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Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes (Basel) 2022; 13:genes13091519. [PMID: 36140690 PMCID: PMC9498922 DOI: 10.3390/genes13091519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.
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2
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Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs. Sci Rep 2021; 11:9986. [PMID: 33976241 PMCID: PMC8113533 DOI: 10.1038/s41598-021-88132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Most individuals chronically infected with hepatitis C virus (HCV) are asymptomatic during the initial stages of infection and therefore the precise timing of infection is often unknown. Retrospective estimation of infection duration would improve existing surveillance data and help guide treatment. While intra-host viral diversity quantifications such as Shannon entropy have previously been utilized for estimating duration of infection, these studies characterize the viral population from only a relatively short segment of the HCV genome. In this study intra-host diversities were examined across the HCV genome in order to identify the region most reflective of time and the degree to which these estimates are influenced by high-risk activities including those associated with HCV acquisition. Shannon diversities were calculated for all regions of HCV from 78 longitudinally sampled individuals with known seroconversion timeframes. While the region of the HCV genome most accurately reflecting time resided within the NS3 gene, the gene region with the highest capacity to differentiate acute from chronic infections was identified within the NS5b region. Multivariate models predicting duration of infection from viral diversity significantly improved upon incorporation of variables associated with recent public, unsupervised drug use. These results could assist the development of strategic population treatment guidelines for high-risk individuals infected with HCV and offer insights into variables associated with a likelihood of transmission.
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Abstract
Protective vaccines for hypervariable pathogens are urgently needed. It has been proposed that amputating highly variable epitopes from vaccine antigens would induce the production of broadly protective antibodies targeting conserved epitopes. However, so far, these approaches have failed, partially because conserved epitopes are occluded in vivo and partially because co-localizing patterns of immunodominance and antigenic variability render variable epitopes the primary target for antibodies in natural infection. In this Perspective, to recast the challenge of vaccine development for hypervariable pathogens, I evaluate convergent mechanisms of adaptive variation, such as intrahost immune-mediated diversification, spatiotemporally defined antigenic space, and infection-enhancing cross-immunoreactivity. The requirements of broadly protective immune responses targeting variable pathogens are formulated in terms of cross-immunoreactivity, stoichiometric thresholds for neutralization, and the elicitation of antibodies targeting physicochemically conserved signatures within sequence variable domains.
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Affiliation(s)
- Alexander I Mosa
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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4
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Hwang HR, Kim SC, Kang SH, Lee CH. Increase in the genetic polymorphism of varicella-zoster virus after passaging in in vitro cell culture. J Microbiol 2019; 57:1033-1039. [PMID: 31659688 DOI: 10.1007/s12275-019-9429-4] [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: 09/06/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022]
Abstract
Primary infections with the varicella-zoster virus (VZV) result in varicella, while latent reactivation leads to herpes zoster. Both varicella and zoster can be prevented by live attenuated vaccines. There have been reports suggesting that both clinical VZV strains and those in vaccine preparations are genetically polymorphic, containing mixtures of both wild-type and vaccine-type sequences at certain vaccine-specific sites. In this study, the genetic polymorphism of the VZV genome was examined by analyzing the frequencies of minor alleles at each nucleotide position. Next-generation sequencing of the clinical VZV strain YC02 passaged in an in vitro cell culture was used to identify genetically polymorphic sites (GPS), where the minor allele frequency (MAF) exceeded 5%. The number of GPS increased by 7.3-fold at high passages (p100) when compared to low passages (p17), although the average MAF remained similar. GPS were found in 6 open reading frames (ORFs) in p17, 35, and 54 ORFs in p60 and p100, respectively. GPS were found more frequently in the dispensable gene group than the essential gene group, but the average MAF was greater in the essential gene group. The most common two major/minor base pairs were A/g and T/c. GPS were found in all three passages at 16 positions, all located in the reiterated (R) region. The population diversity as measured by Shannon entropy increased in p60 and p100. However, the entropy remained unchanged in the R regions.
