Fast subtyping of influenza A virus strains from swine using real-time PT-PCR Short description: The aim of the project is to develop and validate (sensitivity and specificity) real-time RT-PCR as-says 36 for fast subtyping of swine influenza A viruses. Type of project: All Detailed description: Background: Influenza A virus is a group of virus which can infect a number of animals including swine, birds and humans. The influenza virus is subtyped on the basis of the genes HA and NA and water-fowl which is considered the natural reservoir for influenza A viruses, can carry any of the H1 to H16 and N1 to N9 subtypes. In humans and swine it is primarily the subtype combinations H1N1, H1N2, H3N2 which are isolated and known to cause disease. Therefore, four gene variants should be tested for in swine: H1, H3, N1 and N2. Because influenza A virus is an RNA virus, the se-quences of viruses within each subtype are very variable, making it difficult to detect all variants of e.g. H1 in one real-time RT-PCR assay. Presently, swine influenza viruses are routinely subtyped by partial or full length HA and NA gene sequencing followed by phylogenetic analysis, which is a labor- and timeconsuming procedure. The project: This project will design and validate one or more real-time RT-PCR assays for detection of all variants of HA and NA genes that appears in swine. New real-time RT-PCR assays will be desig-ned by comparison (alignment) of known swine influenza virus sequences and by using a real-time PCR design software e.g. AllelelID. It is important that the new assays work under the same PCR conditions, so they can run together in the same PCR set-up. The project work will include purifica-tion of influenza virus RNA genome, set-up of real-time RT-PCR, tests of sensitivity and specificity against known swine influenza virus subtypes. The size of the project can be adjusted by selecting how many HA and NA variants to include. Enquiry: Senior adviser Charlotte Kristiane Hjulsager ckhj@vet.dtu.dk and Molecular biologist Jesper Schak Krog jsck@vet.dtu.dk, Section for Diagnostics and Scientific Advice, and professor Lars Erik Larsen lael@vet.dtu.dk, Section for Virology; DTU Vet, Bülowsvej 27, 1870 Frederiksberg C. ECTS: Flexible
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