Evaluation of two multiplex RT-PCR assays for detection and subtype differentiation of Brazilian swine influenza viruses
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VETERINARY MICROBIOLOGY - SHORT COMMUNICATION
Evaluation of two multiplex RT-PCR assays for detection and subtype differentiation of Brazilian swine influenza viruses Vanessa Haach 1 & Danielle Gava 2 & Maurício Egídio Cantão 2 & Rejane Schaefer 2 Received: 19 September 2019 / Accepted: 20 February 2020 # Sociedade Brasileira de Microbiologia 2020
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. Keywords Influenza A virus . Multiplex RT-PCR . Subtyping . Swine . Diagnosis
Influenza A virus (IAV) belongs to the Orthomyxoviridae family, genus Influenzavirus A and has a segmented genome made up of eight single-stranded RNA molecules [1]. IAV infects several species of birds and mammals and poses a threat to the human population due to its pandemic and zoonotic potential [2, 3]. Swine are considered an important host in the dynamics and epidemiology of IAV, being able to generate reassortant viruses [4]. Interspecies transmission is well documented, exemplified by the infection of pigs with avian influenza viruses and the establishment in swine of human seasonal influenza viruses [3, 5]. Influenza infection causes a significant Responsible Editor: Fernando R. Spilki. * Rejane Schaefer [email protected] 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
2
Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina CEP 89715-899, Brazil
economic impact in the swine production due to its high morbidity and costs with antimicrobials to prevent secondary infection
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