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Affiliation(s)
- Hye Rim Hwang
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Seok Cheon Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Se Hwan Kang
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Chan Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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5
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Prakash S, Shukla S, Ramakrishna V, Jain A. Distribution of hepatitis C genotypes in Uttar Pradesh, India; rare genotype 4 detected. J Med Virol 2018; 90:1875-1881. [PMID: 30085356 DOI: 10.1002/jmv.25277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/07/2018] [Indexed: 12/29/2022]
Abstract
AIM The worldwide prevalence of hepatitis C virus infection (HCV) is nearly 150 to 170 million cases. The prevalence of HCV infection in India is estimated to be around 1%. In India HCV genotype (GT)3 is the predominant GT followed by GT1. Our study aims to establish the prevalent GTs/subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. METHODS The study was a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital from September 2014 to April 2017, and was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried out on a stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger's sequencing of the core region. The phylogenetic analysis of 179 HCV strains with a high-quality sequencing data was performed. RESULTS The distributions of prevalent GTs/subtypes as noted in the current study were ( n [%]): GT1a, 101 (25%); GT1b, 12 (2.9%); GT1c, 1 (0.25%); GT3a, 275 (68.07%); GT3b, 9 (2.2%); GT3g, 2 (0.49%); GT3i, 3 (0.74%); and GT4a, 1 (0.24%). HCV GTs GT2, GT5, and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. CONCLUSIONS HCV GTs 3a and 1a are the commonest circulating GTs in Uttar Pradesh, India.
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Affiliation(s)
- Shantanu Prakash
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Suruchi Shukla
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Vangala Ramakrishna
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Amita Jain
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
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6
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Lisboa Neto G, Malta FM, Gomes-Gouvêa MS, Noble CF, Romano CM, Rebello Pinho JR, Silva MH, Leite AG, Piccoli LZ, Carrilho FJ, Mendes-Correa MC. Characterization of clinical predictors of naturally occurring NS3/NS4A protease polymorphism in genotype 1 hepatitis C virus mono and HIV co-infected patients. J Med Virol 2017; 89:2249-2254. [DOI: 10.1002/jmv.24900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/02/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Gaspar Lisboa Neto
- Department of Infectious Diseases; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
| | - Fernanda M. Malta
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Michele S. Gomes-Gouvêa
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Caroline F. Noble
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Camila M. Romano
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
| | - João R. Rebello Pinho
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Albert Einstein Medicina Diagnóstica; Hospital Israelita Albert Einstein; São Paulo São Paulo Brazil
| | - Mariliza H. Silva
- Centro de Referência e Treinamento em DST/AIDS do Estado de São Paulo; São Paulo São Paulo Brazil
- Clínicas de Especialidades; São Bernardo do Campo São Paulo Brazil
| | | | | | - Flair J. Carrilho
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Maria C. Mendes-Correa
- Department of Infectious Diseases; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
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7
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Hedegaard DL, Tully DC, Rowe IA, Reynolds GM, Bean DJ, Hu K, Davis C, Wilhelm A, Ogilvie CB, Power KA, Tarr AW, Kelly D, Allen TM, Balfe P, McKeating JA. High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. J Hepatol 2017; 66:28-38. [PMID: 27531641 PMCID: PMC5558612 DOI: 10.1016/j.jhep.2016.07.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/22/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The high replication and mutation rate of hepatitis C virus (HCV) results in a heterogeneous population of viral sequences in vivo. HCV replicates in the liver and infected hepatocytes occur as foci surrounded by uninfected cells that may promote compartmentalization of viral variants. Given recent reports showing interferon stimulated gene (ISG) expression in chronic hepatitis C, we hypothesized that local interferon responses may limit HCV replication and evolution. METHODS To investigate the spatial influence of liver architecture on viral replication we measured HCV RNA and ISG mRNA from each of the 8 Couinaud segments of the liver from 21 patients undergoing liver transplant. RESULTS HCV RNA and ISG mRNA levels were comparable across all sites from an individual liver but showed up to 500-fold difference between patients. Importantly, there was no association between ISG and HCV RNA expression across all sites in the liver or plasma. Deep sequencing of HCV RNA isolated from the 8 hepatic sites from two subjects showed a similar distribution of viral quasispecies across the liver and uniform sequence diversity. Single genome amplification of HCV E1E2-envelope clones from 6 selected patients at 2 hepatic sites supported these data and showed no evidence for HCV compartmentalization. CONCLUSIONS We found no differences between the hepatic and plasma viral quasispecies in all patients sampled. We conclude that in end-stage liver disease HCV RNA levels and the genetic pool of HCV envelope sequences are indistinguishable between distant sites in the liver and plasma, arguing against viral compartmentalization. LAY SUMMARY HCV is an RNA virus that exists as a quasispecies of closely related genomes that are under continuous selection by host innate and adaptive immune responses and antiviral drug therapy. The primary site of HCV replication is the liver and yet our understanding of the spatial distribution of viral variants within the liver is limited. High resolution sequencing of HCV and monitoring of innate immune responses at multiple sites across the liver identified a uniform pattern of diversity and argues against viral compartmentalization.
