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Adaptive Immune Responses, Immune Escape and Immune-Mediated Pathogenesis during HDV Infection. Viruses 2022; 14:v14020198. [PMID: 35215790 PMCID: PMC8880046 DOI: 10.3390/v14020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/13/2022] Open
Abstract
The hepatitis delta virus (HDV) is the smallest known human virus, yet it causes great harm to patients co-infected with hepatitis B virus (HBV). As a satellite virus of HBV, HDV requires the surface antigen of HBV (HBsAg) for sufficient viral packaging and spread. The special circumstance of co-infection, albeit only one partner depends on the other, raises many virological, immunological, and pathophysiological questions. In the last years, breakthroughs were made in understanding the adaptive immune response, in particular, virus-specific CD4+ and CD8+ T cells, in self-limited versus persistent HBV/HDV co-infection. Indeed, the mechanisms of CD8+ T cell failure in persistent HBV/HDV co-infection include viral escape and T cell exhaustion, and mimic those in other persistent human viral infections, such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), and HBV mono-infection. However, compared to these larger viruses, the small HDV has perfectly adapted to evade recognition by CD8+ T cells restricted by common human leukocyte antigen (HLA) class I alleles. Furthermore, accelerated progression towards liver cirrhosis in persistent HBV/HDV co-infection was attributed to an increased immune-mediated pathology, either caused by innate pathways initiated by the interferon (IFN) system or triggered by misguided and dysfunctional T cells. These new insights into HDV-specific adaptive immunity will be discussed in this review and put into context with known well-described aspects in HBV, HCV, and HIV infections.
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McMullen K, Bateman K, Stanley A, Combrinck M, Engelbrecht S, Bryer A. Viral protein R polymorphisms in the pathogenesis of HIV-associated acute ischaemic stroke: a case-control study. J Neurovirol 2021; 27:137-144. [PMID: 33462790 DOI: 10.1007/s13365-020-00936-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022]
Abstract
HIV-1 viral proteins have been implicated in endothelial dysfunction, which is a major determinant of ischaemic stroke risk in HIV-infected individuals. Polymorphisms in HIV-1 viral protein R (Vpr) may alter its potential to promote endothelial dysfunction, by modifying its effects on viral replication, reactivation of latent cells, upregulation of pro-inflammatory cytokines and infection of macrophages. We analysed Vpr polymorphisms and their association with acute ischaemic stroke by comparing Vpr signature amino acids between 54 HIV-infected individuals with acute ischaemic stroke, and 80 age-matched HIV-infected non-stroke controls. Isoleucine at position 22 and serine at position 41 were associated with ischaemic stroke in HIV. Individuals with stroke had lower CD4 counts and CD4 nadirs than controls. These polymorphisms are unique to individuals with stroke compared to South African subtype C and the control group consensus sequences. Signature Vpr polymorphisms are associated with acute ischaemic stroke in HIV. These may increase stroke risk by promoting endothelial dysfunction and susceptibility to opportunistic infections. Therapeutic targeting of HIV-1 viral proteins may present an additional mechanism of decreasing stroke risk in HIV-infected individuals.
