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.

我们报告了甲型流感病毒 (IAV) 的全基因组测序，其诊断灵敏度为 100%，并且可在 <24 id=57>n = 19)、商业家禽 ( n = 4) 和猪 ( n = 3) 中获得结果。 IAV 的所有 8 个基因片段，包括来自 18 种公认的血凝素亚型中的 14 种和 11 种神经氨酸酶亚型中的 9 种的基因片段，均以大于 500 倍的覆盖度从评估的 16 个参考病毒分离株中的每一个中进行了整体扩增。以Sanger测序为参考标准获得的3例亚基因组病毒序列与使用MinION方法测序获得的结果相同。实验室间比较表明，在比较 2 个独立实验室时，整个 IAV 基因组测序的重现性≥99.8%。