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  • 1.
    Dagsberg, Jacob
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Förekomst av aviärt influensavirus bland vilda fåglar provtagna vid Ottenby fågelstation under 2017: Detektion och fylogenetisk analys av neuraminidas subtyp 6-virus2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Avian influenza virus (AIV) is divided into subtypes based on two glycoproteins on its surface. Among birds there are 16 subtypes of hemagglutinin (H) and 9 subtypes of neuraminidase (N). Some H subtypes can mutate into highly pathogenic viruses and cause deadly infections. One such highly pathogenic virus was reported in northern Europe in 2017. Spread amongst highly pathogenic H5 is well mapped out. Reverse transcription followed by amplification in real time is used to detect neuraminidase in AIV, based on synthesis of complementary DNA, which gets amplified and detected using fluorescent probe. Sanger sequencing of neuraminidase coding gene segments is used to verify the results from RT-qPCR screening and analysing phylogenetic relationship. To contribute with knowledge about neuraminidase subtype 6, RT-qPCR analysis was used on 282 AIV positive samples from wild birds, sampled at Ottenby bird station in 2017. Gene segments coding for hemaglutinin and neuraminidase among viruses in N6 positive samples was sequenced to validate the N6-RT-qPCR analyses, determine H subtype and to analyse phylogenetic relationship among N6-sequences. The RT-qPCR resulted in 37 N6 positive samples where 26 of these was confirmed as N6 with traditional PCR and sequencing. AIV from the analyses occurred in subtype constellations of: 14 H1N6, 3 H3N6, 8 H4N6 and 1 H5N6. Three samples failed to give H subtype, three different samples gave no N6 sequence. Detected H5N6 was low pathogenic. The phylogenetic analysis showed that AIV N6 sequences from Ottenby, in tandem with sequences from GenBank, formed four genotypes. N6 sequences from two viruses sequenced in this study, associated with subtypes H3N6 and H1N6 formed genotype two, together with four H5N6, possibly high pathogenic viruses from Japan.

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