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

• DOI: 10.1177/1040638720984114
• Publication Date: 2021-02-06T12:46:35Z
• Authors: Beate M. Crossley; Daniel Rejmanek; John Baroch; James B. Stanton; Kelsey T. Young; Mary Lea Killian; Mia K. Torchetti; Sharon K. Hietala
• Keywords: Veterinary sciences; Turkeys; Swine; Sus scrofa; Wild; MinION; Animals, Wild; Microbiology; avian influenza A virus; Vaccine Related; 03 medical and health sciences; Orthomyxoviridae Infections; Genetics; Animals; Veterinary Sciences; nanopore; Poultry Diseases; Swine Diseases; 0303 health sciences; Whole Genome Sequencing; Bird Diseases; Prevention; Biological Sciences; Influenza; 3. Good health; Nanopore Sequencing; Infectious Diseases; Emerging Infectious Diseases; Ducks; whole-genome sequencing; Influenza A virus; Influenza in Birds; Pneumonia & Influenza; Infection; Zoology; Chickens

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.