Browsing by Author "Lakspere, Triin"

Influenza viruses are a group of pathogens in the family Orthomyoviridae, which are classified into 6 genera (A,B,C, Thogotovirus, Isavirus and new unnamed genus). Type A influenza viruses are categorized based on their surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA). So far 17 HA and 9 NA subtypes have been identified. Influenza genome comprises of eight single-stranded negative-sense RNA segments that encode ten to twelve proteins (HA, NA, NP M1/M2, NS1/NS2, PA, PB1 and PB2). Influenza replication cycle depends on the surface proteins binding to host cell receptors, pH mediated fusion and cell-mediated transcription and replication of the viral genome. Virus particles leave the host cell via budding. Influenza viruses cause global epidemic infections each year, the peak is from December to March. These pathogens have also contributed to six global pandemics identified so far. The latest pandemic outbreak was announced by WHO in 2009 which caused over 5000 hospitalizations in Finland. Factors contributing to the severity of clinical outcome can be either genetic, environmental or caused by human host features. This study aims to identify the susceptibility factors for severe influenza A infections and describe the phylodynamics of the latest pandemic A(H1N1)pdm09 from Finnish patient nasopharyngeal aspirates collected between 2009-2013. One-step reverse-transcription PCR was used to amplify all of the 8 segments equally. Fast and precise next-generation sequencing with Illumina 2000 sequencer was used to generate the sequences. Results were bioinformatically analysed using Bayesian modelling with Markov Chain Monte Carlo algorithms of probability distributions. Models analysed showed highest mutation rate in hemagglutinin protein. Phylodynamic analysis revealed higher mutation rate of HA and NA compared to other proteins. Subgroup specific polymorphisms (either in severe or mild cases) were not identified. In total 4657 amino acid substitutions were located in 135 pandemic A(H1N1)pdm09 patient isolates and 238 in 10 seasonal patient samples. Viral HA, NA and PB2 were more frequently mutated than other proteins. Interestingly this study identified double-resistant markers (E119K and S31N) to two antiviral drugs (amantadine and oseltamivir) in one patient isolate (A/Helsinki/598/2013). Previously reported D222 polymorphism (without the signalling peptide)causing more severe clinical outcome was not identified in any of the patient isolates in this study.