Abstract
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.