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&#x2009;h using amplicon-based nanopore sequencing technology (MinION) on clinical material from wild waterfowl (= 19), commercial poultry (= 4), and swine (= 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&#xd7; 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 &#x2265;99.8% across the entirety of the IAV genomes sequenced.