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Complete genome of HBV is almost 3200 base pair long having semicircular shaped double stranded DNA, so far classified into ten genotypes labeled A to J, about 40 sub genotypes and 4 serotypes adr, adw, ayr, ayw. Distribution of HBV genotype D and sub genotype D1 is mostly predominant in Pakistan and India about more than 80% among all genotypes of HBV. While it is less dominant in China where genotype B and C predominates. Focus of this study is the computational analysis of HBV genotype D sub genotype D1 comprising Sequence analysis done using PROBCONS, Phylogenetic analysis performed by MEGA software program, Gene structure analysis using GSDS 2.0 version and Protein structure analysis using BLASTP and SWISS-MODEL.For all these analysis sample of 54 complete genome sequences of HBV genotype D sub genotype D1 were used. Representation of 3 selected countries was subject to the availability of data at Genbank. Six complete genome sequences were obtained from Pakistan 14 from China and 34 sequences were from India. Sequence alignment shows less than 4% divergence in reported sequences from Pakistan, India and China. C and X genes showed divergence of less than 3%. While comparison over the S gene showed similarity ratio of genotype D sub genotype D1 is 97?98%. Phylogenetic analysis suggested that Pakistan HBV, complete genome isolate have the closest evolutionary relationship with its neighboring countries China and India. Sub genotype D1 isolates from China (HQ833466) and Pakistan (AB583680.1) share same ancestor. Gene structure showed coding region exons of ?P? gene is largest about 75% of the gene size while gene ?S? has 2nd largest coding region. However, ?C? and ?X? genes have one smallest exon. Using BLASTP Protein structure showed that similar kind of proteins from different sequences share identical structure format. X proteins were 92% identical, both of Polymerase and Middle S proteins were 99% identical, large surface and pre-core/core proteins have 98% similar structural features relative to its own type. Results from all three X proteins homology models using SWISS MODEL revealed GMQE=0.1. Global and local quality estimate scores including Z-scores for QMEAN CBeta, All Atom, Solvation and Torsion Energy scores were similar indicating good quality, accuracy and reliability of predicted models. 3D visualization showed similar structures and Ramachandran plots showed high percentage of protein residues into favorable region for X Protein Models.
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