Open AccessNanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses
Author(s) -
Beate Crossley,
Daniel Rejmanek,
John A. Baroch,
James B. Stanton,
Kelsey T. Young,
Mary Lea Killian,
Mia Kim Torchetti,
Sharon K. Hietala
Publication year - 2021
Publication title -
journal of veterinary diagnostic investigation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.529
H-Index - 78
eISSN - 1943-4936
pISSN - 1040-6387
DOI - 10.1177/1040638720984114
Subject(s) - minion , nanopore sequencing , biology , sanger sequencing , amplicon , virology , neuraminidase , hemagglutinin (influenza) , genome , influenza a virus , ion semiconductor sequencing , dna sequencing , subgenomic mrna , genetics , computational biology , virus , polymerase chain reaction , gene
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.
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