Pathogen Dynamics in Wild Bird Species: Circulation of Avian Influenza Viruses in Natural Vs
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Pathogen dynamics in wild bird species: circulation of avian influenza viruses in natural vs. anthropic ecosystems and concurrent infections with other agents in waterbirds Olalla Torrontegui Vega 1 Pathogen dynamics in wild bird species; circulation of avian influenza viruses in natural vs. anthropic ecosystems and concurrent infections with other agents in waterbirds Olalla Torrontegui Vega 2017 Work performed at the Animal Health Department of NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario for the degree of Doctor of Phylosophy in Biology with international mention at the University of the Basque Country Thesis directors: Marta Barral DVM, PhD and Ursula Höfle DVM, PhD Department of Zoology and Animal Cell Biology Faculty of Science and Technology University of the Basque Country (c)2017 OLALLA TORRONTEGUI VEGA This thesis was accomplished with financial support from the Spanish National Institute for Agricultural and Food Research and Technology (INIA) (RTA2011-00111-C03 grant), and with financial support from the Department of Agriculture and Fisheries (Basque Government). Olalla Torrontegui was recipient of an INIA predoctoral grant. Index Index List of Content Thesis outline ................................................................................................................... 1 Literature review .............................................................................................................. 5 Avian Influenza Virus: morphology, replication and assembly ............................................................... 7 AIV evolutionary pathways ................................................................................................................... 13 AIV pathogenesis ................................................................................................................................... 15 Epidemiology of AIVs ............................................................................................................................. 17 Effects of host ecology and environment on AIV epidemiology ........................................................... 32 Diagnostic techniques ........................................................................................................................... 39 Chapter 1. Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community ........................................ 41 Abstract ................................................................................................................................................. 43 Introduction ........................................................................................................................................... 45 Material and Methods ........................................................................................................................... 46 Results ................................................................................................................................................... 54 Discussion .............................................................................................................................................. 57 Acknowledgements ............................................................................................................................... 64 Chapter 2. Avian influenza virus prevalence is higher in Passeriformes hosts in the Atlantic bioregion in Spain. .......................................................................................................... 66 Abstract ................................................................................................................................................. 68 Introduction ........................................................................................................................................... 70 Material and methods ........................................................................................................................... 71 Results ................................................................................................................................................... 77 Discussion .............................................................................................................................................. 78 i Index Acknowledgements ............................................................................................................................... 80 Chapter 3. Avian influenza virus in wintering aquatic birds at landfills in south-central Spain. Are these places hotspots for surveillance? ........................................................... 82 Abstract ................................................................................................................................................. 84 Introduction ........................................................................................................................................... 86 Material and Methods ........................................................................................................................... 87 Results ................................................................................................................................................... 89 Discussion .............................................................................................................................................. 91 Acknowledgements ............................................................................................................................... 93 Chapter 4. Mycobacterium sp. and Salmonella sp. are more prevalent when coinfecting with low pathogenic avian influenza virus in wild waterbirds .......................................... 96 Abstract ................................................................................................................................................. 98 Introduction ......................................................................................................................................... 100 Material and methods ......................................................................................................................... 101 Results ................................................................................................................................................. 104 Discussion: ........................................................................................................................................... 108 Acknowledgements ............................................................................................................................. 110 General Discussion ......................................................................................................... 112 Conclusions ................................................................................................................... 120 Summary ....................................................................................................................... 124 Laburpena ..................................................................................................................... 128 Resumen ....................................................................................................................... 132 Acknowledgements ....................................................................................................... 136 Bibliography .................................................................................................................. 140 ii Index Annexes......................................................................................................................... 156 iii Index List of Figures Figure 1. Diagram of an avian influenza virion (Shaw and Palese, 2013). ................................. 8 Figure 2. AIV genome segments and associated proteins after transcription. .......................... 9 Figure 3. Stages of avian influenza virus replication (1-7). ...................................................... 11 Figure 4. Evolution of AIV: antigenic shift vs. antigenic drift. .................................................. 14 Figure 5. Influenza A virus host range and host-associated HA subtypes (H). ......................... 17 Figure 6. AIV replication and transmission in most Anseriformes hosts. ................................ 20 Figure 7. Latest highly pathogenic avian influenza virus outbreak (H5N8) affecting Europe between 26/10/2016 until 22/01/2017. .......................................................................... 32 Figure 8. Main global migratory routes used by wild birds (“Wetlands international,” n.d.) . 34 Figure 9. Sampling effort (grey bars) and AIV prevalence (orange bars) at each sampling time (between brackets). ......................................................................................................... 54 Figure 10. Mean AIV prevalence for each year and counts of Anseriformes and non- Anseriformes breeding pairs in Salburua wetland. .......................................................... 56 Figure 11. Predicted avian influenza virus prevalence at Salburua wetland in relation to waterbird phenology. ....................................................................................................... 58 Figure 12. Avian community composition at Salburua wetland. ............................................