| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Medical Microbiology, University of Edinburgh, Medical School, Teviot Place, Edinburgh EH8 9AG, UK
2 Edinburgh and South East Scotland Blood Transfusion Service, Lauriston Place, Edinburgh EH3 9HB, UK
and3 Chiron Corporation, 4560 Horton Street, Emeryville, California 94608, USA
Variation in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) was investigated in detail by comparing 314 5'NCR sequences of viruses of genotypes 1 to 6. Evidence was obtained for the existence of associations between particular 5'NCR sequence motifs and virus types and subtypes. No recombination was observed between the 5'NCR and coding regions of different genotypes, implying that the sequence of subgenomic regions such as the 5'NCR can be used to deduce virus genotype. The distribution of polymorphic sites within the 5'NCR is used to propose improved oligonucleotide primers for virus detection and quantification that would be equally efficient in detecting RNA of different virus genotypes. The accuracy of two different genotyping methods (RFLP and the line probe assay) based on analysis of sequence polymorphisms in the 5'NCR is predicted from the sequences surveyed to be 97% and 83% respectively for types 1 to 6, with higher accuracies for distinguishing between subtypes 1a/1b, 2a/2b or 3a/3b. Several sites of genotype-specific polymorphism were covariant and maintained the base pairings required for a secondary structure model of the 5'NCR. Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5'NCR
* Author for correspondence. Fax +44 131 650 6531. e-mail dbs@srvl.med.ed.ac.uk
International HCV Collaborative Study Group: J. D. Conradie and A. G. S. Neill, Natal Institute of Immunology and Blood Transfusion Service, Durban, South Africa; G. M. Dusheiko, Royal Free Hospital, London, UK; M. C. Kew and R. Crookes, University of Witwatersrand and Blood Transfusion Service, Johannesburg, South Africa; A. Koshy, Kuwait University, Kuwait; C. K. Lin and C. Lai, Red Cross Blood Transfusion Service, Yaumatei, Hong Kong; I. M. Murray-Lyon, Charing Cross Hospital, London, UK; A. El-Guneid and A. A. Gunaid, Al Thowra Hospitals, Taiz and Sana'a, Yemen; D. Mutimer and M. Ahmed, Queen Elizabeth Hospital, Birmingham, UK; C Nuchprayoon and S. Tanprasert, Red Cross Society, Bangkok, Thailand; F. E. Preston and M. Makris, Royal Hallamshire Hospital, Sheffield, UK; A. Chuansumrit, Ramathibodi Hospital and C. Mahasandana, Siriraj Hospital, Bangkok, Thailand; D. Pritchard, University of Nottingham, UK; E. Riley, University of Edinburgh, Edinburgh, UK; B. M. Greenwood, MRC Laboratories, Fajara, The Gambia; A. A. Saeed and A. M. Al-Rasheed, Riyadh Armed Forces Hospital, Saudi Arabia; M. G. Saleh, I. McFarlane, C. Tibbs and R. Williams, Kings College Hospital, London, UK; J. Power and E. Lawlor, Blood Transfusion Service Board, Republic of Ireland; H. Kiyokawa, Red Cross Blood Centre, Fukuoka, Japan.
Received 21 December 1994;
accepted 28 February 1995.
