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...

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Detalles Bibliográficos
Autores: 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
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
Descripción
Sumario: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.

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