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Affiliation(s)
| | | | - Ian A. Rowe
- Centre for Human Virology, University of Birmingham, Birmingham, UK
| | - Gary M. Reynolds
- NIHR Birmingham Liver Biomedical Research Unit, University of Birmingham, UK
| | - David J. Bean
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ke Hu
- Centre for Human Virology, University of Birmingham, Birmingham, UK
| | | | - Annika Wilhelm
- NIHR Birmingham Liver Biomedical Research Unit, University of Birmingham, UK
| | | | - Karen A. Power
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Alexander W. Tarr
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Deirdre Kelly
- Liver Unit, Birmingham Childrens’ Hospital, Birmingham, UK
| | - Todd M. Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Peter Balfe
- Centre for Human Virology, University of Birmingham, Birmingham, UK.
| | - Jane A. McKeating
- Centre for Human Virology, University of Birmingham, Birmingham, UK,NIHR Birmingham Liver Biomedical Research Unit, University of Birmingham, UK,Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 2a, D-85748 Garching, Germany
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8
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Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses. J Virol 2015; 90:3318-29. [PMID: 26719263 DOI: 10.1128/jvi.02995-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) comprises the first 27 N-terminal amino acid residues of E2. It is classically seen as the most heterogeneous region of the HCV genome. In this study, we assessed HVR1 evolution by using ultradeep pyrosequencing for a cohort of treatment-naive, chronically infected patients over a short, 16-week period. Organization of the sequence set into connected components that represented single nucleotide substitution events revealed a network dominated by highly connected, centrally positioned master sequences. HVR1 phenotypes were observed to be under strong purifying (stationary) and strong positive (antigenic drift) selection pressures, which were coincident with advancing patient age and cirrhosis of the liver. It followed that stationary viromes were dominated by a single HVR1 variant surrounded by minor variants comprised from conservative single amino acid substitution events. We present evidence to suggest that neutralization antibody efficacy was diminished for stationary-virome HVR1 variants. Our results identify the HVR1 network structure during chronic infection as the preferential dominance of a single variant within a narrow sequence space. IMPORTANCE HCV infection is often asymptomatic, and chronic infection is generally well established in advance of initial diagnosis and subsequent treatment. HVR1 can undergo rapid sequence evolution during acute infection, and the variant pool is typically seen to diverge away from ancestral sequences as infection progresses from the acute to the chronic phase. In this report, we describe HVR1 viromes in chronically infected patients that are defined by a dominant epitope located centrally within a narrow variant pool. Our findings suggest that weakened humoral immune activity, as a consequence of persistent chronic infection, allows for the acquisition and maintenance of host-specific adaptive mutations at HVR1 that reflect virus fitness.
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9
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Ren Y, Wang W, Zhang X, Xu Y, Di Bisceglie AM, Fan X. Evidence for deleterious hepatitis C virus quasispecies mutation loads that differentiate the response patterns in IFN-based antiviral therapy. J Gen Virol 2015; 97:334-343. [PMID: 26581744 DOI: 10.1099/jgv.0.000346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Viral quasispecies (QS) have long been considered to affect the efficiency of hepatitis C virus (HCV) antiviral therapy, but a correlation between QS diversity and treatment outcomes has not been established conclusively. We previously measured HCV QS diversity by genome-wide quantification of high-resolution mutation load in HCV genotype 1a patients achieving a sustained virological response (1a/SVR) or a null response (1a/null). The current study extended this work into HCV 1a patients experiencing relapse (1a/relapse, n = 19) and genotype 2b patients with SVR (2b/SVR, n = 10). The mean mutation load per patient in 2b/SVR and 1a/relapse was similar, respectively, to 1a/SVR (517.6 ± 174.3 vs 524 ± 278.8 mutations, P = 0.95) and 1a/null (829.2 ± 282.8 vs 805.6 ± 270.7 mutations, P = 0.78). Notably, a deleterious mutation load, as indicated by the percentage of non-synonymous mutations, was highest in 2b/SVR (33.2 ± 8.5%) as compared with 1a/SVR (23.6 ± 7.8%, P = 0.002), 1a/null (18.2 ± 5.1%, P = 1.9 × 10(-7)) or 1a/relapse (17.8 ± 5.3%, P = 1.8) × 10(-6). In the 1a/relapse group, continuous virus evolution was observed with excessive accumulation of a deleterious load (17.8 ± 5.3% vs 35.4 ± 12.9%, P = 3.5 × 10(-6)), supporting the functionality of Muller's ratchet in a treatment-induced population bottleneck. Taken together, the magnitude of HCV mutation load, particularly the deleterious mutation load, provides an evolutionary explanation for the emergence of multiple response patterns as well as an overall high SVR rate in HCV genotype 2 patients. Augmentation of Muller's ratchet represents a potential strategy to reduce or even eliminate viral relapse in HCV antiviral therapy.
