tetano
Editor, Senior Moderator
J Vet Diagn Invest
. 2021 Feb 6;1040638720984114.
doi: 10.1177/1040638720984114. Online ahead of print.
Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses
Beate M Crossley[SUP] 1 [/SUP], Daniel Rejmanek[SUP] 1 [/SUP], John Baroch[SUP] 2 [/SUP], James B Stanton[SUP] 3 [/SUP], Kelsey T Young[SUP] 3 [/SUP], Mary Lea Killian[SUP] 4 [/SUP], Mia K Torchetti[SUP] 4 [/SUP], Sharon K Hietala[SUP] 1 [/SUP]
Affiliations
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.
Keywords: MinION; avian influenza A virus; nanopore; whole-genome sequencing.
. 2021 Feb 6;1040638720984114.
doi: 10.1177/1040638720984114. Online ahead of print.
Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses
Beate M Crossley[SUP] 1 [/SUP], Daniel Rejmanek[SUP] 1 [/SUP], John Baroch[SUP] 2 [/SUP], James B Stanton[SUP] 3 [/SUP], Kelsey T Young[SUP] 3 [/SUP], Mary Lea Killian[SUP] 4 [/SUP], Mia K Torchetti[SUP] 4 [/SUP], Sharon K Hietala[SUP] 1 [/SUP]
Affiliations
- PMID: 33550926
- DOI: 10.1177/1040638720984114
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.
Keywords: MinION; avian influenza A virus; nanopore; whole-genome sequencing.