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Phylogenetic analysis of GBV-C/hepatitis G virus

Department of Medical Microbiology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK¹
Department of Microbiology, School of Medicine, Universidad del Pais Vasco, 48080 Bilbao, Spain²
Centre for HIV Research, University of Edinburgh, Waddington Building, King’s Buildings, West Mains Road, Edinburgh EH9 3JN, UK³
Centre for Tropical Veterinary Medicine, University of Edinburgh, Easter Bush, Roslin EH25 9RG, UK⁴
Department of Medicine, University of Natal, Congella, South Africa 4013⁵

Author for correspondence: Donald Smith. Present address: Garden Cottage, Clerkington, Haddington, East Lothian EH41 4NJ, UK. e-mail Donald.B.Smith{at}gardencottage.screaming.net

Comparison of 33 epidemiologically distinct GBV-C/hepatitis G virus complete genome sequences suggests the existence of four major phylogenetic groupings that are equally divergent from the chimpanzee isolate GBV-C_tro and have distinct geographical distributions. These four groupings are not consistently reproduced by analysis of the virus 5'-noncoding region (5'-NCR), or of individual genes or subgenomic fragments with the exception of the E2 gene as a whole or of 200–600 nucleotide fragments from its 3' half. This region is upstream of a proposed anti-sense reading frame and contains conserved potential RNA secondary structures that may be capable of directing the internal initiation of translation. Phylogenetic analysis of this region from certain South African isolates is consistent with previous analysis of the 5'-NCR suggesting that these belong to a fifth group. The geographical distribution of virus variants is consistent with a long evolutionary history that may parallel that of pre-historic human migrations, implying that the long-term evolution of this RNA virus is extremely slow.

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