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Affiliation(s)
- Yi Ren
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA.,Wuhan Center for Tuberculosis Control, Wuhan 430030, Hubei, PR China
| | - Weihua Wang
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA
| | - Xiaoan Zhang
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA
| | - Yanjuan Xu
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA
| | - Adrian M Di Bisceglie
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA.,Saint Louis University Liver Center, Saint Louis University School of Medicine, St Louis, MO 63104, USA
| | - Xiaofeng Fan
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA.,Saint Louis University Liver Center, Saint Louis University School of Medicine, St Louis, MO 63104, USA
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10
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Rao X, Hoof I, van Baarle D, Keşmir C, Textor J. HLA Preferences for Conserved Epitopes: A Potential Mechanism for Hepatitis C Clearance. Front Immunol 2015; 6:552. [PMID: 26579127 PMCID: PMC4625101 DOI: 10.3389/fimmu.2015.00552] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infections affect more than 170 million people worldwide. Most of these individuals are chronically infected, but some clear the infection rapidly. Host factors seem to play a key role in HCV clearance, among them are the human leukocyte antigen (HLA) class I molecules. Certain HLA molecules, e.g., B*27 and B*57, are associated with viral clearance. To identify potential mechanisms for these associations, we assess epitope distribution differences between HLA molecules using experimentally verified and in silico predicted HCV epitopes. Specifically, we show that the NS5B protein harbors the largest fraction of conserved regions among all HCV proteins. Such conserved regions could be good targets for cytotoxic T-cell (CTL) responses. We find that the protective HLA-B*27 molecule preferentially presents cytotoxic T-cell (CTL) epitopes from NS5B and, in general, presents the most strongly conserved epitopes among the 23 HLA molecules analyzed. In contrast, HLA molecules known to be associated with HCV persistence do not have similar preferences and appear to target the variable P7 protein. Overall, our analysis suggests that by targeting highly constrained - and thereby conserved - regions of HCV, the protective HLA molecule HLA-B*27 reduces the ability of HCV to escape the cytotoxic T-cell response of the host. For visualizing the distribution of both experimentally verified and predicted epitopes across the HCV genome, we created the HCV epitope browser, which is available at theory.bio.uu.nl/ucqi/hcv.
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Affiliation(s)
- Xiangyu Rao
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Debbie van Baarle
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Johannes Textor
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
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11
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Montoya V, Olmstead AD, Janjua NZ, Tang P, Grebely J, Cook D, Richard Harrigan P, Krajden M. Differentiation of acute from chronic hepatitis C virus infection by nonstructural 5B deep sequencing: a population-level tool for incidence estimation. Hepatology 2015; 61:1842-50. [PMID: 25645961 DOI: 10.1002/hep.27734] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/28/2015] [Indexed: 01/19/2023]
Abstract
UNLABELLED The ability to classify acute versus chronic hepatitis C virus (HCV) infections at the time of diagnosis is desirable to improve the quality of surveillance information. The aim of this study was to differentiate acute from chronic HCV infections utilizing deep sequencing. HCV nonstructural 5B (NS5B) amplicons (n = 94) were generated from 77 individuals (13 acute and 64 chronic HCV infections) in British Columbia, Canada, with documented seroconversion time frames. Amplicons were deep sequenced and HCV genomic diversity was measured by Shannon entropy (SE) and a single nucleotide variant (SNV) analysis. The relationship between each diversity measure and the estimated days since infection was assessed using linear mixed models, and the ability of each diversity measure to differentiate acute from chronic infections was assessed using generalized estimating equations. Both SE and the SNV diversity measures were significantly different for acute versus chronic infections (P < 0.009). NS5B nucleotide diversity continued to increase for at least 3 years postinfection. Among individuals with the least uncertainty with regard to duration of infection (n = 39), the area under the receiver operating characteristic curve (AUROC) was high (0.96 for SE; 0.98 for SNV). Although the AUROCs were lower (0.86 for SE; 0.80 for SNV) when data for all individuals were included, they remain sufficiently high for epidemiological purposes. Synonymous mutations were the primary discriminatory variable accounting for over 78% of the measured genetic diversity. CONCLUSIONS NS5B sequence diversity assessed by deep sequencing can differentiate acute from chronic HCV infections and, with further validation, could become a powerful population-level surveillance tool for incidence estimation.
