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Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses.

ABSTRACT: We report whole-genome sequencing of influenza A virus (IAV) with 100% diagnostic sensitivity and results available in <24-48 h using amplicon-based nanopore sequencing technology (MinION) on clinical material from wild waterfowl (n = 19), commercial poultry (n = 4), and swine (n = 3). All 8 gene segments of IAV including those from 14 of the 18 recognized hemagglutinin subtypes and 9 of the 11 neuraminidase subtypes were amplified in their entirety at >500× coverage from each of 16 reference virus isolates evaluated. Subgenomic viral sequences obtained in 3 cases using Sanger sequencing as the reference standard were identical to those obtained when sequenced using the MinION approach. An inter-laboratory comparison demonstrated reproducibility when comparing 2 independent laboratories at ≥99.8% across the entirety of the IAV genomes sequenced.

SUBMITTER: Crossley BM 

PROVIDER: S-EPMC7953088 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses.

Crossley Beate M BM   Rejmanek Daniel D   Baroch John J   Stanton James B JB   Young Kelsey T KT   Killian Mary Lea ML   Torchetti Mia K MK   Hietala Sharon K SK  

Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 20210206 2

We report whole-genome sequencing of influenza A virus (IAV) with 100% diagnostic sensitivity and results available in <24-48 h using amplicon-based nanopore sequencing technology (MinION) on clinical material from wild waterfowl (<i>n</i> = 19), commercial poultry (<i>n</i> = 4), and swine (<i>n</i> = 3). All 8 gene segments of IAV including those from 14 of the 18 recognized hemagglutinin subtypes and 9 of the 11 neuraminidase subtypes were amplified in their entirety at >500× coverage from ea  ...[more]

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