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Affiliation(s)
- Kate McMullen
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
| | - Kathleen Bateman
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Alan Stanley
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Marc Combrinck
- Division of Geriatric Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Services, Cape Town, South Africa
| | - Alan Bryer
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
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Yin L, Chang KF, Nakamura KJ, Kuhn L, Aldrovandi GM, Goodenow MM. Unique genotypic features of HIV-1 C gp41 membrane proximal external region variants during pregnancy relate to mother-to-child transmission via breastfeeding. JOURNAL OF CLINICAL PEDIATRICS AND NEONATOLOGY 2021; 1:9-20. [PMID: 34553192 PMCID: PMC8454918 DOI: 10.46439/pediatrics.1.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mother-to-child transmission (MTCT) through breastfeeding remains a major source of pediatric HIV-1 infection worldwide. To characterize plasma HIV-1 subtype C populations from infected mothers during pregnancy that related to subsequent breast milk transmission, an exploratory study was designed to apply next generation sequencing and a custom bioinformatics pipeline for HIV-1 gp41 extending from heptad repeat region 2 (HR2) through the membrane proximal external region (MPER) and the membrane spanning domain (MSD). MPER harbors linear and highly conserved epitopes that repeatedly elicits HIV-1 neutralizing antibodies with exceptional breadth. Viral populations during pregnancy from women who transmitted by breastfeeding, compared to those who did not, displayed greater biodiversity, more frequent amino acid polymorphisms, lower hydropathy index and greater positive charge. Viral characteristics were restricted to MPER, failed to extend into flanking HR2 or MSD regions, and were unrelated to predicted neutralization resistance. Findings provide novel parameters to evaluate an association between maternal MPER variants present during gestation and lactogenesis with subsequent transmission outcomes by breastfeeding. IMPORTANCE HIV-1 transmission through breastfeeding accounts for 39% of MTCT and continues as a major route of pediatric infection in developing countries where access to interventions for interrupting transmission is limited. Identifying women who are likely to transmit HIV-1 during breastfeeding would focus therapies, such as broad neutralizing HIV monoclonal antibodies (bn-HIV-Abs), during the breastfeeding period to reduce MTCT. Findings from our pilot study identify novel characteristics of gestational viral MPER quasispecies related to transmission outcomes and raise the possibility for predicting MTCT by breastfeeding based on identifying mothers with high-risk viral populations.
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Affiliation(s)
- Li Yin
- Molecular HIV Host Interaction Section, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Kai-Fen Chang
- Molecular HIV Host Interaction Section, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | | | - Louise Kuhn
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Grace M. Aldrovandi
- Department of Pediatrics, Sabin Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Maureen M. Goodenow
- Molecular HIV Host Interaction Section, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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5
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Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS Comput Biol 2018; 14:e1006498. [PMID: 30543621 PMCID: PMC6314628 DOI: 10.1371/journal.pcbi.1006498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/02/2019] [Accepted: 09/10/2018] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing of viral populations has advanced our understanding of viral population dynamics, the development of drug resistance, and escape from host immune responses. Many applications require complete gene sequences, which can be impossible to reconstruct from short reads. HIV env, the protein of interest for HIV vaccine studies, is exceptionally challenging for long-read sequencing and analysis due to its length, high substitution rate, and extensive indel variation. While long-read sequencing is attractive in this setting, the analysis of such data is not well handled by existing methods. To address this, we introduce FLEA (Full-Length Envelope Analyzer), which performs end-to-end analysis and visualization of long-read sequencing data. FLEA consists of both a pipeline (optionally run on a high-performance cluster), and a client-side web application that provides interactive results. The pipeline transforms FASTQ reads into high-quality consensus sequences (HQCSs) and uses them to build a codon-aware multiple sequence alignment. The resulting alignment is then used to infer phylogenies, selection pressure, and evolutionary dynamics. The web application provides publication-quality plots and interactive visualizations, including an annotated viral alignment browser, time series plots of evolutionary dynamics, visualizations of gene-wide selective pressures (such as dN/dS) across time and across protein structure, and a phylogenetic tree browser. We demonstrate how FLEA may be used to process Pacific Biosciences HIV env data and describe recent examples of its use. Simulations show how FLEA dramatically reduces the error rate of this sequencing platform, providing an accurate portrait of complex and variable HIV env populations. A public instance of FLEA is hosted at http://flea.datamonkey.org. The Python source code for the FLEA pipeline can be found at https://github.com/veg/flea-pipeline. The client-side application is available at https://github.com/veg/flea-web-app. A live demo of the P018 results can be found at http://flea.murrell.group/view/P018. Viral populations constantly evolve and diversify. In this article we introduce a method, FLEA, for reconstructing and visualizing the details of evolutionary changes. FLEA specifically processes data from sequencing platforms that generate reads that are long, but error-prone. To study the evolutionary dynamics of entire genes during viral infection, data is collected via long-read sequencing at discrete time points, allowing us to understand how the virus changes over time. However, the experimental and sequencing process is imperfect, so the resulting data contain not only real evolutionary changes, but also mutations and other genetic artifacts caused by sequencing errors. Our method corrects most of these errors by combining thousands of erroneous sequences into a much smaller number of unique consensus sequences that represent biologically meaningful variation. The resulting high-quality sequences are used for further analysis, such as building an evolutionary tree that tracks and interprets the genetic changes in the viral population over time. FLEA is open source, and is freely available online.
