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

Authors
  • Haach, Vanessa1
  • Gava, Danielle2
  • Cantão, Maurício Egídio2
  • Schaefer, Rejane3
  • 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. , (Brazil)
  • 2 Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil. , (Brazil)
  • 3 Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil. [email protected] , (Brazil)
Type
Published Article
Journal
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]
Publication Date
Sep 01, 2020
Volume
51
Issue
3
Pages
1447–1451
Identifiers
DOI: 10.1007/s42770-020-00250-z
PMID: 32125678
Source
Medline
Keywords
Language
English
License
Unknown

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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