Molecular characterisation of hepatitis A virus strains from clinical and environmental sources in South Africa

Hepatitis A virus (HAV) is the most common cause of acute viral hepatitis worldwide. Hepatitis A virus is classified in the genus Hepatovirus of the family Picornaviridae. The virion has a 7.5 kb positive-sense single-stranded RNA genome and only one serotype of the virus has been identified so far. There are six genotypes of HAV distinguished by nucleotide sequence analysis of the VP1 region. Genotypes I, II and III, each with their subdivisions A and B, infect humans. Genotypes IV, V and VI infect non-human primates. These genotypes have a distinct geographical distribution. In 1997, it was established that genotype IA and IB prevail in South Africa (SA) with IB being predominant. However, no recent data have been published on the types of HAV circulating in SA even though the virus was detected in surface water sources and on fresh produce at the point of retail. There is an effective vaccine for the prevention of hepatitis A, but recent publications have reported the possible emergence of antigenic escape mutants of HAV. The aim of the study was therefore to establish which genotypes and possibly variants thereof of HAV are circulating the community compared to the genotypes present in water and food sources. To identify the different strains of HAV circulating in SA, detection and characterisation of HAV strains was performed on clinical and environmental sources. A total of 117 clinical specimens and 80 water samples (irrigation, surface and wastewater) and 20 fresh produce (tomatoes, lettuce, cabbage) samples were analysed. Samples were collected in SA and neighbouring countries. Hepatitis A virus was detected in 78% of the clinical specimens and in only 46% of the water samples. None of the fresh produce analysed in the study tested positive for HAV even though some of the produce were irrigated with HAV contaminated water. Molecular characterisation of the detected strains revealed the presence of genotype IB in SA. The SA strains have a unique nucleic acid sequence, namely a R298K mutation within the VP1 region and R71S substitution within the VP1/P2B junction, which distinguishes them from strains detected in the rest of the world and even in neighbouring countries. The characterised strains were also analysed for the presence of previously isolated antigenic escape mutants and/or novel ones. One possible vaccine escape mutant, with a I179T substitution next to the neutralisation residue Y181 in the VP1 region, was identified. A variety of strains with mutation(s) at or around the neutralisation sites were also identified as well as circulation of quasispecies among clinical HAV strains. The study revealed the circulation of a potential new HAV genotype among the SA simian population. The data provided by the study stresses the need to implement a proper surveillance system of the circulation of HAV strains in SA.Dissertation (MSc)--University of Pretoria, 2013.Medical VirologyMScUnrestricte