Computational protocol: Hepatitis B virus Genotyping Among Patients With Cirrhosis

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Protocol publication

[…] Sequences were genotyped by phylogenetic reconstructions using reference sequences from all HBV genotypes obtained from Gen Bank comprising of HBsAg region (S). Complete genomes where also obtained from GenBank and phylogenetic analyses were performed. All sequences were aligned using CLUSTAL W. Phylogenetic tree was constructed by the neighbor-joining (N-J) method () with the mid-point rooting option. To confirm the reliability of the phylogenetic tree, bootstrap resampling tests were carried out 1000 times. The accession numbers and country of the reported sequences were as following: genotype A, AB014370 from Japan, AB222707 from Uzbekistan, AF297621 from South Africa, EU410082 from the Philippines, and AB194951 from Cameroon; genotype B, AB073838 from Japan, AF121243 from Sweden, M54923 from Indonesia, AY167098 from Taiwan, X97850 from the UK; genotype C, AB014393 from Japan, AB222714 from Uzbekistan, X75665 from Sweden, X75656 from Polynesia, AB105172 from Hawaii, EU439009 from China; genotype D, AF043593 from Germany, and Z35716 from Poland, X80924. The analyses and calculated nucleotide differences within and between the isolated sequences were carried out by MEGA program, version 4 (). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Homo sapiens, Hepatitis B virus
Diseases Hepatitis B, Hepatitis, Chronic, Infection, Liver Cirrhosis, Chemical and Drug Induced Liver Injury
Chemicals Hepatitis B Surface Antigens