses 2007; 23:309-15. [PMID: 17331038 PMCID: PMC2925658 DOI: 10.1089/aid.2006.0180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate the viral features of long-term nonprogressive HIV-1 infection and the selection of viral genomes, we studied serial complete HIV-1 sequences obtained from a mother-child pair, both long-term nonprogressors. Analysis of four genomic sequences demonstrated that all viral genes were intact, lacking major deletions or premature stop codons to easily explain the slow disease progression. These data suggest that viral attenuation, if present, was caused by subtle sequence variations or virus-host interactions. Serial sequences from an HIV-1-infected mother-child pair afforded us the opportunity to examine the immune selection of HIV-1 sequences years after transmission between individuals. We demonstrated that the daughter's strains were most likely subjected to immunoselection or immunoediting according to the presence of novel MHC class I alleles that differed between mother and daughter. An analysis of nef-specific cytotoxic T-lymphocyte responses in the child, whose HIV-1 nef sequence differed from the maternal nef, supported this interpretation. This study highlights the potential of full genome analysis in the investigation of pathogenesis and immune selection during HIV-1 evolution.
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Affiliation(s)
- Milan Reinis
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
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31
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Cai F, Chen H, Hicks CB, Bartlett JA, Zhu J, Gao F. Detection of minor drug-resistant populations by parallel allele-specific sequencing. Nat Methods 2007; 4:123-5. [PMID: 17206150 DOI: 10.1038/nmeth995] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 11/09/2006] [Indexed: 01/06/2023]
Abstract
We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we successfully detected and quantified minor populations of drug-resistant viruses and performed linkage analysis of multiple-drug resistance mutations. This assay may serve as a useful tool to study drug resistance in HIV and other infectious agents.
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Affiliation(s)
- Fangping Cai
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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32
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Rousseau CM, Birditt BA, McKay AR, Stoddard JN, Lee TC, McLaughlin S, Moore SW, Shindo N, Learn GH, Korber BT, Brander C, Goulder PJR, Kiepiela P, Walker BD, Mullins JI. Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J Virol Methods 2006; 136:118-25. [PMID: 16701907 DOI: 10.1016/j.jviromet.2006.04.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 04/03/2006] [Accepted: 04/06/2006] [Indexed: 11/22/2022]
Abstract
Full-length HIV-1 genome sequencing provides important data needed to address several vaccine design, molecular epidemiologic and pathogenesis questions. A protocol is presented for obtaining near full-length genomes (NFLGs) from subjects infected with HIV-1 subtype C. This protocol was used to amplify NFLGs from 244 of 366 (67%) samples collected at two clinics in Durban, South Africa (SK and PS). Viral load was directly associated with frequency of successful NFLG amplification for both cohorts (PS; p = 0.005 and SK; p < 0.001). Seventeen of 38 initially NFLG-negative SK samples had variation within the PCR primer binding sites, however only 3 of these were successfully re-amplified using re-designed primers homologous to the target viruses. NFLGs were obtained from 7 of 24 PBMC samples processed from subjects whose plasma did not yield a NFLG. Stable plasmid clones were obtained from all 244 NFLG-positive PCR products, and both strands of each genome were sequenced, using a primary set of 46 primers. These methods thus allow the large-scale collection of HIV-1 NFLGs from populations infected primarily with subtype C. The methods are readily adaptable to other HIV-1 subtypes, and provide materials for viral functional analyses and population-based molecular epidemiology studies that include analysis of viral genome chimerization.
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Affiliation(s)
- Christine M Rousseau
- Department of Microbiology, University of Washington, Seattle, WA 98195-8070, USA.
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33
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Fan X, Xu Y, Di Bisceglie AM. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 2006; 346:1163-72. [PMID: 16793008 PMCID: PMC7092855 DOI: 10.1016/j.bbrc.2006.06.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/02/2006] [Indexed: 11/27/2022]
Abstract
Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1 kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Saint Louis University Liver Center, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63110, USA.
