Comprehensive analysis of mutations in the hepatitis delta virus genome based on full- length sequencing in a nationwide cohort study and evolutionary.

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Comprehensive analysis of mutations in the hepatitis delta virus genome based on full- length sequencing in a nationwide cohort study and evolutionary pattern during disease progression E. Shirvani-Dastgerdi, S. Amini-Bavil-Olyaee, S. Moayed Alavian, C. Trautwein, F. Tacke Clinical Microbiology and Infection Volume 21, Issue 5, Pages 510.e11-510.e23 (May 2015) DOI: 10.1016/j.cmi.2014.12.008 Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 1 Phylogenetic analysis of Iranian hepatitis D virus (HDV) isolates based on full genome (a) and large delta antigen (L-HDAg) (b) sequences. The branches represented in these trees are also supported by maximum likelihood analysis (data not shown). Colours represent geographic distribution of the samples, which were collected from different areas of the country. Bootstrap values above 70% are indicated at the branch nodes. Clinical Microbiology and Infection 2015 21, 510.e11-510.e23DOI: (10.1016/j.cmi.2014.12.008) Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 2 Inter-genotypic distances are displayed based on hepatitis D virus (HDV) full-length (a) and large delta antigen (L-HDAg) genome (b) sequences. Iranian samples with highest distances to reference HDV genotype (GT) 1 are marked by circles (isolates D32, D33 and D34). Clinical Microbiology and Infection 2015 21, 510.e11-510.e23DOI: (10.1016/j.cmi.2014.12.008) Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 3 Hepatitis D virus (HDV) isolates sampled simultaneously during a 4-year follow up of an HDV-infected mother (D5) and her son (D39). (a) Large delta antigen (L-HDAg) amino acid alignment of the isolates. (b) Schematic L-HDAg amino acid similarities at initial sampling and after 4 years are depicted. Clinical Microbiology and Infection 2015 21, 510.e11-510.e23DOI: (10.1016/j.cmi.2014.12.008) Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 4 (a) Hepatitis D virus (HDV) ribozyme logo based on 38 aligned sequences. Cleavage sites and important nucleotides for base pairing to form secondary structures are shown (asterisks). Note that there is a base insertion after C67 in anti-genomic strands in some sequences, which affects base numbering onwards. (b) Pseudoknot secondary structure of the ribozyme represented by majority of sequences as well as cleavage sites and conformational domains are shown. Red asterisks indicate the positions at which mutations occur. The P4 domain is highlighted in red due to the high frequency of mutations in this region. Clinical Microbiology and Infection 2015 21, 510.e11-510.e23DOI: (10.1016/j.cmi.2014.12.008) Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 5 (a) Large delta antigen (L-HDAg) sequence alignment logo based on 44 isolates from hepatitis B virus/hepatitis D virus (HBV-HDV) co-infected patients. Functional domains (presented by boxes) and post-transcriptional modification (PTM) sites (illustrated as circles) are indicated. (b) Sites under positive selection in L-HDAg of 44 isolates. A value of dN/dS >1 indicates overabundance of non-synonymous mutations at each codon. The highlighted zone depicts the codons, which are affected by positive selection (codons 136 to 159). Boxes on top of the figure show the immunogenic epitopes of the protein. The alteration of amino acids at immunogenic CD8+ T-cell and B-cell epitopes is noteworthy. Abbreviations: RBD, RNA binding domain; CCD, coiled coil domain; NLS, nuclear localization signal; P, phosphorylation; M, methylation; A, acetylation; I, isoprenylation; BCE, B-cell epitope; CD8+, CD8+ T-cell epitope; CD4+, CD4+ T-cell epitope. Clinical Microbiology and Infection 2015 21, 510.e11-510.e23DOI: (10.1016/j.cmi.2014.12.008) Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions