| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Medical Microbiology, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG
2 Edinburgh and South East Scotland Blood Transfusion Service, Royal Infirmary of Edinburgh, Lauriston Place, Edinburgh EH3 9HB, U.K.
3 Chiron Corporation, 4560 Horton Street, Emeryville, California 94608, U.S.A.
and4 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
Isolates of hepatitis C virus (HCV) show considerable nucleotide sequence variability throughout the genome. Comparisons of complete genome sequences have been used as the basis of classification of HCV into a number of genotypes that show 67 to 77% sequence similarity. In order to investigate whether sequence relationships between genotypes are equivalent in different regions of the genome, we have carried out formal sequence analysis of variants in the 5' non-coding region (5'NCR) and in the genes encoding the core protein, an envelope protein (E1) and a non-structural protein (NS-5). In the E1 region, variants grouped into a series of six major genotypes and a series of subtypes that could be matched to the phylogenetic groupings previously observed for the NS-5 region. Furthermore, core and E1 sequences showed three non-overlapping ranges of sequence similarity corresponding to those between different genotypes, subtypes and isolates previously described in NS-5. Each major genotype could also be reliably identified by sequence comparisons in the well conserved 5'NCR, although many subtypes, such as 1a/1b, 2a/2c and some of those of type 4, could not be reliably distinguished from each other in this region. These data indicate that subgenomic regions such as E1 and NS-5 contain sufficient phylogenetic information for the identification of each of the 11 or 12 known types and subtypes of HCV. No evidence was found for variants of HCV that had sequences of one genotype in the 5'NCR but of a different one in the E1 or NS-5 region. This suggests that recombination between different HCV types is rare or non-existent and does not currently pose a problem in the use of subgenomic regions in classification.
Received 15 November 1993;
accepted 21 December 1993.
This article has been cited by other articles:
|
|
 |
|
  K. J. Herlihy, J. P. Graham, R. Kumpf, A. K. Patick, R. Duggal, and S. T. Shi Development of Intergenotypic Chimeric Replicons To Determine the Broad-Spectrum Antiviral Activities of Hepatitis C Virus Polymerase Inhibitors Antimicrob. Agents Chemother., October 1, 2008; 52(10): 3523 - 3531. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Li, L. V. Thomassen, A. Majid, B. J. McMahon, D. Bruden, S. McArdle, N. Bano, M. Chung, R. L. Carithers, J. D. Perkins, et al. Investigation of Putative Multisubtype Hepatitis C Virus Infections In Vivo by Heteroduplex Mobility Analysis of Core/Envelope Subgenomes J. Virol., August 1, 2008; 82(15): 7524 - 7532. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Noppornpanth, Y. Poovorawan, T. X. Lien, S. L. Smits, A. D. M. E. Osterhaus, and B. L. Haagmans Complete genome analysis of hepatitis C virus subtypes 6t and 6u J. Gen. Virol., May 1, 2008; 89(5): 1276 - 1281. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. G. Murphy, B. Willems, M. Deschenes, N. Hilzenrat, R. Mousseau, and S. Sabbah 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 J. Clin. Microbiol., April 1, 2007; 45(4): 1102 - 1112. [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]
|
|
|
|
|
|
S. Noppornpanth, T. X. Lien, Y. Poovorawan, S. L. Smits, A. D. M. E. Osterhaus, and B. L. Haagmans Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus. J. Virol., August 1, 2006; 80(15): 7569 - 7577. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Colina, D. Casane, S. Vasquez, L. Garcia-Aguirre, A. Chunga, H. Romero, B. Khan, and J. Cristina Evidence of intratypic recombination in natural populations of hepatitis C virus J. Gen. Virol., January 1, 2004; 85(1): 31 - 37. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Gault, P. Soussan, Y. Morice, L. Sanders, A. Berrada, B. Rogers, and P. Deny Evaluation of a New Serotyping Assay for Detection of Anti-Hepatitis C Virus Type-Specific Antibodies in Serum Samples J. Clin. Microbiol., May 1, 2003; 41(5): 2084 - 2087. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Dimitrova, I. Imbert, M. P. Kieny, and C. Schuster Protein-Protein Interactions between Hepatitis C Virus Nonstructural Proteins J. Virol., May 1, 2003; 77(9): 5401 - 5414. