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Evaluation of two multiplex RT-PCR assays for detection and subtype differentiation of Brazilian swine influenza viruses

  • Veterinary Microbiology - Short Communication
  • Published:
Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

Influenza A virus (IAV) subtypes H1N1, H1N2, and H3N2 are endemic in swine herds in most pork producing countries; however, the viruses circulating in different geographic regions are antigenically and genetically distinct. In this sense, the availability of a rapid diagnostic assay to detect locally adapted IAVs and discriminate the virus subtype in clinical samples from swine is extremely important for monitoring and control of the disease. This study describes the development and validation of a multiplex RT-PCR assay for detection and subtyping of IAV from pigs. The analytical and diagnostic specificity of the assays was 100% (94.3–100.0, CI 95%), and the limit of detection was 10−3 TCID50/mL. A total of 100 samples (IAV isolates and clinical specimens) were tested, and the virus subtype was determined for 80 samples (80%; 71.1–86.7, CI 95%). From these, 50% were H1N1, 22.5% were H1N2, and 7.5% were H3N2. Partial subtyping was determined for 8.75% samples (H1pdmNx and HxN2). Additionally, mixed infections with two virus subtypes (H1N2 + H3N2 and H1N1pdm + H1pdmN2; 2.5%) and reassortant viruses (H1pdmN2, 6.25%; and H1N1hu, 2.5%) were detected by the assay. A rapid detection of the most prevalent IAV subtypes and lineages in swine is provided by the assays developed here, improving the IAV diagnosis in Brazilian laboratories, and contributing to the IAV monitoring.

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Acknowledgements

The authors acknowledge Marisete F. Schiochet and Neide L. Simon for laboratory assistance, Arlei Coldebella for statistical analysis, and Marina Schmitt for the graphic design.

Funding

This study was supported by the EMBRAPA (SEG 22.16.05.004.00.03). VH has a grant from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

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Authors and Affiliations

  1. Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, Rio Grande do Sul, CEP 90050-170, Brazil

    Vanessa Haach

  2. Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil

    Danielle Gava, Maurício Egídio Cantão & Rejane Schaefer

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  1. Vanessa Haach
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  3. Maurício Egídio Cantão
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  4. Rejane Schaefer
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Correspondence to Rejane Schaefer.

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Haach, V., Gava, D., Cantão, M.E. et al. Evaluation of two multiplex RT-PCR assays for detection and subtype differentiation of Brazilian swine influenza viruses. Braz J Microbiol 51, 1447–1451 (2020). https://doi.org/10.1007/s42770-020-00250-z

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  • DOI: https://doi.org/10.1007/s42770-020-00250-z

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