| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Medical Microbiology, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
2 National Blood Centre, Thai Red Cross Society, Henri Durant Road, Bangkok 10330, Thailand
3 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity values or evolutionary distances corresponding to divisions of HCV into types, subtypes and isolates. Using these criteria, novel variants of HCV from Vietnam, Thailand and Indonesia have been classified as types 7, 8, 9, 10 and 11, many of which can be further subdivided into between two to four subtypes. In this study, this distance-based method of virus classification was compared with phylogenetic analysis and statistical measures to establish the confidence of the groupings. Using bootstrap resampling of phylogenetic trees in several subgenomic regions (core, E1, NS5) and with complete genomic sequences, we found that one set of novel HCV variants (‘types 7, 8, 9 and 11’) consistently grouped together into a single clade that also contained type 6a, while ‘type 10a’ grouped with type 3. In contrast, no robust higher-order groupings were observed between any of the other five previously described HCV genotypes (types 1–5). In each subgenomic region, the distribution of pairwise distances between members of the type 6 clade were consistently bi-modal and therefore provided no justification for classification of these variants into the three proposed categories (type, subtype, isolate). Based on these results, we propose that a more useful classification would regard all these variants as subtypes of type 6 or type 3, even though the level of sequence diversity within the clade was greater than observed for other genotypes. Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus.
Received 17 June 1996;
accepted 6 August 1996.
This article has been cited by other articles:
|
|
 |
|
  L. Lu, D. Murphy, C. Li, S. Liu, X. Xia, P. H. Pham, Y. Jin, C. H. Hagedorn, and K. Abe Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6 J. Gen. Virol., February 1, 2008; 89(2): 444 - 452. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lu, C. Li, Y. Fu, L. Thaikruea, S. Thongswat, N. Maneekarn, C. Apichartpiyakul, H. Hotta, H. Okamoto, D. Netski, et al. Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses J. Gen. Virol., May 1, 2007; 88(5): 1505 - 1518. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lu, C. Li, Y. Fu, F. Gao, O. G. Pybus, K. Abe, H. Okamoto, C. H. Hagedorn, and D. Murphy Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6 J. Gen. Virol., May 1, 2007; 88(5): 1519 - 1525. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Bouchardeau, J. F. Cantaloube, S. Chevaliez, C. Portal, A. Razer, J.-J. Lefrere, J. M. Pawlotsky, P. De Micco, and S. Laperche Improvement of Hepatitis C Virus (HCV) Genotype Determination with the New Version of the INNO-LiPA HCV Assay J. Clin. Microbiol., April 1, 2007; 45(4): 1140 - 1145. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Noppornpanth, E. Sablon, K. De Nys, T. X. Lien, J. Brouwer, M. Van Brussel, S. L. Smits, Y. Poovorawan, A. D. M. E. Osterhaus, and B. L. Haagmans Genotyping Hepatitis C Viruses from Southeast Asia by a Novel Line Probe Assay That Simultaneously Detects Core and 5' Untranslated Regions J. Clin. Microbiol., November 1, 2006; 44(11): 3969 - 3974. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lu, T. Nakano, C. Li, Y. Fu, S. Miller, C. Kuiken, B. H. Robertson, and C. H. Hagedorn Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J. Gen. Virol., March 1, 2006; 87(Pt 3): 629 - 634. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Laperche, K. Saune, P. Deny, G. Duverlie, S. Alain, M.-L. Chaix, C. Gaudy, F. Lunel, J.-M. Pawlotsky, C. Payan, et al. Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database Is Essential for Standardization of Genotype Determinations in Multicenter Epidemiological Studies J. Clin. Microbiol., February 1, 2006; 44(2): 614 - 616. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hazari, A. Patil, V. Joshi, D. E. Sullivan, C. D. Fermin, R. F. Garry, R. M. Elliott, and S. Dash Alpha interferon inhibits translation mediated by the internal ribosome entry site of six different hepatitis C virus genotypes J. Gen. Virol., November 1, 2005; 86(11): 3047 - 3053. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-F. Cantaloube, P. Gallian, H. Attoui, P. Biagini, P. De Micco, and X. de Lamballerie Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Blood Donors from Southeast France J. Clin. Microbiol., August 1, 2005; 43(8): 3624 - 3629. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Laperche, F. Lunel, J. Izopet, S. Alain, P. Deny, G. Duverlie, C. Gaudy, J.-M. Pawlotsky, J.-C. Plantier, B. Pozzetto, et al. Comparison of Hepatitis C Virus NS5b and 5' Noncoding Gene Sequencing Methods in a Multicenter Study J. Clin. Microbiol., February 1, 2005; 43(2): 733 - 739. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Netski, X.-H. Wang, S. H. Mehta, K. Nelson, D. Celentano, S. Thongsawat, N. Maneekarn, V. Suriyanon, J. Jittiwutikorn, D. L. Thomas, et al. Hepatitis C Virus (HCV) Core Antigen Assay To Detect Ongoing HCV Infection in Thai Injection Drug Users J. Clin. Microbiol., April 1, 2004; 42(4): 1631 - 1636. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. You, D. D. Stump, A. D. Branch, and C. M. Rice A cis-Acting Replication Element in the Sequence Encoding the NS5B RNA-Dependent RNA Polymerase Is Required for Hepatitis C Virus RNA Replication J. Virol., February 1, 2004; 78(3): 1352 - 1366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. S. Lole, J. A. Jha, S. P. Shrotri, B. N. Tandon, V. G. M. Prasad, and V. A. Arankalle Comparison of Hepatitis C Virus Genotyping by 5' Noncoding Region- and Core-Based Reverse Transcriptase PCR Assay with Sequencing and Use of the Assay for Determining Subtype Distribution in India J. Clin. Microbiol., November 1, 2003; 41(11): 5240 - 5244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Morice, D. Roulot, V. Grando, J. Stirnemann, E. Gault, V. Jeantils, M. Bentata, B. Jarrousse, O. Lortholary, C. Pallier, et al. Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns J. Gen. Virol., May 1, 2001; 82(5): 1001 - 1012. [Abstract] [Full Text]
|
|
|
|
|
|
P. Simmonds 2000 Fleming Lecture. The origin and evolution of hepatitis viruses in humans J. Gen. Virol., April 1, 2001; 82(4): 693 - 712. [Abstract] [Full Text]
|
|
|
|
|
|
K. Abid, R. Quadri, A.-L. Veuthey, A. Hadengue, and F. Negro A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3 J. Gen. Virol., June 1, 2000; 81(6): 1485 - 1493. [Abstract] [Full Text]
|
|
|
|
 |
|
 N. N. Zein Clinical Significance of Hepatitis C Virus Genotypes Clin. Microbiol. Rev., April 1, 2000; 13(2): 223 - 235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. E. Khudyakov, M.-e. Cong, B. Nichols, D. Reed, X.-G. Dou, S. O. Viazov, J. Chang, M. W. Fried, I. Williams, W. Bower, et al. Sequence Heterogeneity of TT Virus and Closely Related Viruses J. Virol., April 1, 2000; 74(7): 2990 - 3000. [Abstract] [Full Text]
|
|
|
|
|
|
S. M. Bowyer and J. G. M. Sim Relationships within and between genotypes of hepatitis B virus at points across the genome: footprints of recombination in certain isolates J. Gen. Virol., February 1, 2000; 81(2): 379 - 392. [Abstract] [Full Text]
|
|
|
|
|
|
R Colina, C Azambuja, R Uriarte, C Mogdasy, and J Cristina Evidence of increasing diversification of hepatitis C viruses J. Gen. Virol., June 1, 1999; 80(6): 1377 - 1382. [Abstract]
|
|
|
|
|
|
P. Calvo, J Kansopon, K Sra, S Quan, R DiNello, R Guaschino, G Calabrese, F Danielle, M. Brunetto, F Bonino, et al. Hepatitis C virus heteroduplex tracking assay for genotype determination reveals diverging genotype 2 isolates in Italian hemodialysis patients [In Process Citation] J. Clin. Microbiol., January 1, 1998; 36(1): 227 - 233. [Abstract] [Full Text]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