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Affiliation(s)
- Vincent Montoya
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea D Olmstead
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Naveed Z Janjua
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick Tang
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason Grebely
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Darrel Cook
- BC Center for Disease Control, Vancouver, British Columbia, Canada
| | - P Richard Harrigan
- BC Center for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Mel Krajden
- BC Center for Disease Control, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
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12
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Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity. Proc Natl Acad Sci U S A 2015; 112:6653-8. [PMID: 25941392 DOI: 10.1073/pnas.1422942112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Hepatitis C virus (HCV) has the propensity to cause chronic infection. Continuous immune escape has been proposed as a mechanism of intrahost viral evolution contributing to HCV persistence. Although the pronounced genetic diversity of intrahost HCV populations supports this hypothesis, recent observations of long-term persistence of individual HCV variants, negative selection increase, and complex dynamics of viral subpopulations during infection as well as broad cross-immunoreactivity (CR) among variants are inconsistent with the immune-escape hypothesis. Here, we present a mathematical model of intrahost viral population dynamics under the condition of a complex CR network (CRN) of viral variants and examine the contribution of CR to establishing persistent HCV infection. The model suggests a mechanism of viral adaptation by antigenic cooperation (AC), with immune responses against one variant protecting other variants. AC reduces the capacity of the host's immune system to neutralize certain viral variants. CRN structure determines specific roles for each viral variant in host adaptation, with variants eliciting broad-CR antibodies facilitating persistence of other variants immunoreacting with these antibodies. The proposed mechanism is supported by empirical observations of intrahost HCV evolution. Interference with AC is a potential strategy for interruption and prevention of chronic HCV infection.
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13
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Nelson CW, Hughes AL. Within-host nucleotide diversity of virus populations: insights from next-generation sequencing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:1-7. [PMID: 25481279 PMCID: PMC4316684 DOI: 10.1016/j.meegid.2014.11.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 01/03/2023]
Abstract
Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.
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Affiliation(s)
- Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Larrat S, Kulkarni O, Claude JB, Beugnot R, Blum MGB, Fusillier K, Lupo J, Tremeaux P, Plages A, Marlu A, Duborjal H, Signori-Schmuck A, Francois O, Zarski JP, Morand P, Leroy V. Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients. J Clin Microbiol 2015; 53:389-97. [PMID: 25411182 PMCID: PMC4298514 DOI: 10.1128/jcm.02547-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023] Open
Abstract
Despite the gain in sustained virological responses (SVR) provided by protease inhibitors (PIs), failures still occur. The aim of this study was to determine if a baseline analysis of the NS3 region using ultradeep pyrosequencing (UDPS) can help to predict an SVR. Serum samples from 40 patients with previously nonresponding genotype 1 chronic hepatitis C who were retreated with triple therapy, including a PI, were analyzed. Baseline UDPS of the NS3 gene was performed on plasma and peripheral blood mononuclear cells (PBMC). Mutations conferring resistance to PIs were sought. The overall diversity of the quasispecies was evaluated by calculating the Shannon entropy (SE). Resistance mutations were found in plasma and PBMC but were not discriminating enough to predict an SVR. NS3 quasispecies heterogeneity was significantly lower at baseline in patients achieving an SVR than in those not achieving an SVR (SE of 26.98 ± 16.64 × 10(-3) versus 44.93 ± 19.58 × 10(-3), P = 0.0047). With multivariate analysis, the independent predictors of an SVR were fibrosis of stage F ≤2 (odds ratio [OR], 13.3; 95% confidence interval [CI], 1.25 to 141.096; P < 0.03) and SE below the median (OR, 5.4; 95% CI, 1.22 to 23.87; P < 0.03). More than the presence of minor mutations at the baseline in plasma or in PBMC, the NS3 viral heterogeneity determined by UDPS is an independent factor for an SVR in previously treated patients receiving triple therapy that includes a PI.
