First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype
We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained...
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| Veröffentlicht in: | Clinical microbiology and infection 2016-11, Vol.22 (11), p.947.e1-947.e8 |
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| container_title | Clinical microbiology and infection |
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| creator | Salmona, M. Caporossi, A. Simmonds, P. Thélu, M.-A. Fusillier, K. Mercier-Delarue, S. De Castro, N. LeGoff, J. Chaix, M.-L. François, O. Simon, F. Morand, P. Larrat, S. Maylin, S. |
| description | We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2. |
| doi_str_mv | 10.1016/j.cmi.2016.07.032 |
| format | Article |
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The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2.</description><identifier>ISSN: 1198-743X</identifier><identifier>EISSN: 1469-0691</identifier><identifier>DOI: 10.1016/j.cmi.2016.07.032</identifier><identifier>PMID: 27515394</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Democratic Republic of Congo ; Evolution, Molecular ; Genome, Viral ; Genotype ; Genotype 7b ; Hepacivirus - classification ; Hepacivirus - genetics ; Hepacivirus - isolation & purification ; Hepatitis C virus ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Life Sciences ; Male ; Microbiology and Parasitology ; Middle Aged ; Next-generation sequencing ; Phylogeny ; Polymorphism ; Sequence Analysis, DNA - methods ; Virology</subject><ispartof>Clinical microbiology and infection, 2016-11, Vol.22 (11), p.947.e1-947.e8</ispartof><rights>2016 European Society of Clinical Microbiology and Infectious Diseases</rights><rights>Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. 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All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c496t-7f54404e19f6a4f98be554cce8a0730590b77f3ae561adfdda0e8829bd22a3f23</citedby><cites>FETCH-LOGICAL-c496t-7f54404e19f6a4f98be554cce8a0730590b77f3ae561adfdda0e8829bd22a3f23</cites><orcidid>0000-0002-0991-4381 ; 0000-0001-7111-1865</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27515394$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01996478$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Salmona, M.</creatorcontrib><creatorcontrib>Caporossi, A.</creatorcontrib><creatorcontrib>Simmonds, P.</creatorcontrib><creatorcontrib>Thélu, M.-A.</creatorcontrib><creatorcontrib>Fusillier, K.</creatorcontrib><creatorcontrib>Mercier-Delarue, S.</creatorcontrib><creatorcontrib>De Castro, N.</creatorcontrib><creatorcontrib>LeGoff, J.</creatorcontrib><creatorcontrib>Chaix, M.-L.</creatorcontrib><creatorcontrib>François, O.</creatorcontrib><creatorcontrib>Simon, F.</creatorcontrib><creatorcontrib>Morand, P.</creatorcontrib><creatorcontrib>Larrat, S.</creatorcontrib><creatorcontrib>Maylin, S.</creatorcontrib><title>First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype</title><title>Clinical microbiology and infection</title><addtitle>Clin Microbiol Infect</addtitle><description>We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2.</description><subject>Democratic Republic of Congo</subject><subject>Evolution, Molecular</subject><subject>Genome, Viral</subject><subject>Genotype</subject><subject>Genotype 7b</subject><subject>Hepacivirus - classification</subject><subject>Hepacivirus - genetics</subject><subject>Hepacivirus - isolation & purification</subject><subject>Hepatitis C virus</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Microbiology and Parasitology</subject><subject>Middle Aged</subject><subject>Next-generation sequencing</subject><subject>Phylogeny</subject><subject>Polymorphism</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Virology</subject><issn>1198-743X</issn><issn>1469-0691</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU1v1DAQhi0EoqXwA7ggH-GQMI6dOBanakUp0kpcQOJmOc6461U-trazavn1OErpkdN8PfNKMy8h7xmUDFjz-Vja0ZdVTkuQJfDqBblkolEFNIq9zDlTbSEF_31B3sR4BICKc_GaXFSyZjVX4pLc3_gQE53wIRV3OGEwyc8TjXi_4GT9dEfdMgzraB6R2oMJxiYM_s_GzY4aesBTrpKPdEfPPiyRrnh6PCGVtPdnDLlONC7d2ntLXjkzRHz3FK_Ir5uvP3e3xf7Ht--7631hhWpSIV0tBAhkyjVGONV2WNfCWmwNSA61gk5Kxw3WDTO963sD2LaV6vqqMtxV_Ip82nQPZtCn4EcTHvVsvL693uu1B0ypRsj2zDL7cWNPYc6Hx6RHHy0Og5lwXqJmLa-5bABERtmG2jDHGNA9azPQqyv6qLMrenVFg9TZlbzz4Ul-6Ubsnzf-2ZCBLxuA-SFnj0FH6_P_sfcBbdL97P8j_xcQ756p</recordid><startdate>201611</startdate><enddate>201611</enddate><creator>Salmona, M.