Computational protocol: Evolution of Hepatitis B Virus in a Chronic HBV-Infected Patient over 2 Years

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Protocol publication

[…] Fourteen HBV complete genomes available in GenBank (genotypes A, B and E to H) were applied to phylogenetic analysis. Additionally, 50 published sequences of genotype C were also used in this study for alignment analysis (Genbank accession numbers can be obtained upon request). The whole genome sequences were assembled by BioEdit sequence alignment editor software, version 7.0.5.2 []. Alignment was performed using Clustal X software, version 1.83 []. Phylogenetic and molecular evolutionary analysis of nucleotide differences within and between the isolate sequences were carried out by MEGA program, version 3.1 []. Genetic distance was estimated using the Kimura two-parameter algorithm. The phylogenetic trees were constructed by the neighbor-joining method. Bootstrap re-sampling and reconstruction were carried out for 1,000 times to confirm the reliability of phylogenetic trees. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Applications Phylogenetics, WGS analysis
Organisms Hepatitis B virus, Homo sapiens
Diseases Hepatitis B, Infection