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Affiliation(s)
- Sylvie Larrat
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Om Kulkarni
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | | | - Réjane Beugnot
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Michaël G B Blum
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | - Katia Fusillier
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Julien Lupo
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Pauline Tremeaux
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Agnès Plages
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Alice Marlu
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | | | - Anne Signori-Schmuck
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Olivier Francois
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | - Jean-Pierre Zarski
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France
| | - Patrice Morand
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Vincent Leroy
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France
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Sølund C, Krarup H, Ramirez S, Thielsen P, Røge BT, Lunding S, Barfod TS, Madsen LG, Tarp B, Christensen PB, Gerstoft J, Laursen AL, Bukh J, Weis N. Nationwide experience of treatment with protease inhibitors in chronic hepatitis C patients in Denmark: identification of viral resistance mutations. PLoS One 2014; 9:e113034. [PMID: 25438153 PMCID: PMC4249835 DOI: 10.1371/journal.pone.0113034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/18/2014] [Indexed: 12/15/2022] Open
Abstract
Background and Aims The first standard of care in treatment of chronic HCV genotype 1 infection involving directly acting antivirals was protease inhibitors telaprevir or boceprevir combined with pegylated-interferon and ribavirin (triple therapy). Phase III studies include highly selected patients. Thus, treatment response and development of viral resistance during triple therapy in a routine clinical setting needs to be determined. The aims of this study were to investigate treatment outcome and identify sequence variations after triple therapy in patients with chronic HCV genotype 1 infection in a routine clinical setting. Methods 80 patients, who initiated and completed triple therapy in Denmark between May 2011 and November 2012, were included. Demographic data and treatment response were obtained from the Danish Database for Hepatitis B and C. Direct sequencing and clonal analysis of the RT-PCR amplified NS3 protease were performed in patients without cure following triple therapy. Results 38 (47%) of the patients achieved cure, 15 (19%) discontinued treatment due to adverse events and remained infected, and 27 (34%) experienced relapse or treatment failure of whom 15 of 21 analyzed patients had well-described protease inhibitor resistance variants detected. Most frequently detected protease variants were V36M and/or R155K, and V36M, in patients with genotype 1a and 1b infection, respectively. Conclusions The cure rate after triple therapy in a routine clinical setting was 47%, which is substantially lower than in clinical trials. Resistance variants towards protease inhibitors were seen in 71% of patients failing therapy indicating that resistance could have an important role in treatment response.
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Affiliation(s)
- Christina Sølund
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark; and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Krarup
- Section of Molecular Diagnostics, Clinical Biochemistry and Department of Medical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - Santseharay Ramirez
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark; and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Thielsen
- Department of Gastroenterology, Copenhagen University Hospital, Herlev, Denmark
| | - Birgit T. Røge
- Department of Medicine, Kolding Hospital, Kolding, Denmark
| | - Suzanne Lunding
- Department of Infectious Diseases, Copenhagen University Hospital, Hillerød, Denmark
| | - Toke S. Barfod
- Department of Infectious Diseases, Roskilde Hospital, Roskilde, Denmark
| | - Lone G. Madsen
- Department of Gastroenterology, Køge Hospital, Køge, Denmark
| | - Britta Tarp
- Diagnostic Center, Silkeborg Regional Hospital, Silkeborg, Denmark
| | - Peer B. Christensen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | - Jan Gerstoft
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Alex L. Laursen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Jens Bukh
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark; and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - The DANHEP group
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
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16
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Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing. J Virol 2014; 88:13709-21. [PMID: 25231312 DOI: 10.1128/jvi.01732-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) causes chronic infection in up to 50% to 80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intrahost evolution are poorly understood. In this study, we used ultradeep pyrosequencing (UDPS) to map the viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low-frequency recombinants throughout the study period, implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicate that polyvirus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low for the daughter virions to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response. IMPORTANCE Analysis of ultradeep pyrosequencing data sets derived from virus amplicons frequently relies on software tools that are not optimized for amplicon analysis, assume random incorporation of sequencing errors, and are focused on achieving higher specificity at the expense of sensitivity. Such analysis is further complicated by the presence of hypervariable regions. In this study, we made use of a temporally matched reference sequence data set to inform error correction algorithms. Using this methodology, we were able to (i) detect multiple instances of hepatitis C virus intrasubtype recombination at the E1/E2 junction (a phenomenon rarely reported in the literature) and (ii) interrogate the longitudinal quasispecies complexity of the virome. Parallel to the UDPS, isolation of IgG-bound virions was found to coincide with the collapse of specific viral subpopulations.