This article has been cited by other articles:
|
|
 |
|
  J. Verbeeck, M. J. Stanley, J. Shieh, L. Celis, E. Huyck, E. Wollants, J. Morimoto, A. Farrior, E. Sablon, M. Jankowski-Hennig, et al. Evaluation of Versant Hepatitis C Virus Genotype Assay (LiPA) 2.0 J. Clin. Microbiol., June 1, 2008; 46(6): 1901 - 1906. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Martro, V. Gonzalez, A. J. Buckton, V. Saludes, G. Fernandez, L. Matas, R. Planas, and V. Ausina Evaluation of a New Assay in Comparison with Reverse Hybridization and Sequencing Methods for Hepatitis C Virus Genotyping Targeting Both 5' Noncoding and Nonstructural 5b Genomic Regions J. Clin. Microbiol., January 1, 2008; 46(1): 192 - 197. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Ticehurst, F. M. Hamzeh, and D. L. Thomas Factors Affecting Serum Concentrations of Hepatitis C Virus (HCV) RNA in HCV Genotype 1-Infected Patients with Chronic Hepatitis J. Clin. Microbiol., August 1, 2007; 45(8): 2426 - 2433. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. U. T. Hellen and S. de Breyne A Distinct Group of Hepacivirus/Pestivirus-Like Internal Ribosomal Entry Sites in Members of Diverse Picornavirus Genera: Evidence for Modular Exchange of Functional Noncoding RNA Elements by Recombination J. Virol., June 1, 2007; 81(11): 5850 - 5863. [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]
|
|
|
|
 |
|
 N. Beguiristain, H. D. Robertson, and J. Gomez RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site Nucleic Acids Res., September 16, 2005; 33(16): 5250 - 5261. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. N. Ilina, M. V. Malakhova, E. V. Generozov, E. N. Nikolaev, and V. M. Govorun Matrix-Assisted Laser Desorption Ionization-Time of Flight (Mass Spectrometry) for Hepatitis C Virus Genotyping J. Clin. Microbiol., June 1, 2005; 43(6): 2810 - 2815. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Girard, M. Ravallec, M. Mariller, J.-P. Bossy, A. Cahour, M. Lopez-Ferber, G. Devauchelle, G. Inchauspe, and M. Duonor-Cerutti Effect of the 5' non-translated region on self-assembly of hepatitis C virus genotype 1a structural proteins produced in insect cells J. Gen. Virol., December 1, 2004; 85(12): 3659 - 3670. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Martell, C. Briones, A. de Vicente, M. Piron, J. I. Esteban, R. Esteban, J. Guardia, and J. Gomez Structural analysis of hepatitis C RNA genome using DNA microarrays Nucleic Acids Res., June 24, 2004; 32(11): e90 - e90. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Germer, D. W. Majewski, M. Rosser, A. Thompson, P. S. Mitchell, T. F. Smith, S. Elagin, and J. D.C. Yao Evaluation of the TRUGENE HCV 5'NC Genotyping Kit with the New GeneLibrarian Module 3.1.2 for Genotyping of Hepatitis C Virus from Clinical Specimens J. Clin. Microbiol., October 1, 2003; 41(10): 4855 - 4857. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Quarleri, M. V. Bussy, V. L. Mathet, V. Ruiz, R. Iacono, L. Lu, B. H. Robertson, and J. R. Oubina In Vitro Detection of Dissimilar Amounts of Hepatitis C Virus (HCV) Subtype-Specific RNA Genomes in Mixes Prepared from Sera of Persons Infected with a Single HCV Genotype J. Clin. Microbiol., June 1, 2003; 41(6): 2727 - 2733. [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]
|
|
|
|
|
|
J. E. Levi, D. T. Takaoka, R. H. Garrini, R. M. Fachini, R. Focaccia, E. de Bortholi Santos, H. P. Mitre, J. S. de Mendonca, N. de Paula Cavalheiro, A. A. Barone, et al. Three Cases of Infection with Hepatitis C Virus Genotype 5 among Brazilian Hepatitis Patients J. Clin. Microbiol., July 1, 2002; 40(7): 2645 - 2647. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. P. Fletcher and R. J. Jackson Pestivirus Internal Ribosome Entry Site (IRES) Structure and Function: Elements in the 5' Untranslated Region Important for IRES Function J. Virol., April 16, 2002; 76(10): 5024 - 5033. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. U.T. Hellen and P. Sarnow Internal ribosome entry sites in eukaryotic mRNA molecules Genes & Dev., July 1, 2001; 15(13): 1593 - 1612. [Full Text] [PDF]