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Delaunay C, Brun-Vézinet F, Landman R, Collin G, Peytavin G, Trylesinski A, Flandre P, Miller M, Descamps D. Comparative selection of the K65R and M184V/I mutations in human immunodeficiency virus type 1-infected patients enrolled in a trial of first-line triple-nucleoside analog therapy (Tonus IMEA 021). J Virol 2005; 79:9572-8. [PMID: 16014919 PMCID: PMC1181609 DOI: 10.1128/jvi.79.15.9572-9578.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tonus was a pilot study in which previously untreated human immunodeficiency virus type 1 (HIV-1)-infected patients received the combination of abacavir, lamivudine, and tenofovir once a day. There was a high rate of early virological failure, and the M184V and K65R mutations were frequently detected at week 12 (W12). The objective of this study was to examine the selection dynamics of the K65R and M184V/I mutations. Bulk sequencing of the reverse transcriptase (RT) gene was performed on plasma HIV-1 RNA at baseline, W4, and W12 for 21 patients with detectable viral loads. The RT genes from baseline, W4, and W12 plasma samples from five patients who developed both M184V and K65R but with different mutational patterns were also cloned and screened for the K65R mutation by selective real-time PCR. At baseline, bulk sequencing and clonal analysis showed only wild-type RT sequences. At W4, M184V/I was detected in 12/19 patients and K65K/R in 2 patients by bulk sequencing. At W12, M184V/I was found in 18/20 patient, together with the K65R in 13 patients. At W4, clonal analysis revealed the K65R mutation in 0.6 to 48% of clones in the five patients studied. At W12, the K65R mutation was found in 30 to 100% of clones. K65R and M184V/I seemed to arise in separate clones, followed by an enrichment of viruses containing both mutations. The clinical relevance of this independent evolution is unclear. M184V/I was selected more frequently than K65R at W4. However, K65R was also detected early using a clone-sensitive genotyping method. All three nucleoside analogs are known to select the K65R and/or M184V/I mutation. This convergent genetic pathway to resistance, associated with lower antiretroviral potency, may explain the high selection rate of these mutations in this trial.
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35
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Schroeder TL, Burger H, Weiser B, Bengualid V, Kimani J, Anzala AO, Parker MM, Lamson D, Philpott SM. Characterization of intersubtype recombinant HIV type 1 genomes using a nonradioactive heteroduplex tracking assay. AIDS Res Hum Retroviruses 2005; 21:314-8. [PMID: 15943575 DOI: 10.1089/aid.2005.21.314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic is characterized by the dominance of distinct viral subtypes in different regions of the world, and intersubtype recombinants are common. Traditional subtyping methods analyze only a small fragment of the HIV-1 genome, so the true extent of diversity and recombination has been difficult to examine. We developed a heteroduplex tracking assay (HTA) to identify viral subtypes and rapidly detect recombinant HIV-1 genomes. By using probes that target seven regions across the HIV-1 genome, HTAs can identify intersubtype recombinants on the basis of the heteroduplex mobility pattern. We used this method to analyze HIV-1 strains from 12 patients from the United States and Kenya, comparing the results with those obtained by sequencing. HTA analysis correctly identified the subtype of each region of the genome, revealing that several isolates were recombinants. This method is suitable for studies of HIV-1 diversity and recombination in areas of the world where multiple subtypes are found.
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Affiliation(s)
- Tamara L Schroeder
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
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36
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Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C, Weiser B. Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol 2005; 79:353-63. [PMID: 15596829 PMCID: PMC538688 DOI: 10.1128/jvi.79.1.353-363.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.
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Affiliation(s)
- Sean Philpott
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
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37
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van Marle G, Power C. Human immunodeficiency virus type 1 genetic diversity in the nervous system: Evolutionary epiphenomenon or disease determinant? J Neurovirol 2005; 11:107-28. [PMID: 16036790 DOI: 10.1080/13550280590922838] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Over the past decade there has been a revolution in the understanding and care of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-associated disease. Much of this progress stems from a broader recognition of the importance of differences in viral types, including receptor preference(s), replication properties, and reservoirs, as contributing factors to immunosuppresion and disease progression. In contrast, there is limited conceptualizatin of viral diversity and turnover in the brain and circulation in relation to neurocognitive impairments. Herein, the authors review current concepts regarding viral molecular diversity and phenotypes together with features of HIV-1 neuroinvasion, neurotropism, neurovirulence and neurosusceptiblity. Viral genetic and antigenic diversity is reduced within the brain compared to blood or other systemic organs within individuals. Conversely, viral molecular heterogeneity is greater in patients with HIV-associated dementia compared to nondemented patients, depending on the viral gene examined. Individual viral proteins exert multiple neuropathogenic effects, although the neurological consequences of different viral polymorphisms remain uncertain. Nonetheless, host genetic polymorphisms clearly influence neurological disease outcomes and likely dictate both acquired and innate immune responses, which in turn shape viral evolution within the host. Emerging issues include widespread antiretroviral therapy resistance and increasing awareness of viral superinfections together with viral recombination, all of which are likely to impact on both HIV genetic variation and neuropathogenesis. With the persisting prevalence of HIV-induced neurocognitive disabilities, despite marked improvements in managing immunosuppression, it remains imperative to fully define and understand the mechanisms by which viral dynamics and diversity contribute to neurological disease, permitting the development of new therapeutic strategies.
