Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients
Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-P...
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| creator | Çelik, İnci Karataylı, Ersin Çevik, Emrah Gökçe Kabakçı, S. Karataylı, Senem Ceren Dinç, Bedia Çınar, Kubilay Yalçın, Kendal İdilman, Ramazan Yurdaydın, Cihan Bozdayi, A. Mithat |
| description | Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-PCR using two pairs of primers that cover the entire HDV genome. PCR products were sequenced directly. The results showed that these 9 isolates were approximately 1680 base pairs in length and clustered in the genotype HDV-1 branch when phylogenetic analysis was done with the sequences together with the complete sequences of HDV genomes representing each genotype retrieved from GenBank. Analysis of a portion of the large hepatitis D antigen (L-HDAg) gene showed that sequence similarity among these Turkish isolates is between 87.4 and 97.1%, and the Turkish isolates have the most sequence similarity to HDV-1 (90.5%), while they have the least sequence similarity to HDV-3 (64.1%). Full-genome analysis indicates that the sequence similarity is between 80.7 and 95.4%, and the highest sequence similarity is 84.8% (between the Turkish isolates and HDV-1). The lowest sequence similarity is 56.4% (between the Turkish isolates and HDV-3). In conclusion, phylogenetic analysis shows that the Turkish HDV isolates belong to HDV-1. |
| doi_str_mv | 10.1007/s00705-011-1120-y |
| format | Article |
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Mithat</creator><creatorcontrib>Çelik, İnci ; Karataylı, Ersin ; Çevik, Emrah ; Gökçe Kabakçı, S. ; Karataylı, Senem Ceren ; Dinç, Bedia ; Çınar, Kubilay ; Yalçın, Kendal ; İdilman, Ramazan ; Yurdaydın, Cihan ; Bozdayi, A. Mithat</creatorcontrib><description>Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-PCR using two pairs of primers that cover the entire HDV genome. PCR products were sequenced directly. The results showed that these 9 isolates were approximately 1680 base pairs in length and clustered in the genotype HDV-1 branch when phylogenetic analysis was done with the sequences together with the complete sequences of HDV genomes representing each genotype retrieved from GenBank. Analysis of a portion of the large hepatitis D antigen (L-HDAg) gene showed that sequence similarity among these Turkish isolates is between 87.4 and 97.1%, and the Turkish isolates have the most sequence similarity to HDV-1 (90.5%), while they have the least sequence similarity to HDV-3 (64.1%). Full-genome analysis indicates that the sequence similarity is between 80.7 and 95.4%, and the highest sequence similarity is 84.8% (between the Turkish isolates and HDV-1). The lowest sequence similarity is 56.4% (between the Turkish isolates and HDV-3). In conclusion, phylogenetic analysis shows that the Turkish HDV isolates belong to HDV-1.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-011-1120-y</identifier><identifier>PMID: 21984217</identifier><language>eng</language><publisher>Vienna: Springer Vienna</publisher><subject>Adult ; Amino acids ; Antigens ; Base Sequence ; Biomedical and Life Sciences ; Biomedicine ; DNA Primers - genetics ; Gastroenterology ; Genome, Viral ; Genomes ; Genotype & phenotype ; Hepatitis B ; Hepatitis B virus ; Hepatitis D virus ; Hepatitis D, Chronic - virology ; Hepatitis delta Antigens - genetics ; Hepatitis delta virus ; Hepatitis Delta Virus - classification ; Hepatitis Delta Virus - genetics ; Hepatitis Delta Virus - isolation & purification ; Humans ; Infections ; Infectious Diseases ; Medical Microbiology ; Medicine ; Middle Aged ; Molecular Sequence Data ; Original Article ; Phylogenetics ; Phylogeny ; RNA, Viral - genetics ; Turkey ; Virology ; Viruses</subject><ispartof>Archives of virology, 2011-12, Vol.156 (12), p.2215-2220</ispartof><rights>Springer-Verlag 2011</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-p242t-e2642a364aba4477714219fd7219be205148f3a964f22a9ff331b37c5aa1e7a23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00705-011-1120-y$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00705-011-1120-y$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21984217$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Çelik, İnci</creatorcontrib><creatorcontrib>Karataylı, Ersin</creatorcontrib><creatorcontrib>Çevik, Emrah</creatorcontrib><creatorcontrib>Gökçe Kabakçı, S.</creatorcontrib><creatorcontrib>Karataylı, Senem Ceren</creatorcontrib><creatorcontrib>Dinç, Bedia</creatorcontrib><creatorcontrib>Çınar, Kubilay</creatorcontrib><creatorcontrib>Yalçın, Kendal</creatorcontrib><creatorcontrib>İdilman, Ramazan</creatorcontrib><creatorcontrib>Yurdaydın, Cihan</creatorcontrib><creatorcontrib>Bozdayi, A. Mithat</creatorcontrib><title>Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><addtitle>Arch Virol</addtitle><description>Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-PCR using two pairs of primers that cover the entire HDV genome. PCR products were sequenced directly. The results showed that these 9 isolates were approximately 1680 base pairs in length and clustered in the genotype HDV-1 branch when phylogenetic analysis was done with the sequences together with the complete sequences of HDV genomes representing each genotype retrieved from GenBank. Analysis of a portion of the large hepatitis D antigen (L-HDAg) gene showed that sequence similarity among these Turkish isolates is between 87.4 and 97.1%, and the Turkish isolates have the most sequence similarity to HDV-1 (90.5%), while they have the least sequence similarity to HDV-3 (64.1%). Full-genome analysis indicates that the sequence similarity is between 80.7 and 95.4%, and the highest sequence similarity is 84.8% (between the Turkish isolates and HDV-1). The lowest sequence similarity is 56.4% (between the Turkish isolates and HDV-3). In conclusion, phylogenetic analysis shows that the Turkish HDV isolates belong to HDV-1.