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Fountain-Jones NM, Packer C, Troyer JL, VanderWaal K, Robinson S, Jacquot M, Craft ME. Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions. J Anim Ecol 2017; 86:1469-1482. [PMID: 28884827 DOI: 10.1111/1365-2656.12751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/14/2017] [Indexed: 11/29/2022]
Abstract
Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. Here, we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype-specific transmission pathways in a social carnivore. We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle ) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father- and/or mother-offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype-specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks or co-infection best structured the FIVPle network. While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype-specific. Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
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Affiliation(s)
| | - Craig Packer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN, USA
| | | | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
| | - Stacie Robinson
- National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Maude Jacquot
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
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Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations. Sci Rep 2017; 7:3534. [PMID: 28615687 PMCID: PMC5471223 DOI: 10.1038/s41598-017-03581-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/09/2017] [Indexed: 01/12/2023] Open
Abstract
Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.
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8
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Hayashida T, Tsuchiya K, Kikuchi Y, Oka S, Gatanaga H. Emergence of CXCR4-tropic HIV-1 variants followed by rapid disease progression in hemophiliac slow progressors. PLoS One 2017; 12:e0177033. [PMID: 28472121 PMCID: PMC5417636 DOI: 10.1371/journal.pone.0177033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The association between emergence of CXCR4-tropic HIV-1 variants (X4 variants) and disease progression of HIV-1 infection has been reported. However, it is not known whether the emergence of X4 variants is the cause or result of HIV-1 disease progression. We tried to answer this question. DESIGN HIV-1 env sequences around the V3 region were analyzed in serially stocked samples in order to determine whether X4 variants emerged before or after the fall in CD4+ T-cell count. METHODS The study subjects were five HIV-1-infected hemophiliac slow progressors. Deep sequencing around the HIV-1 env V3 region was conducted in duplicate. Tropism was predicted by geno2pheno [coreceptor] 2.5 with cutoff value of false positive ratio at <5%. When X4 variant was identified in the latest stocked sample before the introduction of antiretroviral therapy, we checked viral genotype in previously stocked samples to determine the time of emergence of X4 variants. RESULTS Emergence of X4 variants was noted in two of the five patients when their CD4+ T-cell counts were still high. The rate of decrease of CD4+ T-cell count or of rise of HIV-1 load accelerated significantly after the emergence of X4 variants in these two cases. Phylogenetic analysis showed that these X4 variants emerged from CCR5-tropic HIV-1 viruses with several amino acid changes in the V3 region. CONCLUSIONS The emergence of X4 variants preceded HIV-1 disease progression in two hemophiliac slow progressors.
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Affiliation(s)
- Tsunefusa Hayashida
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshimi Kikuchi
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
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9
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Lin YY, Hsieh CH, Chen JH, Lu X, Kao JH, Chen PJ, Chen DS, Wang HY. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. BMC Bioinformatics 2017; 18:223. [PMID: 28446139 PMCID: PMC5406902 DOI: 10.1186/s12859-017-1630-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
Background The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. Results In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Conclusions Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1630-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- You-Yu Lin
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan. .,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan.
| | - Chia-Hung Hsieh
- Department of Forestry and Nature Conservation, Chinese Culture University, Taipei, 111, Taiwan
| | - Jiun-Hong Chen
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Xuemei Lu
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Ding-Shinn Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 100, Taiwan.
