Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza
Perlas Puente, Albert (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals)
Reska, Tim
Croville, Guillaume (Université de Toulouse)
Tarrés-Freixas, Ferran (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal)
Guérin, Jean-Luc (Université de Toulouse)
Majó i Masferrer, Natàlia (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal)
Urban, Lara (Technical University of Munich)

Fecha:	2025
Resumen:	Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. We here utilized a well-defined AIV strain to systematically investigate AIV genetic characterization through rapid, portable nanopore sequencing by comparing the latest DNA and RNA nanopore sequencing approaches and various computational pipelines for viral consensus sequence generation and phylogenetic analysis. We show that the latest direct RNA nanopore sequencing updates improve consensus sequence generation, but that the application of the latest DNA nanopore chemistry after reverse transcription and amplification outperforms, such native viral RNA sequencing by achieving higher sequencing accuracy and throughput. We additionally leveraged the direct RNA nanopore sequencing data for the detection of RNA modifications, such as N 6 -methyladenosine and pseudouridine, which play a role in viral immune evasion. Finally, we applied these sequencing approaches together with portable AIV diagnosis and quantification tools to environmental samples from a poultry farm, demonstrating the feasibility of nanopore sequencing for on-site non-invasive AIV monitoring in real-world outbreak scenarios.
Derechos:	Aquest 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.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Avian influenza ; Viral evolution ; RNA modifications ; Nanopore sequencing
Publicado en:	Virus Evolution, Vol. 11 (february 2025) , ISSN 2057-1577

DOI: 10.1093/ve/veaf010
PMID: 40066328

9 p, 3.3 MB

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