1National Institute of Virology, Pune, India
2Malabar Institute of Medical Science, Calicut, India
3Kasturba Medical College, Manipal, India.
There are very few reports for genomic analysis of HAV strains from developing countries. The present study was carried out to detect genotypes and variations in different genomic regions of HAV strains from sporadic infections in Southern and Western parts of India. Serum samples collected from acute hepatitis A patients (n=20) were subjected to RT-PCR by using primers from partial 5’non-coding region, VP1/2A junction and partial 3D regions. PCR products of the specimens indicating amplification of HAV RNA were sequenced. Nucleotide sequence data obtained were aligned with the sequences of HAV strains available in GenBank by using Clustal X version 1.83.The phylogenetic analyses were carried out in MEGA 3.1 by using Kimura 2-parameter and neighbor-joining algorithm. The reliability of different phylogenetic groupings was confirmed by using 1000 bootstrap replications. Using VP1/2A junction region 5 isolates from western India and 15 isolates from southern India were classified as genotype IIIA. Percent nucleotide identities with Nor21 (genotype IIIA) ranged from 98.4% -99.2% in 5’NCR,95%-98% in VP1/2A junction and 94.4% -98.5% in partial 3D regions. Variations between the strains from western and southern regions were detected to be 0.65% in 5’NCR while the same were 2.3% in VP1/2A junction and 2.8% in partial 3D regions.