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Affiliation(s)
- Guido van Marle
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
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38
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Kitchen CMR, Philpott S, Burger H, Weiser B, Anastos K, Suchard MA. Evolution of human immunodeficiency virus type 1 coreceptor usage during antiretroviral Therapy: a Bayesian approach. J Virol 2004; 78:11296-302. [PMID: 15452249 PMCID: PMC521818 DOI: 10.1128/jvi.78.20.11296-11302.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is substantial evidence for ongoing replication and evolution of human immunodeficiency virus type 1 (HIV-1), even in individuals receiving highly active antiretroviral therapy. Viral evolution in the presence of antiviral therapy needs to be considered when developing new therapeutic strategies. Phylogenetic analyses of HIV-1 sequences can be used for this purpose but may give rise to misleading results if rates of intrapatient evolution differ significantly. To improve analyses of HIV-1 evolution relevant to studies of pathogenesis and treatment, we developed a Bayesian hierarchical model that incorporates all available sequence data while simultaneously allowing the phylogenetic parameters of each patient to vary. We used this method to examine evolutionary changes in HIV-1 coreceptor usage in response to treatment. We examined patients whose viral populations exhibited a shift in coreceptor utilization in response to therapy. CXCR4 (X4) strains emerged in each patient but were suppressed following initiation of new antiretroviral regimens, so that CCR5-utilizing (R5) strains predominated. By phylogenetically reconstructing the evolutionary relationship of HIV-1 obtained longitudinally from each patient, it was possible to examine the origin of the reemergent R5 virus. Using our Bayesian hierarchical approach, we found that the reemergent R5 virus detectable after therapy was more closely related to the predecessor R5 virus than to the X4 strains. The Bayesian hierarchical approach, unlike more traditional methods, makes it possible to evaluate competing hypotheses across patients. This model is not limited to analyses of HIV-1 but can be used to elucidate evolutionary processes for other organisms as well.
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Affiliation(s)
- Christina M R Kitchen
- Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095-1772.
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Charpentier C, Dwyer DE, Mammano F, Lecossier D, Clavel F, Hance AJ. Role of minority populations of human immunodeficiency virus type 1 in the evolution of viral resistance to protease inhibitors. J Virol 2004; 78:4234-47. [PMID: 15047838 PMCID: PMC374292 DOI: 10.1128/jvi.78.8.4234-4247.2004] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) drug resistance results from the accumulation of mutations in the viral genes targeted by the drugs. These genetic changes, however, are commonly detected and monitored by techniques that only take into account the dominant population of plasma virus. Because HIV-1-infected patients harbor a complex and diverse mixture of virus populations, the mechanisms underlying the emergence and the evolution of resistance are not fully elucidated. Using techniques that allow the quantification of resistance mutations in minority virus species, we have monitored the evolution of resistance in plasma virus populations from patients failing protease inhibitor treatment. Minority populations with distinct resistance genotypes were detected in all patients throughout the evolution of resistance. The emergence of new dominant genotypes followed two possible mechanisms: (i) emergence of a new mutation in a currently dominant genotype and (ii) emergence of a new genotype derived from a minority virus species. In most cases, these population changes were associated with an increase in resistance at the expense of a reduction in replication capacity. Our findings provide a preliminary indication that minority viral species, which evolve independently of the majority virus population, can eventually become dominant populations, thereby serving as a reservoir of diversity and possibly accelerating the development of drug resistance.
