Genotyping Hepatitis B virus by Next-Generation Sequencing
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to...
| Autores: | , , , , , , , , , , , , , , , , , , , |
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universitat Autònoma de Barcelona |
| Repositorio: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglés |
| OAI Identifier: | oai:ddd.uab.cat:304130 |
| Acceso en línea: | https://ddd.uab.cat/record/304130 https://dx.doi.org/urn:doi:10.3390/ijms25105481 |
| Access Level: | acceso abierto |
| Palabra clave: | Hepatitis B virus Genotypes Next-generation sequencing Quasispecies Conservation Information content Distance-Based discrimination method PreS Hepatitis B X gene RNA interference |
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Genotyping Hepatitis B virus by Next-Generation SequencingDetection of Mixed Infections and Analysis of Sequence ConservationDopico, Eva|||0000-0002-5306-3035Vila, Marta|||0000-0001-9303-5189Tabernero, David|||0000-0002-1146-4084Gregori i Font, Josep|||0000-0002-4253-8015Rando-Segura, Ariadna|||0000-0003-4555-7286Pacín Ruiz, Beatriz|||0000-0001-8718-6589Guerrero, Laura|||0000-0003-1978-9067Ubillos, Itziar|||0000-0002-0993-0058Martínez, Miguel J.|||0000-0002-0682-1075Costa, Josep|||0000-0001-7978-0748Quer, Josep|||0000-0003-0014-084XPérez Garreta, JavierGonzález Sánchez, Alejandra|||0000-0002-1809-3415Antón Pagarolas, Andrés, 1976-|||0000-0002-1476-0815Pumarola Suñé, Tomàs|||0000-0002-5171-7461Riveiro Barciela, Mar|||0000-0001-9309-2052Ferrer Costa, Roser|||0000-0002-8925-3172Buti, Maria|||0000-0002-0732-3078Rodríguez Frías, Francisco|||0000-0002-9128-7013Cortese, Maria Francesca|||0000-0002-4318-532XHepatitis B virusGenotypesNext-generation sequencingQuasispeciesConservationInformation contentDistance-Based discrimination methodPreSHepatitis B X geneRNA interferenceOur aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies. 22024-01-0120242024-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/304130https://dx.doi.org/urn:doi:10.3390/ijms25105481reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2021-126447OB-I00Instituto de Salud Carlos III https://doi.org/10.13039/501100004587 PI19/00301Instituto de Salud Carlos III https://doi.org/10.13039/501100004587 PI22/00258open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:3041302026-06-06T12:50:31Z |
| dc.title.none.fl_str_mv |
Genotyping Hepatitis B virus by Next-Generation Sequencing Detection of Mixed Infections and Analysis of Sequence Conservation |
| title |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| spellingShingle |
Genotyping Hepatitis B virus by Next-Generation Sequencing Dopico, Eva|||0000-0002-5306-3035 Hepatitis B virus Genotypes Next-generation sequencing Quasispecies Conservation Information content Distance-Based discrimination method PreS Hepatitis B X gene RNA interference |
| title_short |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| title_full |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| title_fullStr |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| title_full_unstemmed |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| title_sort |
Genotyping Hepatitis B virus by Next-Generation Sequencing |
| dc.creator.none.fl_str_mv |