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10
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Meng F, Dong X, Hu T, Liu Y, Zhao Y, Lv Y, Chang S, Zhao P, Cui Z. Analysis of Quasispecies of Avain Leukosis Virus Subgroup J Using Sanger and High-throughput Sequencing. Virol J 2016; 13:112. [PMID: 27350157 PMCID: PMC4924251 DOI: 10.1186/s12985-016-0559-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/09/2016] [Indexed: 01/14/2023] Open
Abstract
Background Avian leukosis viruses subgroup J (ALV-J) exists as a complex mixture of different, but closely related genomes named quasispecies subjected to continuous change according to the Principles of Darwinian evolution. Method The present study seeks to compare conventional Sanger sequencing with deep sequencing using MiSeq platform to study quasispecies dynamics of ALV-J. Results The accuracy and reproducibility of MiSeq sequencing was determined better than Sanger sequencing by running each experiment in duplicate. According to the mutational rate of single position and the ability to distinguish dominant quasispecies with two sequencing methods, conventional Sanger sequencing technique displayed high randomness due to few sequencing samples, while deep sequencing could reflect the composition of the quasispecies more accurately. In the mean time, the research of quasispecies via Sanger sequencing was simulated and analyzed with the aid of re-sampling strategy with replacement for 1000 times repeat from high-throughput sequencing data, which indicated that the higher antibody titer, the higher sequence entropy, the harder analyzing with the conventional Sanger sequencing, resulted in lower ratios of dominant variants. Conclusions In sum, deep sequencing is better suited for detecting rare variants comprehensively. The simulation of Sanger sequencing that we propose here will also help to standardize quasispecies researching under different selection pressure based on next-generation sequencing data.
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Affiliation(s)
- Fanfeng Meng
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Xuan Dong
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Tao Hu
- Institute of Pathogen Biology, Taishan Medical College, Taian, 271000, China
| | - Yingnan Liu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Yingjie Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Yanyan Lv
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
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11
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Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA. Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2016; 3:e251. [PMID: 27340685 PMCID: PMC4907805 DOI: 10.1212/nxi.0000000000000251] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 12/13/2022]
Abstract
Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected CNS infections. Methods: In a prospective pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from 10 patients with neurologic problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in 3 patients for whom validation techniques confirmed the pathogens identified by NGS. Although NGS was unable to identify with precision infectious agents in the remaining cases, it contributed to the understanding of neuropathologic processes in 5 others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in 8 of 10 cases, and were noncontributory in the remaining 2. Conclusions: NGS-guided metagenomic studies of brain, spinal cord, or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.
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Affiliation(s)
- Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Anupama Kumar
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Haiping Hao
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Peter Burger
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Fausto J Rodriguez
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Michael Lim
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Alfredo Quiñones-Hinojosa
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Gary L Gallia
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Jeffrey A Tornheim
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Michael T Melia
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Cynthia L Sears
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
| | - Carlos A Pardo
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD
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12
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Lloyd SB, Lichtfuss M, Amarasena TH, Alcantara S, De Rose R, Tachedjian G, Alinejad-Rokny H, Venturi V, Davenport MP, Winnall WR, Kent SJ. High fidelity simian immunodeficiency virus reverse transcriptase mutants have impaired replication in vitro and in vivo. Virology 2016; 492:1-10. [PMID: 26896929 DOI: 10.1016/j.virol.2016.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/15/2022]
Abstract
The low fidelity of HIV replication facilitates immune and drug escape. Some reverse transcriptase (RT) inhibitor drug-resistance mutations increase RT fidelity in biochemical assays but their effect during viral replication is unclear. We investigated the effect of RT mutations K65R, Q151N and V148I on SIV replication and fidelity in vitro, along with SIV replication in pigtailed macaques. SIVmac239-K65R and SIVmac239-V148I viruses had reduced replication capacity compared to wild-type SIVmac239. Direct virus competition assays demonstrated a rank order of wild-type>K65R>V148I mutants in terms of viral fitness. In single round in vitro-replication assays, SIVmac239-K65R demonstrated significantly higher fidelity than wild-type, and rapidly reverted to wild-type following infection of macaques. In contrast, SIVmac239-Q151N was replication incompetent in vitro and in pigtailed macaques. Thus, we showed that RT mutants, and specifically the common K65R drug-resistance mutation, had impaired replication capacity and higher fidelity. These results have implications for the pathogenesis of drug-resistant HIV.
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Affiliation(s)
- Sarah B Lloyd
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Marit Lichtfuss
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Thakshila H Amarasena
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Robert De Rose
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Gilda Tachedjian
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | | | - Vanessa Venturi
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Wendy R Winnall
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia.
