Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants

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 3 Division of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JN and 4 SNBTS Microbiology Reference Unit, Regional Virus Laboratory, Ruchill Hospital, Glasgow G20 9NB, U.K. Sequences obtained in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) were obtained from Scottish blood donors and compared with previously published HCV sequences. Phylogenetic analysis revealed the existence of three distinct groups of sequences; two of these corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species. Nucleotide sequences of this latter group differed from all previously published 5'NCR sequence variants by at least 9%. This new virus type also differed considerably from previously published variants in other regions of the viral genome (core, NS-3 and NS-5), with corrected nucleotide distances of 15, 43 and 49% respectively from the prototype HCV-1 sequence. Formal phylogenetic analysis of each of the coding regions confirmed that HCV type 1 variants could be clearly differentiated into regional variants (Far East and U.S.A./European), in contrast to the clearly overlapping geographical distributions of the main HCV types in U.K. blood donors. We discuss the evidence for and against the hypothesis that the three main phylogenetic groups identified in this study represent separate species of HCV. Received 5 December 1991; accepted 31 January 1992.