Computational protocol: Clade homogeneity and low rate of delta virus despite hyperendemicity of hepatitis B virus in Ethiopia

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Protocol publication

[…] All raw sequences were manually edited and aligned using Geneious software version 6.2.1 (http://www.geneious.com). Neighbor-joining phylogenetic trees and genetic distances were calculated using MEGA5 software (www.megasoftware.net) with Kimura 2-parameter, pair wise deletion option, and 1000 bootstrap replicates. Genotyping was independently performed on the basis of phylogenetic relationship by taking the short fragment non-coding genome region (368pb) and the full HDV genome sequences along with representative reference sequences from different HDV genotypes of 1 to 8 retrieved from the GenBank. Alignment of both the nucleotide sequences and the amino acid residues of the current isolates that encode 19 carboxyl (C)-terminal amino acid (aa 196–214) residues of LHDAg depicting the clathrin heavy chain (CHC) interacting domain (includes clathrin box-binding domain (CBD) (aa 199–203), the isoprenylation (Py) signal site (aa 211–214)) were compared with sequences retrieved from the GenBank. Moreover, nucleotide substitutions variations on the poly(A) signal (nt 946–952), and the RNA editing targets of the anti-genomic HDV RNA (nt 1012) and its corresponding genomic RNA (nt 580) were examined for nucleotide substitution variations. The acetylation (Ac) and phosphorylation (Pi) sites, RNA binding domain (aa 79–107) and the domains of arginine-rich motifs (ARMs) (aa 137–144) of sHDAg were also analysed for possible nucleotide and amino acid residue variations. The nucleotide sequences of both non-coding short fragment genome region and the full HDV genome region used in this study are available in the GenBank/EMBL/DDBJ data bases with an accession numbers from KY463671 to KY463682. […]

Pipeline specifications

Software tools Geneious, MEGA
Databases DDBJ
Application Phylogenetics
Organisms Human poliovirus 1 Mahoney, Hepatitis delta virus, Homo sapiens
Diseases Hepatitis B, Liver Diseases, HIV Infections, Chemical and Drug Induced Liver Injury
Chemicals Amino Acids, Aspartic Acid, Methionine, Nucleotides, Tyrosine, Lamivudine