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13
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Homs M, Rodriguez-Frias F, Gregori J, Ruiz A, Reimundo P, Casillas R, Tabernero D, Godoy C, Barakat S, Quer J, Riveiro-Barciela M, Roggendorf M, Esteban R, Buti M. Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection. PLoS One 2016; 11:e0158557. [PMID: 27362848 PMCID: PMC4928832 DOI: 10.1371/journal.pone.0158557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/19/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV) quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD) treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg). The amber codon encodes the small (unedited) HDAg form and the W codon the large (edited) HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (p<0.05). An accumulation of transition-type changes was found to be responsible for higher evolution rates. The percentages of unedited and edited genomes and the quasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.
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Affiliation(s)
- Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- * E-mail:
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Spain
| | - Alicia Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Pilar Reimundo
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Cristina Godoy
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Salma Barakat
- Gastroenterology Department, National Centre for Gastrointestinal and Liver disease, Khartoum, Sudan
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Diseases Unit, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Michael Roggendorf
- Institut of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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14
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Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One 2015; 10:e0141723. [PMID: 26599538 PMCID: PMC4658132 DOI: 10.1371/journal.pone.0141723] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/12/2015] [Indexed: 02/06/2023] Open
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Michael G Berg
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Beniwende Kabre
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine A Brennan
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - John Hackett
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
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15
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Nascimento-Brito S, Paulo Zukurov J, Maricato JT, Volpini AC, Salim ACM, Araújo FMG, Coimbra RS, Oliveira GC, Antoneli F, Janini LMR. HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA. PLoS One 2015; 10:e0139037. [PMID: 26413773 PMCID: PMC4587555 DOI: 10.1371/journal.pone.0139037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/07/2015] [Indexed: 01/19/2023] Open
Abstract
In order to establish new infections HIV-1 particles need to attach to receptors expressed on the cellular surface. HIV-1 particles interact with a cell membrane receptor known as CD4 and subsequently with another cell membrane molecule known as a co-receptor. Two major different co-receptors have been identified: C-C chemokine Receptor type 5 (CCR5) and C-X-C chemokine Receptor type 4 (CXCR4) Previous reports have demonstrated cellular modifications upon HIV-1 binding to its co-receptors including gene expression modulations. Here we investigated the effect of viral binding to either CCR5 or CXCR4 co-receptors on viral diversity after a single round of reverse transcription. CCR5 and CXCR4 pseudotyped viruses were used to infect non-stimulated and stimulated PBMCs and purified CD4 positive cells. We adopted the SOLiD methodology to sequence virtually the entire proviral DNA from all experimental infections. Infections with CCR5 and CXCR4 pseudotyped virus resulted in different patterns of genetic diversification. CCR5 virus infections produced extensive proviral diversity while in CXCR4 infections a more localized substitution process was observed. In addition, we present pioneering results of a recently developed method for the analysis of SOLiD generated sequencing data applicable to the study of viral quasi-species. Our findings demonstrate the feasibility of viral quasi-species evaluation by NGS methodologies. We presented for the first time strong evidence for a host cell driving mechanism acting on the HIV-1 genetic variability under the control of co-receptor stimulation. Additional investigations are needed to further clarify this question, which is relevant to viral diversification process and consequent disease progression.
