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

Beate M. Crossley, Daniel Rejmanek, John Baroch, James B. Stanton, Kelsey T. Young, Mary Lea Killian, Mia K. Torchetti, Sharon K. Hietala

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish (US)
JournalJournal of Veterinary Diagnostic Investigation
DOIs
StateAccepted/In press - 2021

Keywords

  • avian influenza A virus
  • MinION
  • nanopore
  • whole-genome sequencing

ASJC Scopus subject areas

  • veterinary(all)

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