Unusual HCV Genotype Patterns
L. Tracy, L. Cabuang, R. McCaw & R. Hammond
(Updated September 2006)
The Molecular Microbiology Unit at VIDRL has performed HCV genotyping since 1994. We now have a comprehensive database of results from more than 4000 patients. The commercial kit we use is the Versant HCV Genotyping Assay (LiPA) from Bayer. The region used to identify the genotypes in this assay is the 5’ UTR. It must be noted that recombination events are possible and that in these cases, using only one region may not be sufficient to determine HCV genotype
The interpretation of the significant bands is dependent on their relative intensity and is by its very nature, subjective. With experience, the significant bands are recognized, with the bands for some genotypes being clearer than others. For example, we have found that the bands for genotype 3a are mostly clear, whereas those for genotype 1 subtypes often have faint secondary bands.
As a resource for laboratories using the Versant HCV Genotype Assay (LiPA) we have compiled a set of examples with characteristic banding patterns not represented on the interpretation chart supplied with the kit. It is possible that there are regional differences in genotype sequence, so that the interpretation chart may not be universally suitable. We have sequenced the core region from at least three samples with the same unusual banding pattern before assigning the genotype and placing it on our website.
To begin your search, please click here for the Unusual Banding Interpretation Chart
Note: Brackets – () – denote faint bands.
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Recently, there has been a review of the nomenclature for HCV genotypes. Here is a table outlining the new codes, replacing the previous codes for these genotypes.