|
|
|
|
|
|
L. Krekulova, V. Rehak, A. E. Wakil, E. Harris, and L. W. Riley Nested Restriction Site-Specific PCR To Detect and Type Hepatitis C Virus (HCV): a Rapid Method To Distinguish HCV Subtype 1b from Other Genotypes J. Clin. Microbiol., May 1, 2001; 39(5): 1774 - 1780. [Abstract] [Full Text]
|
|
|
|
|
|
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]
|
|
|
|
|
|
J. Laporte, I. Malet, T. Andrieu, V. Thibault, J.-J. Toulme, C. Wychowski, J.-M. Pawlotsky, J.-M. Huraux, H. Agut, and A. Cahour Comparative Analysis of Translation Efficiencies of Hepatitis C Virus 5' Untranslated Regions among Intraindividual Quasispecies Present in Chronic Infection: Opposite Behaviors Depending on Cell Type J. Virol., November 15, 2000; 74(22): 10827 - 10833. [Abstract] [Full Text]
|
|
|
|
|
|
R. S. Ross, S. O. Viazov, C. D. Holtzer, A. Beyou, A. Monnet, C. Mazure, and M. Roggendorf Genotyping of Hepatitis C Virus Isolates using CLIP Sequencing J. Clin. Microbiol., October 1, 2000; 38(10): 3581 - 3584. [Abstract] [Full Text]
|
|
|
|
|
|
V. G. Kolupaeva, T. V. Pestova, and C. U. T. Hellen An Enzymatic Footprinting Analysis of the Interaction of 40S Ribosomal Subunits with the Internal Ribosomal Entry Site of Hepatitis C Virus J. Virol., July 15, 2000; 74(14): 6242 - 6250. [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]
|
|
|
|
|
|
P. A. White, X. Zhai, I. Carter, Y. Zhao, and W. D. Rawlinson Simplified Hepatitis C Virus Genotyping by Heteroduplex Mobility Analysis J. Clin. Microbiol., February 1, 2000; 38(2): 477 - 482. [Abstract] [Full Text]
|
|
|
|
|
|
R. Rijnbrand, G. Abell, and S. M. Lemon Mutational Analysis of the GB Virus B Internal Ribosome Entry Site J. Virol., January 1, 2000; 74(2): 773 - 783. [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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
S. Jang, L. Wang, M Radkowski, J Rakela, and T Laskus Differences between hepatitis C virus 5' untranslated region quasispecies in serum and liver J. Gen. Virol., March 1, 1999; 80(3): 711 - 716. [Abstract]
|
|
|
|
|
|
S. Tang, A. J. Collier, and R. M. Elliott Alterations to both the Primary and Predicted Secondary Structure of Stem-Loop IIIc of the Hepatitis C Virus 1b 5' Untranslated Region (5'UTR) Lead to Mutants Severely Defective in Translation Which Cannot Be Complemented in trans by the Wild-Type 5'UTR Sequence J. Virol., March 1, 1999; 73(3): 2359 - 2364. [Abstract] [Full Text]
|
|
|
|
|
|
M. Martell, J. Gómez, J. I. Esteban, S. Sauleda, J. Quer, B. Cabot, R. Esteban, and J. Guardia High-Throughput Real-Time Reverse Transcription-PCR Quantitation of Hepatitis C Virus RNA J. Clin. Microbiol., February 1, 1999; 37(2): 327 - 332. [Abstract] [Full Text]
|
|
|
|
|
|
M. Honda, M. R. Beard, L.-H. Ping, and S. M. Lemon A Phylogenetically Conserved Stem-Loop Structure at the 5' Border of the Internal Ribosome Entry Site of Hepatitis C Virus Is Required for Cap-Independent Viral Translation J. Virol., February 1, 1999; 73(2): 1165 - 1174. [Abstract] [Full Text]
|
|
|
|
|
|
D. V. Sizova, V. G. Kolupaeva, T. V. Pestova, I. N. Shatsky, and C. U. T. Hellen Specific Interaction of Eukaryotic Translation Initiation Factor 3 with the 5' Nontranslated Regions of Hepatitis C Virus and Classical Swine Fever Virus RNAs J. Virol., June 1, 1998; 72(6): 4775 - 4782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. McAllister, C. Casino, F. Davidson, J. Power, E. Lawlor, P. L. Yap, P. Simmonds, and D. B. Smith Long-Term Evolution of the Hypervariable Region of Hepatitis C Virus in a Common-Source-Infected Cohort J. Virol., June 1, 1998; 72(6): 4893 - 4905. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Lerat, S. Rumin, F. Habersetzer, F. Berby, M.-A. Trabaud, C. Trepo, and G. Inchauspe In Vivo Tropism of Hepatitis C Virus Genomic Sequences in Hematopoietic Cells: Influence of Viral Load, Viral Genotype, and Cell Phenotype Blood, May 15, 1998; 91(10): 3841 - 3849. [Abstract] [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 | |
