Molecular detection of Hepatitis A RNA and genotyping has been an important tool to characterize the virus and improve the surveillance on the diversity of Hepatitis A strains around the globe.


HAVNET is a global network of scientists working in hepatitis A reference laboratories sharing molecular and epidemiological data on hepatitis A.


Genotyping and comparative phylogenetic analysis of Hepatitis A strains have been crucial to support and help to identify the source of infection, or track Hepatitis A foodborne outbreaks.
Due to a longer incubation time, most of the times it is difficult to link to an origin source, especially for foodborne transmission. Therefore, once clinical symptoms develop, taking a food history is not very reliable, unless cases are linked to a common food establishment or event.

Molecular typing and comparative studies of Hepatitis A strains can provide additional support to elucidate sequence relatedness and can be correlated with the geographical origin of the virus. However, the robustness and level of resolution of this correlation depends on the choice of the genome targets that are used as well as on the quality and completeness of the reference set to which the sequence is compared.

Genotype definition

The initial criteria to define different genotypes was based in the molecular characterization and comparison of one region the Hepatitis A virus genome, the junction region between the C-terminus of VP1 protein and N-terminal protein 2A (VP1/2A region) from isolates from different parts of the world (see typing protocol at HAVNET).

A genotype is defined as a group of viruses possessing nucleotide sequences having less than 15% variation and sub-genotypes have 7 to 7.5% nucleotide variations. Molecular epidemiology studies have shown that genotype III and I are the most prevalent genotypes isolated from humans.