IDENTIFICATION OF GENETIC-VARIANTS OF HEPATITIS-A VIRUS

Although detection of hepatitis A virus (HAV) has been greatly aided b y the development of polymerase chain reaction (PCR) technology, ident ification of genetic variants requires sequencing PCR products, which necessarily limits the length of the HAV genome (typically 2%) that ca n be analyzed. From a regulatory standpoint, identification of the spe cific strain detected by PCR is a prerequisite not only to overrule co ntamination of test samples in the diagnostic laboratory, but also to possibly locate the origin of the virus detected by PCR. We explored a lternatives to sequencing PCR products to achieve these goals. The fin dings indicate that restriction fragment length polymorphism (RFLP) an alysis of PCR products from two noncontiguous regions of the HAV genom e encompassing 765 nucleotides (approximately 10% of the genome) by th e restriction endonucleases HinfI and AluI, which cut frequently withi n the HAV genome, can distinguish the common tissue culture adapted st rains of HAV from stool isolates. The resolution can be greatly enhanc ed by combining single strand conformation polymorphism (SSCP) analysi s with restriction enzyme digestion, when most of the seventeen strain s analyzed could be identified. (C) 1997 Elsevier Science B.V.