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17
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Jackowiak P, Kuls K, Budzko L, Mania A, Figlerowicz M, Figlerowicz M. Phylogeny and molecular evolution of the hepatitis C virus. INFECTION GENETICS AND EVOLUTION 2013; 21:67-82. [PMID: 24200590 DOI: 10.1016/j.meegid.2013.10.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022]
Abstract
The hepatitis C virus (HCV) is a globally prevalent human pathogen that causes persistent liver infections in most infected individuals. HCV is classified into seven phylogenetically distinct genotypes, which have different geographical distributions and levels of genetic diversity. Some of these genotypes are endemic and highly divergent, whereas others disseminate rapidly on an epidemic scale but display lower variability. HCV phylogeny has an important impact on disease epidemiology and clinical practice because the viral genotype may determine the pathogenesis and severity of the resultant chronic liver disease. In addition, there is a clear association between the HCV genotype and its susceptibility to antiviral treatment. Similarly to other RNA viruses, in a single host, HCV exists as a combination of related but genetically different variants. The whole formation is the actual target of selection exerted by a host organism and antiviral therapeutics. The genetic structure of the viral population is largely shaped by mutations that are constantly introduced during an error-prone replication. However, it appears that genetic recombination may also contribute to this process. This heterogeneous collection of variants has a significant ability to evolve towards the fitness optimum. Interestingly, negative selection, which restricts diversity, emerges as an essential force that drives HCV evolution. It is becoming clear that HCV evolves to become stably adapted to the host environment. In this article we review the HCV phylogeny and molecular evolution in the context of host-virus interactions.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Kuls
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Mania
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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18
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Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Mol Biol Evol 2013; 30:1916-28. [PMID: 23686658 DOI: 10.1093/molbev/mst094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Gene overlapping is widely employed by RNA viruses to generate genetic novelty while retaining a small genome size. However, gene overlapping also increases the deleterious effect of mutations as they affect more than one gene, thereby reducing the evolutionary rate of RNA viruses and hence their adaptive capacity. Although there is general agreement on the benefits of gene overlapping as a mechanism of genomic compression for rapidly evolving organisms, its effect on the pace of RNA virus evolution remains a source of debate. To address this issue, we collected sequence data from 117 instances of gene overlapping across 19 families, 30 genera, and 55 species of RNA viruses. On these data, we analyzed how genetic distances, selective pressures, and the distribution of RNA secondary structures and conserved protein functional domains vary between overlapping (OV) and nonoverlapping (NOV) regions. We show that gene overlapping generally results in a decrease in the rate of RNA virus evolution through a reduction in the frequency of synonymous mutations. However, this effect is less pronounced in genes with a terminal rather than an internal gene overlap, which might result from a greater proportion of protein functional conserved domains in NOV than in OV regions, in turn reducing the number of nonsynonymous mutations in the former. Overall, our analyses clarify the role of gene overlapping as a modulator of the evolutionary rates exhibited by RNA viruses and shed light on the factors that shape the genetic diversity of this important group of pathogens.
