A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus

Autores
Techera, Claudia; Tomás, Gonzalo; Grecco, Sofía; Williman, Joaquín; Hernández, Martín; Olivera, Valeria Soledad; Bandac, Alejandro; Vagnozzi, Ariel Eduardo; Panzera, Yanina; Marandino, Ana; Pérez, Ruben
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión aceptada
Descripción
The infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.
Instituto de Virología
Fil: Techera, Claudia. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Tomás, Gonzalo. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Grecco, Sofía. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Williman, Joaquín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Hernández, Martín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Olivera, Valeria Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina
Fil: Banda, Alejandro. Mississippi State University. College of Veterinary Medicine. Poultry Research and Diagnostic Laboratory; Estados Unidos
Fil: Vagnozzi, Ariel Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina
Fil: Panzera, Yanina. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Marandino, Ana. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Pérez, Ruben. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fuente
Journal of Virological Methods 322 : 114807 (2023)
Materia
Infectious Bursal Disease Virus
Genome-wide Association Studies
Genomes
Evolution
PCR
Phylogenetic Analysis
Chickens
Virus Bursitis Infecciosa
Estudios de Asociación del Genoma Completo
Genomas
Evolución
Análisis Filogenético
Pollo
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/15281
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oai_identifier_str oai:localhost:20.500.12123/15281
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virusTechera, ClaudiaTomás, GonzaloGrecco, SofíaWilliman, JoaquínHernández, MartínOlivera, Valeria SoledadBandac, AlejandroVagnozzi, Ariel EduardoPanzera, YaninaMarandino, AnaPérez, RubenInfectious Bursal Disease VirusGenome-wide Association StudiesGenomesEvolutionPCRPhylogenetic AnalysisChickensVirus Bursitis InfecciosaEstudios de Asociación del Genoma CompletoGenomasEvoluciónAnálisis FilogenéticoPolloThe infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.Instituto de VirologíaFil: Techera, Claudia. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Tomás, Gonzalo. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Grecco, Sofía. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Williman, Joaquín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Hernández, Martín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Olivera, Valeria Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; ArgentinaFil: Banda, Alejandro. Mississippi State University. College of Veterinary Medicine. Poultry Research and Diagnostic Laboratory; Estados UnidosFil: Vagnozzi, Ariel Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; ArgentinaFil: Panzera, Yanina. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Marandino, Ana. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayFil: Pérez, Ruben. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; UruguayElsevierinfo:eu-repo/date/embargoEnd/2024-09-212023-09-21T14:20:33Z2023-09-21T14:20:33Z2023-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/15281https://www.sciencedirect.com/science/article/pii/S01660934230013251879-0984https://doi.org/10.1016/j.jviromet.2023.114807Journal of Virological Methods 322 : 114807 (2023)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2026-09-24T11:38:59Zoai:localhost:20.500.12123/15281instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2026-09-24 11:39:00.999INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
title A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
spellingShingle A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
Techera, Claudia
Infectious Bursal Disease Virus
Genome-wide Association Studies
Genomes
Evolution
PCR
Phylogenetic Analysis
Chickens
Virus Bursitis Infecciosa
Estudios de Asociación del Genoma Completo
Genomas
Evolución
Análisis Filogenético
Pollo
title_short A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
title_full A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
title_fullStr A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
title_full_unstemmed A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
title_sort A rapid and affordable amplicon-based method for next generation genome sequencing of the infectious bursal disease virus
dc.creator.none.fl_str_mv Techera, Claudia
Tomás, Gonzalo
Grecco, Sofía
Williman, Joaquín
Hernández, Martín
Olivera, Valeria Soledad
Bandac, Alejandro
Vagnozzi, Ariel Eduardo
Panzera, Yanina
Marandino, Ana
Pérez, Ruben
author Techera, Claudia
author_facet Techera, Claudia
Tomás, Gonzalo
Grecco, Sofía
Williman, Joaquín
Hernández, Martín
Olivera, Valeria Soledad
Bandac, Alejandro
Vagnozzi, Ariel Eduardo
Panzera, Yanina
Marandino, Ana
Pérez, Ruben
author_role author
author2 Tomás, Gonzalo
Grecco, Sofía
Williman, Joaquín
Hernández, Martín
Olivera, Valeria Soledad
Bandac, Alejandro
Vagnozzi, Ariel Eduardo
Panzera, Yanina
Marandino, Ana
Pérez, Ruben
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Infectious Bursal Disease Virus
Genome-wide Association Studies
Genomes
Evolution
PCR
Phylogenetic Analysis
Chickens
Virus Bursitis Infecciosa
Estudios de Asociación del Genoma Completo
Genomas
Evolución
Análisis Filogenético
Pollo
topic Infectious Bursal Disease Virus
Genome-wide Association Studies
Genomes
Evolution
PCR
Phylogenetic Analysis
Chickens
Virus Bursitis Infecciosa
Estudios de Asociación del Genoma Completo
Genomas
Evolución
Análisis Filogenético
Pollo
dc.description.none.fl_txt_mv The infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.
Instituto de Virología
Fil: Techera, Claudia. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Tomás, Gonzalo. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Grecco, Sofía. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Williman, Joaquín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Hernández, Martín. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Olivera, Valeria Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina
Fil: Banda, Alejandro. Mississippi State University. College of Veterinary Medicine. Poultry Research and Diagnostic Laboratory; Estados Unidos
Fil: Vagnozzi, Ariel Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina
Fil: Panzera, Yanina. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Marandino, Ana. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
Fil: Pérez, Ruben. Universidad de la República. Facultad de Ciencias. Instituto de Biología. Sección Genética Evolutiva; Uruguay
description The infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.
publishDate 2023
dc.date.none.fl_str_mv 2023-09-21T14:20:33Z
2023-09-21T14:20:33Z
2023-12
info:eu-repo/date/embargoEnd/2024-09-21
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/15281
https://www.sciencedirect.com/science/article/pii/S0166093423001325
1879-0984
https://doi.org/10.1016/j.jviromet.2023.114807
url http://hdl.handle.net/20.500.12123/15281
https://www.sciencedirect.com/science/article/pii/S0166093423001325
https://doi.org/10.1016/j.jviromet.2023.114807
identifier_str_mv 1879-0984
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Journal of Virological Methods 322 : 114807 (2023)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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