Dopico, Eva|||0000-0002-5306-3035 Vila, Marta|||0000-0001-9303-5189 Tabernero, David|||0000-0002-1146-4084 Gregori i Font, Josep|||0000-0002-4253-8015 Rando-Segura, Ariadna|||0000-0003-4555-7286 Pacín Ruiz, Beatriz|||0000-0001-8718-6589 Guerrero, Laura|||0000-0003-1978-9067 Ubillos, Itziar|||0000-0002-0993-0058 Martínez, Miguel J.|||0000-0002-0682-1075 Costa, Josep|||0000-0001-7978-0748 Quer, Josep|||0000-0003-0014-084X Pérez Garreta, Javier González Sánchez, Alejandra|||0000-0002-1809-3415 Antón Pagarolas, Andrés, 1976-|||0000-0002-1476-0815 Pumarola Suñé, Tomàs|||0000-0002-5171-7461 Riveiro Barciela, Mar|||0000-0001-9309-2052 Ferrer Costa, Roser|||0000-0002-8925-3172 Buti, Maria|||0000-0002-0732-3078 Rodríguez Frías, Francisco|||0000-0002-9128-7013 Cortese, Maria Francesca|||0000-0002-4318-532X |
| author |
Dopico, Eva|||0000-0002-5306-3035 |
| author_facet |
Dopico, Eva|||0000-0002-5306-3035 Vila, Marta|||0000-0001-9303-5189 Tabernero, David|||0000-0002-1146-4084 Gregori i Font, Josep|||0000-0002-4253-8015 Rando-Segura, Ariadna|||0000-0003-4555-7286 Pacín Ruiz, Beatriz|||0000-0001-8718-6589 Guerrero, Laura|||0000-0003-1978-9067 Ubillos, Itziar|||0000-0002-0993-0058 Martínez, Miguel J.|||0000-0002-0682-1075 Costa, Josep|||0000-0001-7978-0748 Quer, Josep|||0000-0003-0014-084X Pérez Garreta, Javier González Sánchez, Alejandra|||0000-0002-1809-3415 Antón Pagarolas, Andrés, 1976-|||0000-0002-1476-0815 Pumarola Suñé, Tomàs|||0000-0002-5171-7461 Riveiro Barciela, Mar|||0000-0001-9309-2052 Ferrer Costa, Roser|||0000-0002-8925-3172 Buti, Maria|||0000-0002-0732-3078 Rodríguez Frías, Francisco|||0000-0002-9128-7013 Cortese, Maria Francesca|||0000-0002-4318-532X |
| author_role |
author |
| author2 |
Vila, Marta|||0000-0001-9303-5189 Tabernero, David|||0000-0002-1146-4084 Gregori i Font, Josep|||0000-0002-4253-8015 Rando-Segura, Ariadna|||0000-0003-4555-7286 Pacín Ruiz, Beatriz|||0000-0001-8718-6589 Guerrero, Laura|||0000-0003-1978-9067 Ubillos, Itziar|||0000-0002-0993-0058 Martínez, Miguel J.|||0000-0002-0682-1075 Costa, Josep|||0000-0001-7978-0748 Quer, Josep|||0000-0003-0014-084X Pérez Garreta, Javier González Sánchez, Alejandra|||0000-0002-1809-3415 Antón Pagarolas, Andrés, 1976-|||0000-0002-1476-0815 Pumarola Suñé, Tomàs|||0000-0002-5171-7461 Riveiro Barciela, Mar|||0000-0001-9309-2052 Ferrer Costa, Roser|||0000-0002-8925-3172 Buti, Maria|||0000-0002-0732-3078 Rodríguez Frías, Francisco|||0000-0002-9128-7013 Cortese, Maria Francesca|||0000-0002-4318-532X |
| author2_role |
author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Hepatitis B virus Genotypes Next-generation sequencing Quasispecies Conservation Information content Distance-Based discrimination method PreS Hepatitis B X gene RNA interference |
| topic |
Hepatitis B virus Genotypes Next-generation sequencing Quasispecies Conservation Information content Distance-Based discrimination method PreS Hepatitis B X gene RNA interference |
| description |
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies. |
| publishDate |
2024 |
| dc.date.none.fl_str_mv |
2 2024-01-01 2024 2024-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/304130 https://dx.doi.org/urn:doi:10.3390/ijms25105481 |
| url |
https://ddd.uab.cat/record/304130 https://dx.doi.org/urn:doi:10.3390/ijms25105481 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2021-126447OB-I00 Instituto de Salud Carlos III https://doi.org/10.13039/501100004587 PI19/00301 Instituto de Salud Carlos III https://doi.org/10.13039/501100004587 PI22/00258 |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona |
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