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. S. Nolte, A. M. Green, K. R. Fiebelkorn, A. M. Caliendo, C. Sturchio, A. Grunwald, and M. Healy Clinical Evaluation of Two Methods for Genotyping Hepatitis C Virus Based on Analysis of the 5' Noncoding Region J. Clin. Microbiol., April 1, 2003; 41(4): 1558 - 1564. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Chen and K. E. Weck Hepatitis C Virus Genotyping: Interrogation of the 5' Untranslated Region Cannot Accurately Distinguish Genotypes 1a and 1b J. Clin. Microbiol., September 1, 2002; 40(9): 3127 - 3134. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schroter, B. Zollner, P. Schafer, O. Landt, U. Lass, R. Laufs, and H.-H. Feucht Genotyping of Hepatitis C Virus Types 1, 2, 3, and 4 by a One-Step LightCycler Method Using Three Different Pairs of Hybridization Probes J. Clin. Microbiol., June 1, 2002; 40(6): 2046 - 2050. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Kalinina, H. Norder, S. Mukomolov, and L. O. Magnius A Natural Intergenotypic Recombinant of Hepatitis C Virus Identified in St. Petersburg J. Virol., March 19, 2002; 76(8): 4034 - 4043. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J C L Booth, J O'Grady, and J Neuberger Clinical guidelines on the management of hepatitis C Gut, July 1, 2001; 49(0): I1 - 21. [Full Text] [PDF]
|
|
|
|
|
|
J. F. Quarleri, B. H. Robertson, V. L. Mathet, M. Feld, L. Espínola, M. P. Requeijo, O. Mandó, G. Carballal, and J. R. Oubiña Genomic and Phylogenetic Analysis of Hepatitis C Virus Isolates from Argentine Patients: a Six-Year Retrospective Study J. Clin. Microbiol., December 1, 2000; 38(12): 4560 - 4568. [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]
|
|
|
|
|
|
D. B. Smith, M. Basaras, S. Frost, D. Haydon, N. Cuceanu, L. Prescott, C. Kamenka, D. Millband, M. A. Sathar, and P. Simmonds Phylogenetic analysis of GBV-C/hepatitis G virus J. Gen. Virol., March 1, 2000; 81(3): 769 - 780. [Abstract] [Full Text]
|
|
|
|
|
|
R. N. Charrel, P. De Micco, and X. de Lamballerie Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts J. Gen. Virol., September 1, 1999; 80(9): 2329 - 2335. [Abstract] [Full Text]
|
|
|
|
|
|
G V Papatheodoridis, S G R G Barton, D Andrew, G Clewley, S Davies, A P Dhillon, G Dusheiko, B Davidson, K Rolles, and A K Burroughs Longitudinal variation in hepatitis C virus (HCV) viraemia and early course of HCV infection after liver transplantation for HCV cirrhosis: the role of different immunosuppressive regimens Gut, September 1, 1999; 45(3): 427 - 434. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schröter, H.-H. Feucht, P. Schäfer, B. Zöllner, and R. Laufs Serological Determination of Hepatitis C Virus Subtypes 1a, 1b, 2a, 2b, 3a, and 4a by a Recombinant Immunoblot Assay J. Clin. Microbiol., August 1, 1999; 37(8): 2576 - 2580. [Abstract] [Full Text]
|
|
|
|
|
|
J. J. Germer, P. N. Rys, J. N. Thorvilson, and D. H. Persing Determination of Hepatitis C Virus Genotype by Direct Sequence Analysis of Products Generated with the Amplicor HCV Test J. Clin. Microbiol., August 1, 1999; 37(8): 2625 - 2630. [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]
|
|
|
|
|
|
M. E. Major, K. Mihalik, J. Fernandez, J. Seidman, D. Kleiner, A. A. Kolykhalov, C. M. Rice, and S. M. Feinstone Long-Term Follow-Up of Chimpanzees Inoculated with the First Infectious Clone for Hepatitis C Virus J. Virol., April 1, 1999; 73(4): 3317 - 3325. [Abstract] [Full Text]
|
|
|
|
|
|
Y.-M. Wang, S. C. Ray, O. Laeyendecker, J. R. Ticehurst, and D. L. Thomas Assessment of Hepatitis C Virus Sequence Complexity by Electrophoretic Mobilities of Both Single-and Double-Stranded DNAs J. Clin. Microbiol., October 1, 1998; 36(10): 2982 - 2989. [Abstract] [Full Text]
|
|
|
|
|
|
D. O'Meara, Z. Yun, A. Sönnerborg, and J. Lundeberg Cooperative Oligonucleotides Mediating Direct Capture of Hepatitis C Virus RNA from Serum J. Clin. Microbiol., September 1, 1998; 36(9): 2454 - 2459. [Abstract] [Full Text]
|
|
|
|
|
|
G H Haydon, L M Jarvis, C S Blair, P Simmonds, D J Harrison, K J Simpson, and P C Hayes Clinical significance of intrahepatic hepatitis C virus levels in patients with chronic HCV infection Gut, April 1, 1998; 42(4): 570 - 575. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 H. J. Worman Molecular biological methods in diagnosis and treatment of liver diseases Clin. Chem., August 1, 1997; 43(8): 1476 - 1486. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Ridzon, K. Gallagher, C. Ciesielski, E. E. Mast, M. B. Ginsberg, B. J. Robertson, C.-C. Luo, and A. DeMaria Simultaneous Transmission of Human Immunodeficiency Virus and Hepatitis C Virus from a Needle-Stick Injury N. Engl. J. Med., March 27, 1997; 336(13): 919 - 922. [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
