The influence of hepatitis C virus genetic region on phylogenetic clustering analysis

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Lamoury, François M J ^a   Jacka, Brendan ^a   Bartlett, Sofia ^a   Bull, Rowena A ^b   Wong, Arthur ^a   Amin, Janaki ^a   Schinkel, Janke ^c   Poon, Art F ^d,e   Matthews, Gail V ^a   Grebely, Jason ^a   Dore, Gregory J ^a,f   Applegate, Tanya L ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c ACADEMIC MEDICAL CENTER   (Netherlands)

^d BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^e UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^f ST VINCENT S HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BOOTSTRAPPING; CLUSTER ANALYSIS; COHORT ANALYSIS; CONTROLLED STUDY; GENE SEQUENCE; GENETIC DISTANCE; GENETIC VARIABILITY; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROSPECTIVE STUDY; VIRUS CORE; VIRUS ENVELOPE; VIRUS GENOME; VIRUS STRAIN; GENETICS; GENOTYPE; HEPACIVIRUS; MOLECULAR EVOLUTION; SEQUENCE ANALYSIS;

VIRUS RNA;

CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENOTYPE; HEPACIVIRUS; HUMANS; PHYLOGENY; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EID: 84941337578     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0131437     Document Type: Article

References (50)

1. Bartenschlager R, Lohmann V. Replication of hepatitis C virus. The Journal of general virology. 2000; 81(Pt 7):1631-48. PMID: 10859368.
2. Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nature reviews Genetics. 2008; 9(4):267-76. doi:10.1038/nrg2323PMID: 18319742.
3. 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: journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2014; 21:67-82. doi:10.1016/j.meegid.2013.10.021 PMID: 24200590.
4. Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, et al. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology. 2014; 59(1):318-27. doi:10.1002/hep.26744 PMID: 24115039; PubMed Central PMCID: PMC4063340.
5. Jacka B, Lamoury F, Simmonds P, Dore GJ, Grebely J, Applegate T. Sequencing of the Hepatitis C Virus: A Systematic Review. PloS one. 2013; 8(6):e67073. Epub 2013/07/05. doi:10.1371/journal.pone.0067073 PMID: 23826196; PubMed Central PMCID: PMC3694929.
6. Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S, et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology. 2005; 42(4):962-73. Epub 2005/09/09. doi:10.1002/hep.20819 PMID: 16149085.
7. Simmonds P, Holmes EC, Cha TA, Chan SW, McOmish F, Irvine B, et al. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. The Journal of general virology. 1993; 74 (Pt 11):2391-9. Epub 1993/11/01. PMID: 8245854.
8. Bukh J, Purcell RH, Miller RH. At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proceedings of the National Academy of Sciences of the United States of America. 1993; 90(17):8234-8. Epub 1993/09/01. PMID: 8396266; PubMed Central PMCID: PMC47323.
9. Bukh J, Miller RH, Purcell RH. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Seminars in liver disease. 1995; 15(1):41-63. Epub 1995/02/01. doi:10.1055/s-2007-1007262 PMID: 7597443.
10. Svennblad B, Britton T. Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences. Statistical applications in genetics and molecular biology. 2007; 6:Article35. Epub 2008/01/04. doi:10.2202/1544-6115.1313 PMID: 18171319.
11. Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC evolutionary biology. 2011; 11:131. Epub 2011/05/21. doi:10.1186/1471-2148-11-131 PMID: 21595904; PubMed Central PMCID: PMC3112090.
12. Zhang EZ, Bartels DJ, Frantz JD, Seepersaud S, Lippke JA, Shames B, et al. Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples. Virology journal. 2013; 10:53. Epub 2013/02/14. doi:10.1186/1743-422X-10-53PMID: 23402332; PubMed Central PMCID: PMC3575352.
13. Matthews GV, Hellard M, Haber P, Yeung B, Marks P, Baker D, et al. Characteristics and treatment outcomes among HIV-infected individuals in the Australian Trial in Acute Hepatitis C. Clinical infectious diseases: An official publication of the Infectious Diseases Society of America. 2009; 48(5):650-8.Epub 2009/02/05. doi:10.1086/596770PMID: 19191653; PubMed Central PMCID: PMC2895679.
14. Dore GJ, Hellard M, Matthews GV, Grebely J, Haber PS, Petoumenos K, et al. Effective treatment of injecting drug users with recently acquired hepatitis C virus infection. Gastroenterology. 2010; 138 (1):123-35 e1-2. Epub 2009/09/29. doi:10.1053/j.gastro.2009.09.019 PMID: 19782085; PubMed Central PMCID: PMC2813391.