</description><subject>Adult</subject><subject>Amino acids</subject><subject>Antigens</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>DNA Primers - genetics</subject><subject>Gastroenterology</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Hepatitis B</subject><subject>Hepatitis B virus</subject><subject>Hepatitis D virus</subject><subject>Hepatitis D, Chronic - virology</subject><subject>Hepatitis delta Antigens - genetics</subject><subject>Hepatitis delta virus</subject><subject>Hepatitis Delta Virus - classification</subject><subject>Hepatitis Delta Virus - genetics</subject><subject>Hepatitis Delta Virus - isolation & purification</subject><subject>Humans</subject><subject>Infections</subject><subject>Infectious Diseases</subject><subject>Medical Microbiology</subject><subject>Medicine</subject><subject>Middle Aged</subject><subject>Molecular Sequence Data</subject><subject>Original Article</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>RNA, Viral - genetics</subject><subject>Turkey</subject><subject>Virology</subject><subject>Viruses</subject><issn>0304-8608</issn><issn>1432-8798</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkUtLxDAUhYMozvj4AW4kuHFVzatNupTBFwhuxnXITG9nMrZNTVKh_96UUQQ3bm7Ivd89JOcgdEHJDSVE3oZUSJ4RSjNKGcnGAzSngrNMyVIdojnhRGSqIGqGTkLYEZIaPD9GM0ZLJRiVc-QXru0biIA30LkWcICPAbo1BGy6CvfbsXFpAtGuU8M0Y7ABuxpvoTfRxnSpoIkGf1o_hLRkg2tMhArX3rW4sx3g5eDfbdjiaQG6GM7QUW2aAOff5yl6e7hfLp6yl9fH58XdS9YzwWIGrBDM8EKYlRFCSknTi8u6kqmugJGcClVzUxaiZsyUdc05XXG5zo2hIA3jp-h6r9t7l_4Uom5tWEPTmA7cEHTJCqVEzov_SaKSd6WYNK_-kDs3-OTLBEkiWE4muctvaFi1UOne29b4Uf-4ngC2B0IadRvwvyqU6ClavY9Wp2j1FK0e-RdGQZUB</recordid><startdate>20111201</startdate><enddate>20111201</enddate><creator>Çelik, İnci</creator><creator>Karataylı, Ersin</creator><creator>Çevik, Emrah</creator><creator>Gökçe Kabakçı, S.</creator><creator>Karataylı, Senem Ceren</creator><creator>Dinç, Bedia</creator><creator>Çınar, Kubilay</creator><creator>Yalçın, Kendal</creator><creator>İdilman, Ramazan</creator><creator>Yurdaydın, Cihan</creator><creator>Bozdayi, A. 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Mithat</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients</atitle><jtitle>Archives of virology</jtitle><stitle>Arch Virol</stitle><addtitle>Arch Virol</addtitle><date>2011-12-01</date><risdate>2011</risdate><volume>156</volume><issue>12</issue><spage>2215</spage><epage>2220</epage><pages>2215-2220</pages><issn>0304-8608</issn><eissn>1432-8798</eissn><abstract>Hepatitis delta virus (HDV) is a subviral agent of hepatitis B virus (HBV), and its life cycle is dependent on HBV. It is commonly accepted that HDV has eight distinct genotypes. In this study, the complete nucleotide sequences of HDV genomes isolated from nine Turkish patients were obtained by RT-PCR using two pairs of primers that cover the entire HDV genome. PCR products were sequenced directly. The results showed that these 9 isolates were approximately 1680 base pairs in length and clustered in the genotype HDV-1 branch when phylogenetic analysis was done with the sequences together with the complete sequences of HDV genomes representing each genotype retrieved from GenBank. Analysis of a portion of the large hepatitis D antigen (L-HDAg) gene showed that sequence similarity among these Turkish isolates is between 87.4 and 97.1%, and the Turkish isolates have the most sequence similarity to HDV-1 (90.5%), while they have the least sequence similarity to HDV-3 (64.1%). Full-genome analysis indicates that the sequence similarity is between 80.7 and 95.4%, and the highest sequence similarity is 84.8% (between the Turkish isolates and HDV-1). The lowest sequence similarity is 56.4% (between the Turkish isolates and HDV-3). In conclusion, phylogenetic analysis shows that the Turkish HDV isolates belong to HDV-1.</abstract><cop>Vienna</cop><pub>Springer Vienna</pub><pmid>21984217</pmid><doi>10.1007/s00705-011-1120-y</doi><tpages>6</tpages></addata></record> |
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| subjects | Adult Amino acids Antigens Base Sequence Biomedical and Life Sciences Biomedicine DNA Primers - genetics Gastroenterology Genome, Viral Genomes Genotype & phenotype Hepatitis B Hepatitis B virus Hepatitis D virus Hepatitis D, Chronic - virology Hepatitis delta Antigens - genetics Hepatitis delta virus Hepatitis Delta Virus - classification Hepatitis Delta Virus - genetics Hepatitis Delta Virus - isolation & purification Humans Infections Infectious Diseases Medical Microbiology Medicine Middle Aged Molecular Sequence Data Original Article Phylogenetics Phylogeny RNA, Viral - genetics Turkey Virology Viruses |
| title | Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients |
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