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A universal RT-qPCR assay for “One Health” detection of influenza A viruses
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A universal RT-qPCR assay for “One Health” detection of influenza A viruses
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Journal Article
A universal RT-qPCR assay for “One Health” detection of influenza A viruses
2021
Overview
The mutual dependence of human and animal health is central to the One Health initiative as an integrated strategy for infectious disease control and management. A crucial element of the One Health includes preparation and response to influenza A virus (IAV) threats at the human-animal interface. The IAVs are characterized by extensive genetic variability, they circulate among different hosts and can establish host-specific lineages. The four main hosts are: avian, swine, human and equine, with occasional transmission to other mammalian species. The host diversity is mirrored in the range of the RT-qPCR assays for IAV detection. Different assays are recommended by the responsible health authorities for generic IAV detection in birds, swine or humans. In order to unify IAV monitoring in different hosts and apply the One Health approach, we developed a single RT-qPCR assay for universal detection of all IAVs of all subtypes, species origin and global distribution. The assay design was centred on a highly conserved region of the IAV matrix protein (MP)-segment identified by a comprehensive analysis of 99,353 sequences. The reaction parameters were effectively optimised with efficiency of 93–97% and LOD
95%
of approximately ten IAV templates per reaction. The assay showed high repeatability, reproducibility and robustness. The extensive
in silico
evaluation demonstrated high inclusivity, i.e. perfect sequence match in the primers and probe binding regions, established as 94.6% for swine, 98.2% for avian and 100% for human H3N2, pandemic H1N1, as well as other IAV strains, resulting in an overall predicted detection rate of 99% on the analysed dataset. The theoretical predictions were confirmed and extensively validated by collaboration between six veterinary or human diagnostic laboratories on a total of 1970 specimens, of which 1455 were clinical and included a diverse panel of IAV strains.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
/ Animals
/ Assaying
/ Design
/ DNA
/ Editing
/ Funding
/ Genomes
/ Hogs
/ Humans
/ Influenza A virus - genetics
/ Influenza A virus - isolation & purification
/ Influenza A Virus, H1N1 Subtype - genetics
/ Influenza A Virus, H1N1 Subtype - isolation & purification
/ Influenza A Virus, H3N2 Subtype - genetics
/ Influenza A Virus, H3N2 Subtype - isolation & purification
/ Influenza in Birds - diagnosis
/ Influenza in Birds - virology
/ Influenza, Human - diagnosis
/ Medicine and health sciences
/ Methods
/ Molecular diagnostic techniques
/ Orthomyxoviridae Infections - diagnosis
/ Orthomyxoviridae Infections - virology
/ Research and Analysis Methods
/ Reverse Transcriptase Polymerase Chain Reaction - methods
/ Reviews
/ Species
/ Swine
/ Vaccines
/ Viruses
/ Zoonoses