15. Murphy DG, Willems B, Deschenes M, Hilzenrat N, Mousseau R, Sabbah S. Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5' untranslated region sequences. Journal of clinical microbiology. 2007; 45(4):1102-12. Epub 2007/02/09. doi:10.1128/JCM.02366-06PMID: 17287328; PubMed Central PMCID: PMC1865836.
16. Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, et al. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic acids research. 2009; 37(Web Server issue):W634-W42. Epub 2009/06/02. doi:10.1093/nar/gkp455PMID: 19483099; PubMed Central PMCID: PMC2703899.
17. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22(21):2688-90. Epub 2006/08/25. doi:10.1093/bioinformatics/btl446 PMID: 16928733.
18. Ragonnet-Cronin M, Hodcroft E, Hue S, Fearnhill E, Delpech V, Brown AJ, et al. Automated analysis of phylogenetic clusters. BMC bioinformatics. 2013; 14(1):317. Epub 2013/11/07. doi:10.1186/1471-2105-14-317 PMID: 24191891.
19. Fourment M, Gibbs MJ. PATRISTIC: A program for calculating patristic distances and graphically comparing the components of genetic change. BMC evolutionary biology. 2006; 6:1. Epub 2006/01/04. doi:10.1186/1471-2148-6-1 PMID: 16388682; PubMed Central PMCID: PMC1352388.
20. Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS biology. 2011; 9(3):e1000602. Epub 2011/03/23doi:10.1371/journal.pbio.1000602 PMID: 21423652; PubMed Central PMCID: PMC3057953.
21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution. 2013; 30(12):2725-9. Epub 2013/10/18doi:10.1093/molbev/mst197PMID: 24132122; PubMed Central PMCID: PMC3840312.
22. Robinson DF, Foulds LR. Comparison of phylogenic trees. Mathematical biosciences 53:131-147 (1981). 1981;131-147.
23. Day WHE. Optimal algorithms for comparing trees with labeled leaves. Journal of classification. 1985; 2:7-28.
24. Nei M, Kumar S. Molecular Evolution and Phylogenetics. Oxford University Press 2000.
25. Brocchieri L. Phylogenetic inferences from molecular sequences: review and critique. Theoretical population biology. 2001; 59(1):27-40. Epub 2001/03/13. doi:10.1006/tpbi.2000.1485 PMID: 11243926.
26. Leache AD, Rannala B. The accuracy of species tree estimation under simulation: A comparison of methods. Systematic biology. 2011; 60(2):126-37. Epub 2010/11/20. doi:10.1093/sysbio/syq073 PMID: 21088009.
27. Urbanus AT, van de Laar TJ, Stolte IG, Schinkel J, Heijman T, Coutinho RA, et al. Hepatitis C virus infections among HIV-infected men who have sex with men: An expanding epidemic. AIDS. 2009; 23 (12):F1-F7. doi:10.1097/QAD.0b013e32832e5631 PMID: 19542864.
28. Samimi-Rad K, Asgari F, Nasiritoosi M, Esteghamati A, Azarkeyvan A, Eslami SM, et al. Patient-to- Patient Transmission of Hepatitis C at Iranian Thalassemia Centers Shown by Genetic Characterization of Viral Strains. Hepatitis monthly. 2013; 13(1):e7699. Epub 2013/04/16. doi:10.5812/hepatmon.7699 PMID: 23585766; PubMed Central PMCID: PMC3622054.
29. Sacks-Davis R, Daraganova G, Aitken C, Higgs P, Tracy L, Bowden S, et al. Hepatitis C virus phylogenetic clustering is associated with the social-injecting network in a cohort of people who inject drugs. PloS one. 2012; 7(10):e47335. Epub 2012/10/31. doi:10.1371/journal.pone.0047335 PMID: 23110068; PubMed Central PMCID: PMC3482197.
30. Sultana C, Oprisan G, Szmal C, Vagu C, Temereanca A, Dinu S, et al. Molecular epidemiology of hepatitis C virus strains from Romania. Journal of gastrointestinal and liver diseases: JGLD. 2011; 20 (3):261-6. Epub 2011/10/01. PMID: 21961093.
31. Danielsson A, Palanisamy N, Golbob S, Yin H, Blomberg J, Hedlund J, et al. Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden. Infection ecology & epidemiology. 2014; 4. Epub 2014/01/24. doi:10.3402/iee.v4.22251 PMID: 24455107; PubMed Central PMCID: PMC3895264.
32. Lampe E, Lewis-Ximenez L, Espirito-Santo MP, Delvaux NM, Pereira SA, Peres-da-Silva A, et al. Genetic diversity of HCV in Brazil. Antiviral therapy. 2013; 18(3 Pt B):435-44. Epub 2013/06/26. doi:10.3851/IMP2606PMID: 23792792.
33. Saludes V, Esteve M, Casas I, Ausina V, Martro E. Hepatitis C virus transmission during colonoscopy evidenced by phylogenetic analysis. Journal of clinical virology: The official publication of the Pan American Society for Clinical Virology. 2013; 57(3):263-6. Epub 2013/04/10. doi:10.1016/j.jcv.2013.03.007 PMID: 23567025.
34. Feray C, Bouscaillou J, Falissard B, Mohamed MK, Arafa N, Bakr I, et al. A novel method to identify routes of hepatitis C virus transmission. PloS one. 2014; 9(1):e86098. Epub 2014/01/28. doi:10.1371/journal.pone.0086098PMID: 24465895; PubMed Central PMCID: PMC3900465.
