Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza

Indexed in

License and use

Citations

Altmetrics

Grant support

We would like to acknowledge Dr Ana Moreno from the Istituto Zooprofilattico Sperimentale della Lombardia e dell' Emilia Romagna (Brescia, Italy) who kindly provided us with the A/duck/Italy/281904/2006 LPAIV H1N1 isolate.

Analysis of institutional authors

Tarrés-Freixas, FerranAuthorMajo, NataliaAuthor

Publications

Article

Publicated to:Virus Evolution. 11 (1): veaf010- - 2025-03-10 11(1), DOI: 10.1093/ve/veaf010

Authors: Perlas, Albert; Reska, Tim; Croville, Guillaume; Tarres-Freixas, Ferran; Guerin, Jean-Luc; Majo, Natalia; Urban, Lara

Affiliations

Campus Univ Autonoma Barcelona UAB, Ctr Recerca Sanitat Anim CReSA, IRTA, Programa Sanitat Anim, Bellaterra 08193, Spain - Author

Campus Univ Autonoma Barcelona UAB, Ctr Recerca Sanitat Anim CReSA, Unitat Mixta Invest IRTA UAB Sanitat Anim, Bellaterra 08193, Catalonia, Spain - Author

Cent Univ Catalonia UVic UCC, Univ Vic, Fac Sci Technol & Engn, Dept Biosci, Vic 08500, Spain - Author

Helmholtz Zentrum Muenchen, Computat Hlth Ctr, Ingolstaedter Landstr 1, D-85764 Neuherberg, Germany - Author

Tech Univ Munich, Sch Life Sci, Alte Akad 8, D-85354 Freising Weihenstephan, Germany - Author

Univ Autonoma Barcelona UAB, Dept Sanitat & Anat Anim, Fac Vet, Campus UAB, Bellaterra 08193, Catalonia, Spain - Author

Univ Toulouse, IHAP, INRAE, ENVT, F-31300 Toulouse, France - Author

Abstract

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 N6-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.

Keywords

Avian influenzaNanopore sequencinRna modificationsViral evolution

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Virus Evolution due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 6/41, thus managing to position itself as a Q1 (Primer Cuartil), in the category Virology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-05-13:

Scopus: 1

Impact and social visibility

Leadership analysis of institutional authors