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40
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Fang G, Weiser B, Kuiken C, Philpott SM, Rowland-Jones S, Plummer F, Kimani J, Shi B, Kaul R, Bwayo J, Anzala O, Burger H. Recombination following superinfection by HIV-1. AIDS 2004; 18:153-9. [PMID: 15075531 DOI: 10.1097/00002030-200401230-00003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND There is increasing recognition of recombinant HIV-1 strains globally, but it has been unclear whether recombination results from superinfection during untreated, chronic infection. OBJECTIVE To search for evidence of recombination and superinfection in Africa, where multiple HIV-1 subtypes facilitate identification of strains. METHODS Serial blood samples from highly exposed, chronically infected women in Nairobi's Pumwani sex workers cohort were examined. Serial, complete HIV-1 RNA sequence analyses were performed for seven untreated long-term survivors. Sequences were subjected to computational analysis. RESULTS One woman had evidence of both superinfection and recombination. Complete HIV-1 RNA sequences were first derived from plasma obtained in 1986, when the woman had been HIV seropositive for at least 21 months; this sequence was entirely subtype A. The sequences obtained from plasma in 1995 and 1997, however, were subtype A/C recombinants with a SimPlot demonstrating that the subtype A fragment in 1995 and 1997 was derived from the original 1986 A sequence. Heteroduplex tracking assays demonstrated that the subtype C sequences were not detectable as minor species in 1986. CONCLUSION Intersubtype recombination took place between the original non-recombinant subtype A strain and the superinfecting subtype C strain in an untreated, chronically infected woman. This finding helps to explain the rising prevalence of recombinant HIV-1 worldwide. Recombination resulting from superinfection with diverse strains may pose problems for eliciting broad immune responses necessary for an effective vaccine.
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Affiliation(s)
- Guowei Fang
- Wadsworth Center, NY State Department of Health, Albany, 12208, USA
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41
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Bernardin F, Herring BL, Peddada L, Delwart EL. Primary infection of a male plasma donor with divergent HIV variants from the same source followed by rapid fluctuations in their relative frequency and viral recombination. AIDS Res Hum Retroviruses 2003; 19:1009-15. [PMID: 14678608 DOI: 10.1089/088922203322588369] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The replication of two HIV-1 variants (>4.0% divergent in the env gene) was observed during primary infection of a frequent plasma donor. Phylogenetic analysis indicated that both HIV-1 variants likely originated from the same source. Heteroduplex tracking analysis of the env V3-V5 region indicated that one of these variant emerged in the plasma at the time of seroconversion, 15 days after the initial detection of HIV-1 RNA. Sequencing of the entire protein-coding region of plasma viruses from Days 2, 22, and 31 showed possible regions of recombination in the pol locus occurring within the first month of infection. The very rapid fluctuations of HIV-1 variant frequencies and their recombination during primary infection may reflect changes in their relative fitness in the face of developing immunological responses.
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Affiliation(s)
- Flavien Bernardin
- Department of Medicine, University of California, San Francisco, California 94118, USA
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42
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Kemal KS, Foley B, Burger H, Anastos K, Minkoff H, Kitchen C, Philpott SM, Gao W, Robison E, Holman S, Dehner C, Beck S, Meyer WA, Landay A, Kovacs A, Bremer J, Weiser B. HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation. Proc Natl Acad Sci U S A 2003; 100:12972-7. [PMID: 14557540 PMCID: PMC240729 DOI: 10.1073/pnas.2134064100] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Worldwide, 90% of HIV-1 infections are transmitted heterosexually. Because the genital mucosa are the sites of initial contact with HIV-1 for most exposed individuals, study of the virus from the genital tract is critical for the development of vaccines and therapeutics. Previous analyses of HIV-1 in various tissues have documented compartmentalization of viral genomes. Whether compartmentalization was associated with viral phenotypic differences or immune status, however, was not well understood. We compared HIV-1 gp120 env sequences from the genital tract and plasma of 12 women. Eight women displayed compartmentalized HIV-1 RNA genomes, with viral sequences from each site that were clearly discrete, yet phylogenetically related. The remaining four exhibited env sequences that were intermingled between the two sites. Women with compartmentalized HIV-1 genomes had higher CD4+ cell counts than those displaying intermingled strains (P = 0.02). Intrapatient HIV-1 recombinants comprising sequences that were characteristic of both sites were identified. We next compared viral phenotypes in each compartment. HIV-1 coreceptor usage was often compartmentalized (P 0.01). The number of N-linked glycosylation sites, associated with neutralization resistance, also differed between compartments (P < 0.01). Furthermore, disparities between the density of gp120 glycosylations in each compartment correlated with higher CD4+ counts (P = 0.03). These data demonstrate that the genital tract and plasma can harbor populations of replicating HIV-1 with different phenotypes. The association of higher CD4+ cell counts with compartmentalization of viral genomes and density of gp120 glycosylations suggests that the immune response influences the development of viral genotypes in each compartment. These findings are relevant to the prevention and control of HIV-1 infection.