35. Sunbul M, Khan A, Kurbanov F, Leblebicioglu H, Sugiyama M, Tanaka Y, et al. Tracing the spread of hepatitis C virus in Turkey: A phylogenetic analysis. Intervirology. 2013; 56(3):201-5. Epub 2013/04/04. doi:10.1159/000346775 PMID: 23548552.
36. Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, Rasachak B, et al. Genetic history of hepatitis C virus in East Asia. Journal of virology. 2009; 83(2):1071-82. Epub 2008/10/31. doi:10.1128/JVI.01501-08PMID: 18971279; PubMed Central PMCID: PMC2612398.
37. Ciccozzi M, Zehender G, Cento V, Lo Presti A, Teoharov P, Pavlov I, et al. Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users. Journal of medical virology. 2011; 83(9):1565-70. Epub 2011/07/09. doi:10.1002/jmv.22154 PMID: 21739447.
38. Sulbaran MZ, Di Lello FA, Sulbaran Y, Cosson C, Loureiro CL, Rangel HR, et al. Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2. PloS one. 2010; 5(12):e14315. Epub 2010/12/24. doi:10.1371/journal.pone.0014315 PMID: 21179440; PubMed Central PMCID: PMC3001475.
39. Gadagkar SR, Rosenberg MS, Kumar S. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. Journal of experimental zoology Part B, Molecular and developmental evolution. 2005; 304(1):64-74. Epub 2004/12/14. doi:10.1002/jez.b.21026 PMID: 15593277.
40. Cai Q, Zhao Z, Liu Y, Shao X, Gao Z. Comparison of three different HCV genotyping methods: core, NS5B sequence analysis and line probe assay. International journal of molecular medicine. 2013; 31 (2):347-52. Epub 2012/12/18. doi:10.3892/ijmm.2012.1209 PMID: 23241873.
41. Avo AP, Agua-Doce I, Andrade A, Padua E. Hepatitis C virus subtyping based on sequencing of the C/E1 and NS5B genomic regions in comparison to a commercially available line probe assay. Journal of medical virology. 2013; 85(5):815-22. Epub 2013/03/20. doi:10.1002/jmv.23545 PMID: 23508907.
42. Galli A, Bukh J. Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus. Trends in microbiology. 2014; 22(6):354-64. Epub 2014/03/19. doi:10.1016/j.tim.2014.02.005PMID: 24636243.
43. Gonzalez-Candelas F, Bracho MA, Wrobel B, Moya A. Molecular evolution in court: Analysis of a large hepatitis C virus outbreak from an evolving source. BMC biology. 2013; 11:76. Epub 2013/07/23. doi:10.1186/1741-7007-11-76 PMID: 23870105; PubMed Central PMCID: PMC3717074.
44. Escobar-Gutierrez A, Vazquez-Pichardo M, Cruz-Rivera M, Rivera-Osorio P, Carpio-Pedroza JC, Ruiz-Pacheco JA, et al. Identification of hepatitis C virus transmission using a next-generation sequencing approach. Journal of clinical microbiology. 2012; 50(4):1461-3. Epub 2012/02/04. doi:10.1128/JCM.00005-12 PMID: 22301026; PubMed Central PMCID: PMC3318530.
45. Cruz-Rivera M, Carpio-Pedroza JC, Escobar-Gutierrez A, Lozano D, Vergara-Castaneda A, Rivera- Osorio P, et al. Rapid hepatitis C virus divergence among chronically infected individuals. Journal of clinical microbiology. 2013; 51(2):629-32. Epub 2012/12/12. doi:10.1128/JCM.03042-12 PMID: 23224093; PubMed Central PMCID: PMC3553878.
46. de Bruijne J, Schinkel J, Prins M, Koekkoek SM, Aronson SJ, van Ballegooijen MW, et al. Emergence of hepatitis C virus genotype 4: phylogenetic analysis reveals three distinct epidemiological profiles. Journal of clinical microbiology. 2009; 47(12):3832-8. Epub 2009/10/02doi:10.1128/JCM.01146-09 PMID: 19794040; PubMed Central PMCID: PMC2786681.
47. Vanhommerig JW, Thomas XV, van der Meer JT, Geskus RB, Bruisten SM, Molenkamp R, et al. Hepatitis C Virus (HCV) Antibody Dynamics following Acute HCV Infection and Reinfection among HIVInfected Men who have Sex with Men. Clinical infectious diseases: An official publication of the Infectious Diseases Society of America. 2014. Epub 2014/09/05. doi:10.1093/cid/ciu695 PMID: 25186590.
48. Cantarel BL, Morrison HG, Pearson W. Exploring the relationship between sequence similarity and accurate phylogenetic trees. Molecular biology and evolution. 2006; 23(11):2090-100. Epub 2006/08/08. doi:10.1093/molbev/msl080 PMID: 16891377.
49. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic biology. 2007; 56(4):564-77. Epub 2007/07/27doi:10.1080/10635150701472164 PMID: 17654362.
50. Simmonds P. Genetic diversity and evolution of hepatitis C virus-15 years on. The Journal of general virology. 2004; 85(Pt 11):3173-88. Epub 2004/10/16. doi:10.1099/vir.0.80401-0 PMID: 15483230.