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Affiliation(s)
- Etienne Simon-Loriere
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
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19
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Shahid I, Gull S, Ijaz B, Ahmad W, Ansar M, Asad S, Kausar H, Sarwar MT, Khan MK, Hassan S. Stable Huh-7 cell lines expressing non-structural proteins of genotype 1a of hepatitis C virus. J Virol Methods 2013; 189:65-9. [PMID: 23352716 DOI: 10.1016/j.jviromet.2013.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 12/25/2012] [Accepted: 01/14/2013] [Indexed: 01/03/2023]
Abstract
Hepatitis C virus (HCV) infection has infected approximately 3% of the world population. HCV genotype 1a is distributed throughout the world, and along with genotype 1b, is relatively resistant to current standards of therapy compared to other HCV genotypes. The present study was designed to produce stable Huh-7 cell lines expressing non-structural proteins of HCV genotype la, representing an in vitro system to facilitate the development of new antiviral drugs against chronic HCV infection. The non-structural genes of HCV genotype 1a were amplified and cloned in a mammalian expression vector pCR 3.1/FIagTag. Huh-7 cells were transfected with one of two expression plasmids, the first containing the NS2, NS3, and NS4a cassette, and second containing the NS5a and NS5b genes. Stable cell lines were produced under the selection of gentamycin (G418). mRNA and protein expression analysis was performed by RT-PCR and Western blotting. The RT-PCR and Western blot results confirmed the stable expression of each of the gene products. Stable Huh-7 cell lines with HCV la non-structural proteins may be helpful for evaluating the role of HCV proteins in molecular pathogenesis, and could facilitate the development of new therapeutic drugs.
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Affiliation(s)
- Imran Shahid
- Applied and Functional Genomics Laboratory, Centre of Excellence in Molecular Biology, 87-West Canal Bank Road, 53700 Lahore, Pakistan.
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20
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Yang CW. A comparative study of short linear motif compositions of the influenza A virus ribonucleoproteins. PLoS One 2012; 7:e38637. [PMID: 22715401 PMCID: PMC3371030 DOI: 10.1371/journal.pone.0038637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/08/2012] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions through short linear motifs (SLiMs) are an emerging concept that is different from interactions between globular domains. The SLiMs encode a functional interaction interface in a short (three to ten residues) poorly conserved sequence. This characteristic makes them much more likely to arise/disappear spontaneously via mutations, and they may be more evolutionarily labile than globular domains. The diversity of SLiM composition may provide functional diversity for a viral protein from different viral strains. This study is designed to determine the different SLiM compositions of ribonucleoproteins (RNPs) from influenza A viruses (IAVs) from different hosts and with different levels of virulence. The 96 consensus sequences (regular expressions) of SLiMs from the ELM server were used to conduct a comprehensive analysis of the 52,513 IAV RNP sequences. The SLiM compositions of RNPs from IAVs from different hosts and with different levels of virulence were compared. The SLiM compositions of 845 RNPs from highly virulent/pandemic IAVs were also analyzed. In total, 292 highly conserved SLiMs were found in RNPs regardless of the IAV host range. These SLiMs may be basic motifs that are essential for the normal functions of RNPs. Moreover, several SLiMs that are rare in seasonal IAV RNPs but are present in RNPs from highly virulent/pandemic IAVs were identified. The SLiMs identified in this study provide a useful resource for experimental virologists to study the interactions between IAV RNPs and host intracellular proteins. Moreover, the SLiM compositions of IAV RNPs also provide insights into signal transduction pathways and protein interaction networks with which IAV RNPs might be involved. Information about SLiMs might be useful for the development of anti-IAV drugs.
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Affiliation(s)
- Chu-Wen Yang
- Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan, Republic of China.
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Li H, Atkins E, Bruckner J, McArdle S, Qiu WC, Thomassen LV, Scott J, Shuhart MC, Livingston S, Townshend-Bulson L, McMahon BJ, Harris M, Griffin S, Gretch DR. Genetic and functional heterogeneity of the hepatitis C virus p7 ion channel during natural chronic infection. Virology 2012; 423:30-7. [DOI: 10.1016/j.virol.2011.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/01/2011] [Accepted: 11/11/2011] [Indexed: 01/19/2023]
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22
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Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol 2012; 86:3952-60. [PMID: 22278255 DOI: 10.1128/jvi.06627-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) is the leading cause of liver disease worldwide. In this study, we analyzed four treatment-naïve patients infected with subtype 1a and performed Roche/454 pyrosequencing across the coding region. We report the presence of low-level drug resistance mutations that would most likely have been missed using conventional sequencing methods. The approach described here is broadly applicable to studies of viral diversity and could help to improve the efficacy of direct-acting antiviral agents (DAA) in the treatment of HCV-infected patients.
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