Next Generation Sequencing for identification of new influenza A virus variants from birds, swine, mink, seals etc. Short description: Influenza A virus isolates from birds, swine, mink or seal will be genetically characterized by sequen-cing 34 of the whole virus genome with Next Generation Sequencing technique. The emergence of new variants and/or the phylogenetic relatedness to other virus strains will be investigated by bioinformatics analyses. Type of project: All Detailed description: Background: Influenza A virus is a group of viruses, which can affect a number of animals, such as swine, birds and humans. In general, the influenza viruses circulating within a population are species-specific, which means that the viruses circulating in e.g. swine and birds, normally will stay within their host. However, is it a well-known that influenza A viruses on some occasions have jumped from one species to another, either by transmission of “a whole virus” or by the making of a new virus, by mixing genes with other influenza A virus strains (reassortments). Influenza A virus is an RNA virus with a genome consisting of 8 gene segments (HA, NA, PB2, PB1, PA, NP, M and NS) which together form the whole virus genome at about 13,5 kb. Influenza A virus is named as subtypes based on HA and NA. All variants of HA and NA (H1 to H16 and N1 to N9) found in birds, and this species is considered the natural reservoir for influenza A virus. In humans and swine it is mainly subtypes H1N1, H1N2 and H3N2, which are causing disease. To be able to discover new influenza A virus strains, it is, besides from the subtype, also important or necessary to determine the whole virus genome, since new viruses from time to time develops by reassortment (genetic shift), e.g. the pandemic H1N1 virus which spread among humans and swine in 2009/2010 (H1N1pdm09), which is believed to have evolved by a mix of minimum two different swine influenzas viruses. The project: The project will be based on influenza A viruses isolated in cell culture or eggs, to obtain a high con-centration of the virus. The influenza virus genome will be determined by Next Generation Sequencing (NGS) technique performed on PCR products of each of the 8 gene segments or directly on viral RNA. Prior to the actual sequencing, the influenza virus RNA genome shall be purified and different PCR as-says will be used for detection and partial sequencing. Afterwards, the achieved results will be investi-gated using different bioinformatic analyses, such as assembly of sequence data (contigs), comparison (alignment) to other virus sequences, and relatedness to other viruses (phylogenetic tree). The infor-mations are used in the study of molecular epidemiology of influenza A viruses. 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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