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Affiliation(s)
- Sieberth Nascimento-Brito
- Departamento de Microbiologia e Imunologia Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Rio de Janeiro, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Juliana T. Maricato
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Angela C. Volpini
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Anna Christina M. Salim
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Flávio M. G. Araújo
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Roney S. Coimbra
- Biosystems Informatics Group, CPqRR, FIOCRUZ, Belo Horizonte, Brazil
| | - Guilherme C. Oliveira
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, EPM, UNIFESP, São Paulo, Brazil
- Laboratório de Biocomplexidade e Genômica Evolutiva, EPM, UNIFESP, São Paulo, Brazil
| | - Luiz Mário R. Janini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Departamento de Medicina, EPM, UNIFESP, São Paulo, Brazil
- * E-mail:
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16
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Isakov O, Bordería AV, Golan D, Hamenahem A, Celniker G, Yoffe L, Blanc H, Vignuzzi M, Shomron N. Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum. ACTA ACUST UNITED AC 2015; 31:2141-50. [PMID: 25701575 PMCID: PMC4481840 DOI: 10.1093/bioinformatics/btv101] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 02/11/2015] [Indexed: 12/22/2022]
Abstract
Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Availability and implementation: Freely available on the web at http://www.vivanbioinfo.org Contact: nshomron@post.tau.ac.il Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Antonio V Bordería
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amir Hamenahem
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liron Yoffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hervé Blanc
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marco Vignuzzi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Bioinformatics tools for the investigation of viral evolution and molecular epidemiology. INFECTION GENETICS AND EVOLUTION 2014; 28:349-50. [PMID: 25471675 DOI: 10.1016/j.meegid.2014.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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19
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Abstract
The notoriously low fidelity of HIV-1 replication is largely responsible for the virus's rapid mutation rate, facilitating escape from immune or drug control. The error-prone activity of the viral reverse transcriptase (RT) is predicted to be the most influential mechanism for generating mutations. The low fidelity of RT has been successfully exploited by nucleoside and nucleotide analogue reverse transcriptase inhibitors (NRTIs) that halt viral replication upon incorporation. Consequently, drug-resistant strains have arisen in which the viral RT has an increased fidelity of replication, thus reducing analogue incorporation. Higher fidelity, however, impacts on viral fitness. The appearance of compensatory mutations in combination with higher fidelity NRTI resistance mutations and the subsequent reversion of NRTI-resistant mutations upon cessation of antiretroviral treatment lend support to the notion that higher fidelity exacts a fitness cost. Potential mechanisms for reduced viral fitness are a smaller pool of mutant strains available to respond to immune or drug pressure, slower rates of replication, and a limitation to the dNTP tropism of the virus. Unraveling the relationship between replication fidelity and fitness should lead to a greater understanding of the evolution and control of HIV.
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Affiliation(s)
- Sarah B. Lloyd
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Wendy R. Winnall
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
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20
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Yin L, Hou W, Liu L, Cai Y, Wallet MA, Gardner BP, Chang K, Lowe AC, Rodriguez CA, Sriaroon P, Farmerie WG, Sleasman JW, Goodenow MM. IgM Repertoire Biodiversity is Reduced in HIV-1 Infection and Systemic Lupus Erythematosus. Front Immunol 2013; 4:373. [PMID: 24298273 PMCID: PMC3828670 DOI: 10.3389/fimmu.2013.00373] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/30/2013] [Indexed: 12/25/2022] Open
Abstract
Background: HIV-1 infection or systemic lupus erythematosus (SLE) disrupt B cell homeostasis, reduce memory B cells, and impair function of IgG and IgM antibodies. Objective: To determine how disturbances in B cell populations producing polyclonal antibodies relate to the IgM repertoire, the IgM transcriptome in health and disease was explored at the complementarity determining region 3 (CDRH3) sequence level. Methods: 454-deep pyrosequencing in combination with a novel analysis pipeline was applied to define populations of IGHM CDRH3 sequences based on absence or presence of somatic hypermutations (SHM) in peripheral blood B cells. Results: HIV or SLE subjects have reduced biodiversity within their IGHM transcriptome compared to healthy subjects, mainly due to a significant decrease in the number of unique combinations of alleles, although recombination machinery was intact. While major differences between sequences without or with SHM occurred among all groups, IGHD and IGHJ allele use, CDRH3 length distribution, or generation of SHM were similar among study cohorts. Antiretroviral therapy failed to normalize IGHM biodiversity in HIV-infected individuals. All subjects had a low frequency of allelic combinations within the IGHM repertoire similar to known broadly neutralizing HIV-1 antibodies. Conclusion: Polyclonal expansion would decrease overall IgM biodiversity independent of other mechanisms for development of the B cell repertoire. Applying deep sequencing as a strategy to follow development of the IgM repertoire in health and disease provides a novel molecular assessment of multiple points along the B cell differentiation pathway that is highly sensitive for detecting perturbations within the repertoire at the population level.
