Background: Hepatitis C virus infection is a great issue in China; however, there is very little information on genotyping investigations based on sequence variability in the 5'untranslated (5'UTR) reported. The present study was to define the sequence variability based on the sequence divergences of the 5'UTR of the virus.
Methods: Sequences of 91 isolates from patients with chronic hepatitis C from Yunnan, southwest China, were sequenced and genotypes were defined according to the sequence divergences of the 5'UTR of the virus.
Results: Eighty-six isolates were classified into 3 clades (previously termed groups or major types) by the methods proposed by Chan et al in 1992 and phylogenetic analysis based on nucleotide sequence divergences within the 5'UTR. Fifty-six percent of the isolates were classified into clade 3, 35% into clade 1, and 34.9% into clade 2. New genotypes 1f, 2h, 3h and 3i were defined. In addition, 3 novel sequences were discovered, respectively with an 18-nt sequence deletion (corresponding to nucleotide position -173 to -156), a 28-nt sequence insertion, and a 40-nt sequence insertion, between -56 and -55. Of these isolates, 56% possessed a "G" at position -66 in place of the "T" that is present in all previously reported sequences.
Conclusions: These HCV variants, evolved or remained in this area, may be of great significance in diagnosis and treatment of hepatitis C patients.