Analysing the evolutionary history of HCV: Puzzle of ancient phylogenetic discordance

Infection, Genetics and Evolution

Volumn 7, Issue 3, 2007, Pages 354-360

  Magiorkinis, G ^a   Ntziora, F ^a   Paraskevis, D ^a   Magiorkinis, E ^a   Hatzakis, A ^a  

^a UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

Author keywords

HCV; Interferon resistance; Phylogenetic discordance; Recombination

Indexed keywords

INTERFERON;

ARTICLE; CONVERGENT EVOLUTION; DATA ANALYSIS; DATA BASE; DATA EXTRACTION; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOTYPE; HEPATITIS C VIRUS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; VIRUS GENE; VIRUS GENOME; VIRUS RECOMBINATION; VIRUS RESISTANCE; VIRUS STRAIN;

EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOTYPE; HEPACIVIRUS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC;

HEPATITIS C VIRUS; RNA VIRUSES;

EID: 34247619334     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2006.04.003     Document Type: Article

References (32)

1. Abdo A.A., and Lee S.S. Management of hepatitis C virus genotype 4. J. Gastroenterol. Hepatol. 19 (2004) 1233-1239
2. Abdulkarim A.S., Zein N.N., Germer J.J., Kolbert C.P., Kabbani L., Krajnik K.L., Hola A., Agha M.N., Tourogman M., and Persing D.H. Hepatitis C virus genotypes and hepatitis G virus in hemodialysis patients from Syria: identification of two novel hepatitis C virus subtypes. Am. J. Trop. Med. Hyg. 59 (1998) 571-576
3. Bukh J., Purcell R.H., and Miller R.H. At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative El gene of isolates collected worldwide. Proc. Natl. Acad. Sci. USA 90 (1993) 8234-8238
4. Bukh J., Purcell R.H., and Miller R.H. Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc. Natl. Acad. Sci. USA 91 (1994) 8239-8243
5. Cha T.A., Beall E., Jrvine B., Kolberg J., Chien D., Kuo G., and Urdea M.S. At least five related, but distinct, hepatitis C viral genotypes exist. Proc. Natl. Acad. Sci. USA 89 (1992) 7144-7148
6. Chamberlain R.W., Adams N., Saeed A.A., Simmonds P., and Elliott R.M. Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J. Gen. Virol. 78 Pt 6 (1997) 1341-1347
7. Colina R., Casane D., Vasquez S., Garcia-Aguirre L., Chunga A., Romero H., Khan B., and Cristina J. Evidence of intratypic recombination in natural populations of hepatitis C virus. J. Gen. Virol. 85 (2004) 31-37
8. Dusheiko G., Schmilovitz-Weiss H., Brown D., McOmish F., Yap P.L., Sherlock S., McIntyre N., and Simmonds P. Hepatitis C virus genotypes: an investigation of type-specific differences in geographic origin and disease. Hepatology 19 (1994) 13-18
9. Huang F., Zhao G.Z., and Li Y. HCV genotypes in hepatitis C patients and their clinical significances. World J. Gastroenterol. 5 (1999) 547-549
10. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
11. Kalinina O., Norder H., Mukomolov S., and Magnius L.O. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J. Virol. 76 (2002) 4034-4043
12. McOmish F., Yap P.L., Dow B.C., Follett E.A., Seed C., Keller A.J., Cobain T.J., Krusius T., Kolho E., Naukkarinen R., et al. Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J. Clin. Microbiol. 32 (1994) 884-892
13. Nolte F.S. Hepatitis C virus genotyping: clinical implications and methods. Mol. Diagn. 6 (2001) 265-277
14. Nousbaum J.B., Pol S., Nalpas B., Landais P., Berthelot P., and Brechot C. Hepatitis C virus type lb (II) infection in France and Italy. Collaborative Study Group. Ann. Int. Med. 122 (1995) 161-168
15. Paraskevis D., Deforche K., Lemey P., Magiorkinis G., Hatzakis A., and Vandamme A.M. SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics 21 (2005) 1274-1275
16. Pawlotsky J.M., Tsakiris L., Roudot-Thoraval F., Pellet C., Stuyver L., Duval J., and Dhumeaux D. Relationship between hepatitis C virus genotypes and sources of infection in patients with chronic hepatitis C. J. Infect. Dis. 171 (1995) 1607-1610
17. Robertson B., Myers G., Howard C., Brettin T., Bukh J., Gaschen B., Gojobori T., Maertens G., Mizokami M., Nainan O., Netesov S., Nishioka K., Shin i T., Simmonds P., Smith D., Stuyver L., and Weiner A. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch. Virol. 143 (1998) 2493-2503
18. Saiz J.C., Lopez-Labrador F.X., Ampurdanes S., Dopazo J., Forns X., Sanchez-Tapias J.M., and Rodes J. The prognostic relevance of the nonstructural 5A gene interferon sensitivity determining region is different in infections with genotype lb and 3a isolates of hepatitis C virus. J. Infect. Dis. 177 (1998) 839-847
19. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
20. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
21. Simmonds P. The origin and evolution of hepatitis viruses in humans. J. Gen. Virol. 82 (2001) 693-712
22. Simmonds P., Holmes E.C., Cha T.A., Chan S.W., McOmish F., Jrvine B., Beall E., Yap P.L., Kolberg J., and Urdea M.S. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J. Gen. Virol. 74 Pt 11 (1993) 2391-2399
23. Swofford, D., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Mehods). Version 4.
24. Takada N., Takase S., Takada A., and Date T. Differences in the hepatitis C virus genotypes in different countries. J. Hepatol. 17 (1993) 277-283
25. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
26. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
27. Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Lesmana L.A., Miyakawa Y., and Mayumi M. Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups. J. Gen. Virol. 77 Pt 2 (1996) 293-301
28. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., and Mayumi M. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc. Natl. Acad. Sci. USA 91 (1994) 11022-11026
29. Tuffley C., and Steel M. Modeling the covarion hypothesis of nucleotide substitution. Math Biosci. 147 (1998) 63-91
30. Xia X., and Xie Z. DAMBE: data analysis in molecular biology and evolution. J. Heredity 92 (2001) 371-373
31. Zein N.N. Clinical significance of hepatitis C virus genotypes. Clin. Microbiol. Rev. 13 (2000) 223-235
32. Zein N.N., Rakela J., Krawitt E.L., Reddy K.R., Tominaga T., and Persing D.H. Hepatitis C virus genotypes in the United States: epidemiology, pathogenicity, and response to interferon therapy. Collaborative Study Group. Ann. Int. Med. 125 (1996) 634-639