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

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 >500x 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.

Automated summary

This study conducted whole-genome sequencing of influenza A virus (IAV) using MinION technology, showing high diagnostic sensitivity and accuracy in clinical samples from wild waterfowl, commercial poultry, and swine. Results demonstrated concordance between sequences obtained by MinION and Sanger sequencing methods, as well as reproducibility across different laboratories with >=99.8% consistency in the entirety of the IAV genomes sequenced.