Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.
Guatemala
Illumina
blue‐winged teal
influenza A virus
next‐generation sequencing
wild bird
Journal
Ecology and evolution
ISSN: 2045-7758
Titre abrégé: Ecol Evol
Pays: England
ID NLM: 101566408
Informations de publication
Date de publication:
Jun 2019
Jun 2019
Historique:
received:
29
12
2018
revised:
10
04
2019
accepted:
12
04
2019
entrez:
26
6
2019
pubmed:
27
6
2019
medline:
27
6
2019
Statut:
epublish
Résumé
The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
Identifiants
pubmed: 31236242
doi: 10.1002/ece3.5232
pii: ECE35232
pmc: PMC6580304
doi:
Banques de données
Dryad
['10.5061/dryad.3h2n106']
Types de publication
Journal Article
Langues
eng
Pagination
6534-6546Subventions
Organisme : NIAID NIH HHS
ID : HHSN272201400006C
Pays : United States
Organisme : NIAID NIH HHS
ID : HHSN272201400008C
Pays : United States
Déclaration de conflit d'intérêts
None declared.
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