A universal RT-qPCR assay for "One Health" detection of influenza A viruses

PLoS One. 2021 Jan 20;16(1):e0244669. doi: 10.1371/journal.pone.0244669. eCollection 2021.

Abstract

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 LOD95% 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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Birds / virology
  • Humans
  • 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 A virus / genetics
  • Influenza A virus / isolation & purification*
  • Influenza in Birds / diagnosis*
  • Influenza in Birds / virology
  • Influenza, Human / diagnosis*
  • Influenza, Human / virology
  • One Health
  • Orthomyxoviridae Infections / diagnosis*
  • Orthomyxoviridae Infections / virology
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Swine
  • Swine Diseases / diagnosis*
  • Swine Diseases / virology

Grants and funding

State Veterinary Institute Prague, Czech Republic and Veterinary Institute Zvolen, Slovak Republic: The work was performed in connection with the activities of the National Reference Laboratory for Avian Influenza Viruses and was not funded by additional financial sources. Animal and Plant Health Agency, United Kingdom: The work was funded by the Department of Environment, Food and Rural Affairs (Defra, UK) and the Devolved Administrations of Scotland and Wales through the Programmes of Work (i) “FLUFUTURES - Reducing Influenza A Virus (avian and mammalian) hazards in the UK” (SE2211) and (ii) “FLUFUTURES 2.0 - Understanding the diverse spectrum of influenza virus based threats to the UK” (SE2213); plus two Defra Contract C programmes, namely (iii) the National Reference Laboratory for Statutory and Exotic Virus Diseases of Avian Species and Relevant Hosts (SV3400), and (iv) the International Reference Laboratory for Avian Influenza and Swine Influenza (SV3006). Danam.Vet.Molbiol, Budapest, Hungary; SCG Diagnosztika Ltd., Délegyháza, Hungary; Prophyl Animal Health Ltd., Mohács, Hungary: The companies own budgets were used. The funders provided support in the form of salaries for authors [ÁD, TV, MM] but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. No funding by any additional financial sources. National Institute of Public Health, Czech Republic: The work was supported by Ministry of Health, Czech Republic - conceptual development of research organization („The National Institute of Public Health – NIPH, 75010330“).