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Affiliation(s)
- Kimdar Sherefa Kemal
- New York State Department of Health, Wadsworth Center, 120 New Scotland Avenue, Albany, NY 12208, USA
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Ait-Khaled M, Rakik A, Griffin P, Stone C, Richards N, Thomas D, Falloon J, Tisdale M. HIV-1 Reverse Transcriptase and Protease Resistance Mutations Selected during 16–72 Weeks of Therapy in Isolates from Antiretroviral Therapy-Experienced Patients Receiving Abacavir/Efavirenz/Amprenavir in the CNA2007 Study. Antivir Ther 2003. [DOI: 10.1177/135965350300800205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective To determine HIV-1 reverse transcriptase (RT) and protease (PRO) mutations selected in isolates from antiretroviral therapy (ART)-experienced patients receiving an efavirenz/abacavir/amprenavir salvage regimen. Methods Open-label, single arm of abacavir, 300 mg twice daily, amprenavir, 1200 mg twice daily and efavirenz, 600 mg once daily, in ART-experienced patients of which 42% were non-nucleoside reverse transcriptase inhibitor-naive. The virology population examined consisted of all patients who took at least 16 weeks of study drugs (n=74). Plasma population sequencing was carried out at baseline and last time point at which patients were still taking the three study drugs ± other ART. The median follow-up was 48 weeks (range week 16–72). Results Baseline (n=73) and on-therapy (n=49) genotypes were obtained. By 48 weeks, 51% of isolates had ≥3 non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations. NNRTI mutations selected on therapy were K103N (51%), substitutions at position 190 (17/49, 35%): G to A (n=11) / S (n=4) / E (n=1) and T (n=1); L100I (37%) and V108I (20%) mutations. P225H was not observed in this study. L100I and G190A/S/E/T mutations were rarely detected in the same viral population and baseline Y181C favoured the G190 mutations (OR=8.9, P<0.001), rather than the L100I. The NRTI mutations selected were in accordance with abacavir known resistance profile, no new TAMs were observed, new L74V or I mutations developed in 39 and 16% of isolates, respectively, however, new M184V mutations were only detected in isolates from two patients, one of whom had added lamivudine + didanosine. M184V was common at baseline (55%) and maintained in 22/27 (81%) isolates (five of these 22 added lamivudine or didanosine, or both). The PRO mutations selected were in accordance with the distinct resistance profile of amprenavir compared with other protease inhibitors. Mutations D30N, G48V, N88D/S, L90M and I54V were de-selected, and mutations I50V, I or V to 54M/L, I84V, M46I/L, L33F, I47V as well mutations at position 10 were observed in 20/49 (41%) isolates. Conclusion Prior NNRTI and NRTI therapy influences the pathway of resistance to efavirenz. In this study, the prevalence of mutations selected by efavirenz were different from those described in less ART-experienced patients. Baseline Y181C was associated with the development of mutations at position 190, but not L100I or K103N. In this patient population, abacavir with efavirenz preferentially selected for L74V but not for thymidine analogue mutations. M184V was rarely selected and was maintained in only 77% of patients who did not add lamivudine or didanosine. Finally, amprenavir-specific mutations were selected in the background of other primary protease inhibitor mutations, confirming the distinct resistance profile of amprenavir.
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Affiliation(s)
- Mounir Ait-Khaled
- GlaxoSmithKline, HIV Clinical Development and Medical Affairs Europe, Greenford, UK
| | | | - Philip Griffin
- GlaxoSmithKline, International Clinical Virology, Stevenage, UK
| | - Chris Stone
- GlaxoSmithKline, International Clinical Virology, Stevenage, UK
| | | | - Deborah Thomas
- GlaxSmithKline, North American Medical Affairs, Research Triangle Park, NC, USA
| | - Judith Falloon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md., USA
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Iglesias-Sánchez MJ, López-Galíndez C. Analysis, quantification, and evolutionary consequences of HIV-1 in vitro recombination. Virology 2002; 304:392-402. [PMID: 12504578 DOI: 10.1006/viro.2002.1657] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HIV-1 recombination was studied in vitro by viral cocultivation of four combinations of strains of subtypes B, D, and F. Viral cocultivations were performed in MT-4 cells and maintained for 22 days. The parental and recombinant forms were quantified by a specific PCR system in an env fragment of 2500 nucleotides. On day 5, there was a close correlation between the proportion of recombination and the genetic distance between strains. In three of the four viral combinations studied, a steady increase in the proportion of recombinant genomes was observed over time. This rise coincided with the progressive loss of one of the parental strains, resulting in less diverse viral populations. Nucleotide sequencing of biological recombinant clones from the B/D cocultivation revealed a higher number of recombination events in pol than in env gene, and an increasing number of crossovers per clone with time.
