Browsing by Subject "Next generation sequencing Influenza"

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    Epidemiology and molecular diversity of influenza A viruses in pigs
    (2015-11) Diaz, Carlos
    Influenza A viruses (IAVs) infect many animal species including humans and pigs. Zoonotic IAV infections happen worldwide and are considered a major public health risk because IAVs can cause human pandemics. A novel IAV caused the 1st human pandemic of the 21st century and highlighted the role of pigs in the ecology of IAVs because the 2009 pandemic virus emerged from IAVs circulating in pigs in North America and Asia. However the epidemiology and molecular evolution of IAVs in pigs is not completely understood. Overall we hypothesize that the immune status of the pig is a key driver of the molecular evolution of the virus and that viral diversity alters the course of IAV infection. We also propose that different pig subpopulations on swine farms play unique roles in the persistence of IAVs over time. Therefore the main objective of this dissertation was to characterize the genetic diversity of IAVs during infection of pigs to better understand the epidemiology and molecular evolution of swine influenza, focusing in particular on what happens at the herd level. Classical epidemiological methods and novel experimental designs were integrated with deep genome sequencing technologies and bioinformatics algorithms to produce robust evidence that supports the genetic plasticity of IAVs and contributed to the understanding of virus persistence at the herd level. To understand the epidemiology and molecular evolution of IAV in pigs we design a longitudinal study and followed 5 pig breeding herds for one year (Chapters 2 and 3). We confirmed the persistence of IAV over time in breeding herds and the co-circulation of more than one IAV subtype at a single sampling event (Chapter 2). We proved that this long-term persistence of IAVs in pig breeding herds resulted in a higher odds of IAV infection in groups of new gilts (on farm for less than 4 weeks) and piglets compared to resident gilts (on farm for more than 4 weeks). Additionally, in these herds we found a strong association between IAV infection and year quarter indicating a seasonal pattern of IAV infection. Furthermore, we demonstrated that the continuous detection of IAV within farm could imply the presence of different genetic lineages and not necessarily the persistence of the same IAV over time (chapter 3). However, we also identified the same genetic lineage for prolonged periods of time (283 days). We demonstrated that different pig subpopulations within a farm could harbor different IAVs over time and that the co-circulation of multiple genotypes within a subpopulation could facilitate IAV reassortment. Once pigs are weaned from pig breeding herds they can serve as a source of IAVs to downstream swine sites and their respective regions. Therefore to better understand the molecular evolution of IAV during infection of weaned pigs we evaluated the genetic and antigenic diversity of the virus under different immune statuses in 3-week old weaned pigs. First we compared the antigenic differences at the HA level of IAVs among pigs with or without MDA against IAVs (chapter 4); subsequently we compared the complete genome plasticity of the virus in pigs with active immunity to IAVs (chapter 5); and finally we studied the transmission pattern and IAV genome diversity during infection of pigs after weaning under field conditions (chapter 6). In pigs with or without MDA against IAVs (Chapter 4) we found that nucleotide substitutions at the HA level can happen shortly after infection. Using deep genome sequencing we proved that the genetic diversity of IAVs during infection of weaned vaccinated pigs (chapter 5) is dynamic, within and between pigs, and not limited to the main antigenic genes of the virus. Our results also illustrated the importance of the internal gene segments on the assessment of IAV diversity during infection of pigs. Additionally, we confirmed that pigs can bring IAVs to other swine farms at weaning and that the long-term persistence of IAVs in pigs after weaning could be the result of different epidemic waves of IAV infection (Chapter 6). Furthermore, we found that different IAVs coexisted as a population of viruses that were either closely related to each other in the form of viral groups (VGs) or clearly distinct representing distinct IAV genetic lineages. In conclusion we demonstrated that the complex dynamic of IAV diversity at the herd level is the result of the plasticity of IAV genome during infection of pigs regardless of their immune status. The plasticity of IAV genome during infection of pigs at the individual level indicated that there is a dynamic “cloud” of genotypes during virus replication that are closely related to each other, which might be translated at the population as different virus groups that can co-circulate with other influenza A virus groups over time. Additionally our results demonstrate that IAV infections are not evenly distributed among all subpopulations present in pig breeding herds or in pigs after weaning and indicated that the long-term persistence of IAVs in pig farms could be associated with the continuous occurrence of IAV epidemics at the herd level. Hence, we hypothesize that the most important epidemiological factor for IAV persistence at the population level is the continuous availability of susceptible animals to IAV infections that allow this dynamic cloud of IAV genotypes to replicate over time. We suggest that health interventions to control IAV in swine populations and reduce its zoonotic potential should aim to reduce the transmission and persistence of IAVs among those pig subpopulations that are continuously introduced into pig farms (new gilts, newborn pigs, and weaned pigs). The work presented in this thesis contributes significantly to the understanding of IAV diversity, persistence and evolution in pigs and provides useful information to mitigate IAV infections in pigs and its zoonotic potential.