</creator><creator>Caporossi, A.</creator><creator>Simmonds, P.</creator><creator>Thélu, M.-A.</creator><creator>Fusillier, K.</creator><creator>Mercier-Delarue, S.</creator><creator>De Castro, N.</creator><creator>LeGoff, J.</creator><creator>Chaix, M.-L.</creator><creator>François, O.</creator><creator>Simon, F.</creator><creator>Morand, P.</creator><creator>Larrat, S.</creator><creator>Maylin, S.</creator><general>Elsevier Ltd</general><general>Elsevier for the European Society of Clinical Microbiology and Infectious Diseases</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0002-0991-4381</orcidid><orcidid>https://orcid.org/0000-0001-7111-1865</orcidid></search><sort><creationdate>201611</creationdate><title>First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype</title><author>Salmona, M. ; Caporossi, A. ; Simmonds, P. ; Thélu, M.-A. ; Fusillier, K. ; Mercier-Delarue, S. ; De Castro, N. ; LeGoff, J. ; Chaix, M.-L. ; François, O. ; Simon, F. ; Morand, P. ; Larrat, S. ; Maylin, S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c496t-7f54404e19f6a4f98be554cce8a0730590b77f3ae561adfdda0e8829bd22a3f23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Democratic Republic of Congo</topic><topic>Evolution, Molecular</topic><topic>Genome, Viral</topic><topic>Genotype</topic><topic>Genotype 7b</topic><topic>Hepacivirus - classification</topic><topic>Hepacivirus - genetics</topic><topic>Hepacivirus - isolation & purification</topic><topic>Hepatitis C virus</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Microbiology and Parasitology</topic><topic>Middle Aged</topic><topic>Next-generation sequencing</topic><topic>Phylogeny</topic><topic>Polymorphism</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Salmona, M.</creatorcontrib><creatorcontrib>Caporossi, A.</creatorcontrib><creatorcontrib>Simmonds, P.</creatorcontrib><creatorcontrib>Thélu, M.-A.</creatorcontrib><creatorcontrib>Fusillier, K.</creatorcontrib><creatorcontrib>Mercier-Delarue, S.</creatorcontrib><creatorcontrib>De Castro, N.</creatorcontrib><creatorcontrib>LeGoff, J.</creatorcontrib><creatorcontrib>Chaix, M.-L.</creatorcontrib><creatorcontrib>François, O.</creatorcontrib><creatorcontrib>Simon, F.</creatorcontrib><creatorcontrib>Morand, P.</creatorcontrib><creatorcontrib>Larrat, S.</creatorcontrib><creatorcontrib>Maylin, S.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Clinical microbiology and infection</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Salmona, M.</au><au>Caporossi, A.</au><au>Simmonds, P.</au><au>Thélu, M.-A.</au><au>Fusillier, K.</au><au>Mercier-Delarue, S.</au><au>De Castro, N.</au><au>LeGoff, J.</au><au>Chaix, M.-L.</au><au>François, O.</au><au>Simon, F.</au><au>Morand, P.</au><au>Larrat, S.</au><au>Maylin, S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype</atitle><jtitle>Clinical microbiology and infection</jtitle><addtitle>Clin Microbiol Infect</addtitle><date>2016-11</date><risdate>2016</risdate><volume>22</volume><issue>11</issue><spage>947.e1</spage><epage>947.e8</epage><pages>947.e1-947.e8</pages><issn>1198-743X</issn><eissn>1469-0691</eissn><abstract>We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>27515394</pmid><doi>10.1016/j.cmi.2016.07.032</doi><orcidid>https://orcid.org/0000-0002-0991-4381</orcidid><orcidid>https://orcid.org/0000-0001-7111-1865</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Democratic Republic of Congo Evolution, Molecular Genome, Viral Genotype Genotype 7b Hepacivirus - classification Hepacivirus - genetics Hepacivirus - isolation & purification Hepatitis C virus High-Throughput Nucleotide Sequencing - methods Humans Life Sciences Male Microbiology and Parasitology Middle Aged Next-generation sequencing Phylogeny Polymorphism Sequence Analysis, DNA - methods Virology |
| title | First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype |
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