Computational protocol: Variability in the Precore and Core Promoter Regions of HBV Strains in Morocco: Characterization and Impact on Liver Disease Progression

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Protocol publication

[…] We initially identified the consensus sequences of pre-C/CP regions for HBV genotype A from 49 reference sequences subgenotype A2 and for HBV genotype D from 162 genotype D reference sequences. The sequences were aligned using Clustal X v2.0 software and edited using BioEdit v7.0 program , . A nucleotide with the highest frequency at each site in the regions pre-C/CP was defined as wild-type nucleotide. All reference sequences were isolated from asymptomatic carriers (blood donors or pregnant women) and their GenBank accession numbers were listed in . Nucleotide sequences generated in this work were analyzed and compared to consensus sequence of corresponding genotype in both directions using SeqScape®v2.5 software (Applied Biosystems). We analyzed BCP mutations in the functional region bound by nt 1742 and 1791 (implicated in the synthesis of pre-C RNA). URR and pre-C mutations were analyzed in the entire regions. The nucleotide mutation was defined by difference to the consensus sequence and dual signals (mixed type) were considered as a mutant type. […]

Pipeline specifications

Software tools Clustal W, BioEdit, SeqScape
Application Sanger sequencing
Organisms Hepatitis B virus, Homo sapiens
Diseases Hepatitis B, Carcinoma, Hepatocellular, Liver Diseases, Myopathy, Central Core, Chemical and Drug Induced Liver Injury