Major human Hepatitis A virus genotype in Hong Kong marine waters and detection by real-time PCR

Marine waters from seven sites around Hong Kong with varying levels of sewage pollution were analyzed for Hepatitis A virus (HAV) by PCR cloning and DNA sequencing of the highly variable VP1/2A junction of the HAV genome. Phylogenetic analysis of 10 PCR clones from each of the HAV-positive marine sites indicated that human HAV genotype IB is the most widely distributed type in Hong Kong waters. A sensitive and quantitative TaqMan-based PCR method targeting the 5′-noncoding region (5′-NCR) of HAV was used to quantify HAV particles in marine water samples along with the total Escherichiacoli counts being enumerated on TBX medium for comparison. Our results showed that no correlation of any significance between HAV and E. coli counts was observed which underscores the inadequacy in using E. coli as a sanitary standard to predict the levels of HAV in marine waters.