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1 Department of Medical Microbiology, Medical School, 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 Hong Kong Red Cross Blood Transfusion Service, 15 King's Park Rise, Yaumatei, Kowloon, Hong Kong
4 Department of Medicine, Royal Free Hospital, London NW3 2PS, U.K.
5 Riyadh Armed Forces Hospital, Riyadh 11159, Saudi Arabia
and6 Division of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JN, U.K.
We have analysed the pattern of nucleotide sequence variability in the 5' non-coding region (5' NCR) of geographically dispersed variants of hepatitis C virus (HCV). Phylogenetic analysis of sequences in this region indicated the existence of a new virus type, provisionally termed type 4, the identity of which was confirmed by further analysis of the more variable part of the HCV core protein coding region. The geographical distribution of HCV type 4 was distinct from that of other HCV types, it being particularly widespread in Africa and absent or rare in Europe and the Far East. Much of the variability in the 5' NCR appears to be constrained by a requirement for specific secondary structures in the viral RNA. In one of the most variable regions of the 5' NCR (positions - 169 to - 114), most of the nucleotide changes that are characteristic of different HCV types were covariant, with complementary substitutions at other positions. According to the proposed secondary structure of the 5' NCR, such changes preserved base pairing within a stem-loop structure, whereas the nucleotide insertions found in a proportion of 5' NCR sequences, including those of type 4, localized exclusively to the non-base-paired terminal loop. The specific nucleotide substitutions in the 5' NCR that differentiate each of the four HCV types can be detected by restriction enzyme cleavage, providing a rapid and reliable method for virus typing.
Received 3 November 1992;
accepted 9 December 1992.
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