Knowledge of the nucleotide sequence in the region of the putative VP1/2A junction of the Hepatitis A virus (HAV) genome has enabled differentiation of HAV strains and their classification into seven genotypes, in some of which sub-genotypes A and B can be defined. A 168 base segment encompassing the putative VP1/2A junction of 27 clinical wild-type isolates of HAV from Cuba was amplified by reverse transcriptase-polymerase chain reaction and then sequenced. The Cuban isolates are clustered within sub-genotype IA. A single amino acid substitution, which does not correspond with any of the reported changes for other strains, was observed. A new sub-genotype variant is therefore postulated. This study provides new data on the genetic relatedness of HAVs from Cuba and on the distribution of sub-genotype IA in the Caribbean area.

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