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Fang G, Burger H, Chappey C, Rowland-Jones S, Visosky A, Chen CH, Moran T, Townsend L, Murray M, Weiser B. Analysis of transition from long-term nonprogressive to progressive infection identifies sequences that may attenuate HIV type 1. AIDS Res Hum Retroviruses 2001; 17:1395-404. [PMID: 11679152 DOI: 10.1089/088922201753197060] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Long-term nonprogressive human immunodeficiency virus type 1 (HIV-1) infection and its transition to progressive infection presents an opportunity to identify the molecular determinants of HIV-1 attenuation and pathogenesis. We studied an individual who underwent a transition from long-term nonprogressive to rapidly progressive infection. Because HIV-1 RNA genomes in plasma represent replicating virus, we developed a technique to clone full-length HIV-1 RNA genomes from plasma and used this technique to obtain clones from this individual before and during the transition. Most clones assayed were infectious, demonstrating that the RNA genomes encoded viable virus. Analysis of 20 complete HIV-1 RNA genomic sequences revealed one major difference between sequences found during the two phases of infection. During the nonprogressive phase, the predominant sequences had a large deletion in an Sp1-binding site and adjacent promoter in the U3 part of the long terminal repeat (LTR); when the infection became progressive, all viruses had intact Sp1 and promoter sequences and were derived from a minor species present earlier. Analysis of 184 clones of the LTR region obtained at five time points spanning a 7-year period confirmed this switch. In an in vitro assay, the deletion downregulated LTR-driven transcription of a reporter gene. In addition, analysis of cytotoxic T lymphocyte (CTL) epitopes predicted from the complete viral RNA genomes revealed multiple potential escape mutants that accumulated by the time of progression. These studies suggest that during the nonprogressive phase, the Sp1 enhancer-promoter deletion is likely to have played a role in decreasing replication, thereby attenuating HIV-1. The accumulation of CTL escape mutants suggests that a breakdown in immunologic surveillance may have allowed proliferation of intact virus, thus leading to rapid disease progression. These data reveal the viral and immune interactions characterizing a transition from long-term nonprogressive to rapidly progressive infection.
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Affiliation(s)
- G Fang
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA
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Hance AJ, Lemiale V, Izopet J, Lecossier D, Joly V, Massip P, Mammano F, Descamps D, Brun-Vézinet F, Clavel F. Changes in human immunodeficiency virus type 1 populations after treatment interruption in patients failing antiretroviral therapy. J Virol 2001; 75:6410-7. [PMID: 11413308 PMCID: PMC114364 DOI: 10.1128/jvi.75.14.6410-6417.2001] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and protease that confer resistance to antiretroviral agents are usually accompanied by a reduction in the viral replicative capacity under drug-free conditions. Consequently, when antiretroviral treatment is interrupted in HIV-1-infected patients harboring drug-resistant virus, resistant quasi-species appear to be most often replaced within several weeks by wild-type virus. Using a real-time PCR-based technique for the selective quantification of resistant viral sequences in plasma, we have studied the kinetics of the switch from mutant to wild-type virus and evaluated the extent to which minority populations of resistant viruses not detected by genotyping persist in these individuals. Among 12 patients with viruses expressing the V82A or L90M resistance mutation who had undergone a 3-month interruption of therapy and for whom conventional genotyping had revealed an apparent total reconversion to wild-type virus, minority populations expressing these mutations, representing 0.1 to 21% of total virus, were still detectable in 9 cases. Kinetic studies demonstrated that viruses expressing resistance mutations could be detected for >5 months after the discontinuation of treatment in some patients. Most of the minority resistant genomes detected more than 3 months after the interruption of therapy carried only part of the mutations present in the resistant viruses prior to treatment interruption and appeared to result from the emergence of existing strains selected at earlier stages in the development of drug resistance. Thus, following the interruption of treatment, viral populations containing resistance mutations can persist for several months after the time when conventional genotyping techniques detect only wild-type virus. These populations include viral strains with only some of the resistance mutations initially present, strains that presumably express better fitness under drug-free conditions.
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Affiliation(s)
- A J Hance
- INSERM U552, Hôpital Bichat-Claude Bernard, 46, rue Henri Huchard, 75018 Paris, France.
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