Your browser doesn't support javascript.
loading
Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing.
Croville, Guillaume; Le Loc'h, Guillaume; Zanchetta, Catherine; Manno, Maxime; Camus-Bouclainville, Christelle; Klopp, Christophe; Delverdier, Maxence; Lucas, Marie-Noëlle; Donnadieu, Cécile; Delpont, Mattias; Guérin, Jean-Luc.
Afiliación
  • Croville G; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Le Loc'h G; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Zanchetta C; GeT-PlaGe, INRA, Genotoul, US1426, 31326, Castanet-Tolosan Cedex, France.
  • Manno M; GeT-PlaGe, INRA, Genotoul, US1426, 31326, Castanet-Tolosan Cedex, France.
  • Camus-Bouclainville C; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Klopp C; Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France.
  • Delverdier M; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Lucas MN; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Donnadieu C; GeT-PlaGe, INRA, Genotoul, US1426, 31326, Castanet-Tolosan Cedex, France.
  • Delpont M; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France.
  • Guérin JL; Université de Toulouse, ENVT, INRA, UMR 1225, 31076 Toulouse, France. Electronic address: jl.guerin@envt.fr.
J Virol Methods ; 261: 34-39, 2018 11.
Article en En | MEDLINE | ID: mdl-30086381
Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history. The increasing performances of next-generation sequencing (NGS) opened new opportunities for surveillance of poxviruses, based on timely and affordable workflows. We investigated the application of the 3rd generation Oxford Nanopore Minion technology to achieve real-time whole-genome sequencing directly from lesions, without any enrichment or isolation step. Fowlpox lesions were sampled on hens, total DNA was extracted and processed for sequencing on a MinION, Oxford Nanopore. We readily generated whole APV genomes from cutaneous or tracheal lesions, without any isolation or PCR-based enrichment: Fowlpox virus reads loads ranged from 0.75% to 2.62% and reads up to 61 kbp were generated and readily assembled into 3 APV complete genomes. This long read size eases the assembly step and lowers the bioinformatics capacity requirements and processing time compared to huge sets of short reads. The complete genome analysis confirmed that these Fowlpox viruses cluster within clade A1 and host full length reticuloendotheliovirus (REV) inserts. The pathobiological relevance of REV insert, although a classical feature of fowlpoxviruses (FPVs), should be further investigated. Surveillance of emerging poxviruses could greatly benefit from real-time whole genome sequencing.
Asunto(s)
Palabras clave

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Enfermedades de las Aves de Corral / Análisis de Secuencia de ADN / Avipoxvirus / Infecciones por Poxviridae / Técnicas de Genotipaje / Secuenciación Completa del Genoma Tipo de estudio: Screening_studies Límite: Animals Idioma: En Revista: J Virol Methods Año: 2018 Tipo del documento: Article País de afiliación: Francia

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Enfermedades de las Aves de Corral / Análisis de Secuencia de ADN / Avipoxvirus / Infecciones por Poxviridae / Técnicas de Genotipaje / Secuenciación Completa del Genoma Tipo de estudio: Screening_studies Límite: Animals Idioma: En Revista: J Virol Methods Año: 2018 Tipo del documento: Article País de afiliación: Francia