SURVEY OF TYPE-6 GROUP VARIANTS OF HEPATITIS-C VIRUS IN SOUTHEAST-ASIA BY USING A CORE-BASED GENOTYPING ASSAY

Previous surveys of the prevalences of genotypes of hepatitis C virus (HCV) in different populations have often used genotyping assays based upon analysis of amplified sequences from the 5' noncoding region (5' NCR), such as restriction fragment length polymorphism (RFLP) or hybri dization with type-specific probes (e.g., InnoLipa). Although highly c onserved, this region contains several type-specific nucleotide polymo rphisms that allow major genotypes 1 to 6 to be reliably identified. R ecently, however, novel HCV variants found in Vietnam and Thailand tha t are distantly related to the type 6a genotype (type 6 group) by phyl ogenetic analysis of coding regions of the genome often have sequences in the 5'NCR that are similar or identical to those of type 1 and cou ld therefore not be identified by any assay of sequences in this regio n. We developed a new genotyping assay based upon RFLP of sequences am plified from the more variable core region to investigate their distri bution elsewhere in southeast (SE) Asia. Among 108 samples from blood donors in seven areas that were identified as type 1 by RFLP in the 5' NCR, type 6 group variants were found in Thailand (7 from 28 samples o riginally identified as type 1) and Burma (Myanmar) (1 of 3) but were not found in Hong Kong (n = 43), Macau (n = 8), Taiwan (n = 6), Singap ore (n = 2), or Malaysia (n = 18). Although this small survey suggests a relatively limited distribution for type 6 group variants in SE Asi a, larger studies will be required to explore their distribution in ot her geographical regions and the extent to which their presence would limit the practical usefulness of 5'NCR-based genotyping assays for cl inical or epidemiological purposes.