Evaluation of genomic regions of hepatitis A virus for phylogenetic analysis: Suitability of the 2C region for genotyping

The use of different genomic fragments of hepatitis A virus (HAV) has been described for classification of strains available globally. However, the limitations of these fragments have been reported in several studies. The present study was conducted to evaluate the genomic fragments of HAV, spanning from the 5′NCR to 3′NCR to employ them in molecular diagnosis and genotyping. The different phylogenetic methods confirmed the use of the 5′NCR and the VP4 region in diagnosis due to their conserved nature. The entire genome, 2A, 2C and 3D were identified as the suitable genomic regions comparable to the VP1 region recommended earlier for genotyping. Likelihood mapping analysis indicated the full-length genome sequence as the region of choice for genotyping of HAV. This was followed by a short 2C region (1005 nt), which needs to be explored.