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 (1005nt), which needs to be explored.
Joshi
Madhuri S
MS
National Institute of Virology, 20-A, Dr. Ambedkar Road, P.O. Box No. 11, Pune 411001, India.
Walimbe
Atul M
AM
Chitambar
Shobha D
SD
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D003546:Cysteine Endopeptidases / Q000235:genetics; D016679:Genome, Viral; D030041:Hepatitis A virus / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics*; D015678:Viral Structural Proteins / Q000235:genetics
D020413:3' Untranslated Regions; C085421:3D protein, Hepatitis A virus; D020121:5' Untranslated Regions; D012367:RNA, Viral; C096539:VP1 protein, hepatitis A virus; D014764:Viral Proteins; D015678:Viral Structural Proteins; C108899:protein 2C, Hepatitis A virus; D003546:Cysteine Endopeptidases; C057400:picornain 2A, Picornavirus