In the spring of 2006 we had our first outbreak of avian influenza of highly pathogenic H5N1 (HPAI) among wild birds in Sweden. This disease have impact on poultry industries world wide. Sporadically the virus infects other species than birds and we now know it can even cause fatal infection of humans. There are not yet any confirmed cases of transmission of the disease between humans though a suspected case in an Indonesian family is under investigation. If a mutation occurs that changes the pathogenicity and host affinity to humans we are at a risk of a new pandemia, perhaps like the Spanish flu in 1918-1920. To understand the underlying genetical mechanisms it is important to study the genome of different subtypes of Avian influenza virus (AIV). The aim of this study was to characterize a selected number of AIV isolated from wild birds and minks to see if there are different genetic variants among species. AIV are influenza A viruses and belong to the Orthomyxoviridae family. Influenza A have linear, negative, single-stranded RNA genome consisting of 8 segments. This study focuses on the non structural (NS1) protein because its ability to antagonize the host innate immunity, especially the expression of interferons and Matrix-protein which is important for ribonucleo-protein (RNP) transport and budding. Thirteen low pathogenic AI (LPAI) and 10 HPAI isolates were characterized in terms of subtypes, viral RNA was extracted, cDNA for NS1 and Matrix genes were synthetized, PCR amplified and sequenced. The nucleotide sequences were translated to amino acids and analyzed phylogenetically and the amino acids were compared to public sequences downloaded from National Center for Biotechnology Information (NCBI). We found that two H5N3 and one H10N7 differed significantly from other LPAI in both cladograms and proteinsequences. The cladograms were also different when comparing NS1 and M to each other. HPAI was more homologous as a group, had aspartic acid in p...