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Affiliation(s)
- Li Yin
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida , Gainesville, FL , USA ; Florida Center for AIDS Research, University of Florida , Gainesville, FL , USA
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21
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Prosperi MCF, Yin L, Nolan DJ, Lowe AD, Goodenow MM, Salemi M. Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Sci Rep 2013; 3:2837. [PMID: 24089188 PMCID: PMC3789152 DOI: 10.1038/srep02837] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/13/2013] [Indexed: 11/22/2022] Open
Abstract
Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing platform. The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones. Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent lineages, but none were able to provide a high precision/recall tradeoff. Estimated variant frequencies mildly correlated with the original. Given the limitations of currently available algorithms identified by our empirical validation, the development and exploitation of additional data sets is needed, in order to establish an efficient framework for viral population reconstruction using NGS.
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Affiliation(s)
- Mattia C. F. Prosperi
- University of Manchester, Faculty of Medical and Human Sciences, Northwest Institute of Bio-Health Informatics, Centre for Health Informatics, Institute of Population Health, Manchester, UK
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
| | - Li Yin
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
- Florida Center for AIDS Research, Gainesville, Florida, USA
| | - David J. Nolan
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
| | - Amanda D. Lowe
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
- Florida Center for AIDS Research, Gainesville, Florida, USA
| | - Maureen M. Goodenow
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
- Florida Center for AIDS Research, Gainesville, Florida, USA
| | - Marco Salemi
- University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, Florida, USA
- Florida Center for AIDS Research, Gainesville, Florida, USA
- Emerging Pathogens Institute, Gainesville, Florida, USA
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22
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Selinger C, Katze MG. Mathematical models of viral latency. Curr Opin Virol 2013; 3:402-7. [PMID: 23896280 DOI: 10.1016/j.coviro.2013.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 06/21/2013] [Accepted: 06/26/2013] [Indexed: 10/26/2022]
Abstract
While viral latency remains one of the biggest challenges for successful antiviral therapy, it has also inspired mathematical modelers to develop dynamical system approaches with the aim of predicting the impact of drug efficacy on disease progression and the persistence of latent viral reservoirs. In this review we present several differential equation models and assess their relative success in giving advice to the working clinician and their predictive power for inferring long term viral eradication from short term abatement. Many models predict that there is a considerable likelihood of viral rebound due to continuous reseeding of latent reservoirs. Most mathematical models of HIV latency suffer from being reductionist by ignoring the growing variety of different cell types harboring latent virus, the considerable intercellular delay involved in reactivation, and host-related epigenetic modifications which may alter considerably the dynamical system of immune cell populations.
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Affiliation(s)
- Christian Selinger
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195-8070, USA.
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23
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Salemi M. The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective. Infect Dis Rep 2013; 5:e3. [PMID: 24470967 PMCID: PMC3892624 DOI: 10.4081/idr.2013.s1.e3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 02/19/2013] [Indexed: 01/09/2023] Open
Abstract
The intra-host evolutionary and population dynamics of the human immunodeficiency virus type 1 (HIV-1), the cause of the acquired immunodeficiency syndrome, have been the focus of one of the most extensive study efforts in the field of molecular evolution over the past three decades. As HIV-1 is among the fastest mutating organisms known, viral sequence data sampled over time from infected patients can provide, through phylogenetic analysis, significant insights about the tempo and mode of evolutionary processes shaped by complex interaction with the host milieu. Five main aspects are discussed: the patterns of HIV-1 intra-host diversity and divergence over time in relation to different phases of disease progression; the impact of selection on the temporal structure of HIV-1 intra-host genealogies inferred from longitudinally sampled viral sequences; HIV-1 intra-host sub-population structure; the potential relationship between viral evolutionary rate and disease progression and the central evolutionary role played by recombination occurring in super-infected cells.
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Affiliation(s)
- Marco Salemi
- Department of Pathology Immunology and Laboratory Medicine and Emerging Pathogens Institute, University of Florida , Gainesville, USA
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24
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Abstract
Pathogen discovery is critically important to infectious diseases and public health. Nearly all new outbreaks are caused by the emergence of novel viruses. Genomic tools for pathogen discovery include consensus PCR, microarrays, and deep sequencing. Downstream studies are often necessary to link a candidate novel virus to a disease.
Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease.
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