THE COMPLETE CODING SEQUENCE OF HEPATITIS-C VIRUS GENOTYPE 5A, THE PREDOMINANT GENOTYPE IN SOUTH-AFRICA

Hepatitis C virus (HCV) genotype 5a is the predominant genotype in sou thern Africa with a high prevalence amongst infected blood donors from areas in South Africa. We have determined the nucleotide sequence cor responding to the complete coding region of an HCV isolate, EUH1480, p reviously classified as genotype 5a, from and Edinburgh haemophiliac. The sequence contained a single open reading frame (ORF) coding for a polyprotein of 3014 amino acids. Comparison with the polyprotein seque nces from other HCB genotypes, where the ORF varies from 3008 to 3037 amino acids, showed the observed variation in size was due to differen ces in lengths of the envelope 2 and the nonstructural 5A proteins. Th e sequence divergence of HCV genotype 5 ranged from 29.4% nucleotide d ifferences (24.9% amino acid differences) compared with genotype 1c to 32.5% nucleotide differences (30.3% amino acid differences) compared with 2a. Phylogenetic analysis of the available full length nucleotide sequences showed EUH1480 to form a branch distinct from the other HCV types, confirming the classification of type 5a as a separate genotyp e. (C) 1997 Academic Press.