A newly developed tetraplex real-time RT-PCR for simultaneous screening of influenza virus types A, B, C and D

Influenza Other Respir Viruses. 2019 Jan;13(1):71-82. doi: 10.1111/irv.12613. Epub 2018 Oct 22.

Abstract

Background: Human- or avian-to-swine transmissions have founded several autonomously circulating influenza A virus (IAV) lineages in swine populations that cause economically important respiratory disease. Little is known on other human influenza virus types, like B (IBV) and C (ICV) in European swine, and of the recently detected novel animal influenza virus type D (IDV).

Objectives: Development of a cost-effective diagnostic tool for large-scale surveillance programmes targeting all four influenza virus types.

Methods: An influenza ABCD tetraplex real-time RT-PCR (RT-qPCR) was developed in the frame of this study. A selection of reference virus strains and more than 4000 porcine samples from a passive IAV surveillance programme in European swine with acute respiratory disease were examined.

Results: Two IBV, a single IDV but no ICV infections were identified by tetraplex RT-qPCR. IBV and IDV results were confirmed by conventional RT-PCR and partial sequence analysis.

Conclusions: The tetraplex RT-qPCR proved fit for purpose as a sensitive, specific and high-throughput tool to study influenza virus transmission at the human-animal interface. Complementing close-meshed active virological and serological surveillance is required to better understand the true incidence and prevalence of influenza virus type B, C and D infections in swine.

Keywords: European surveillance; influenza virus types A, B, C and D; multiplex RT-qPCR; swine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA Primers / genetics
  • Epidemiological Monitoring / veterinary*
  • Europe
  • Gammainfluenzavirus / isolation & purification
  • High-Throughput Screening Assays / methods*
  • Influenza A virus / isolation & purification
  • Influenza B virus / isolation & purification
  • Multiplex Polymerase Chain Reaction / methods*
  • Orthomyxoviridae / isolation & purification*
  • Orthomyxoviridae Infections / diagnosis
  • RNA, Viral / genetics
  • Sensitivity and Specificity
  • Sus scrofa
  • Swine
  • Swine Diseases / virology
  • Thogotovirus / isolation & purification

Substances

  • DNA Primers
  • RNA, Viral

Associated data

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  • GENBANK/CY045781
  • GENBANK/EPI248511
  • GENBANK/EPI248525
  • GENBANK/FJ970928
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