Introduction: Equine influenza virus, an influenza type A virus, belongs to the family of Orthomyxoviridae. Equine influenza is a major cause of respiratory disease in horses and outbreaks have severe economical repercussions for the horse industry. It is considered to be endemic in Sweden and between 1997 and 2006 there have been around 10 to 40 outbreaks every year. The objective of this study was to do a phylogenetic characterization of equine influenza outbreaks that occurred in Sweden during a twenty year period. Methods: The haemagglutinin and neuraminidase gene of 14 samples and the complete genome of three samples collected over the span of 20 years were sequenced. The viral RNA were extracted, amplified with OneStep RT-PCR and sequenced. Results & Discussion: The phylogenetic tree and deduced amino acid sequence of HA1 illustrated that different lineages of equine influenza virus has circulated simultaneously in the Swedish horse population. The isolates mainly belonged to pre-divergence-, Eurasian- and American lineages. To characterize equine influenza viruses is important for vaccine strain selection, to fully understand the disease and how the virus evolves.

<p> Traditionally, seasonal forcing has been considered to be the major cause of the influenza seasonality. However, Andreasen [2003] showed that repetitive introductions of new strains can lead to cyclic dynamics. The cyclic dynamic produced by his model is not seasonal, because the length of seasons cannot be defined in his model. In this report, we develop a model that combines a stochastic mutation process with a two-strain competition process governing the spread of the mutant strain. This model can produce stable seasonal dynamics. If we introduce a small seasonal forcing to the transmission rate, the length of a season can be regulated to one year if the unforced system oscillates with a period close to one year. If the system has a period that is far from one year, then the forced system may behave chaotically.</p> / Thesis / Master of Science (MSc)

<p>Evolution by natural selection can occur at multiple biological scales. This is particularly the case for host-pathogen systems, where selection occurs both within each infected host as well as through transmission between hosts. Despite there being established mathematical models for understanding evolution at a single biological scale, fewer tractable models exist for multiscale evolutionary dynamics. Here I present mathematical approaches using tools from probability and stochastic processes as well as dynamical systems to handle multiscale evolutionary systems. The first problem I address concerns the antigenic evolution of influenza. Using a combination of ordinary differential equations and inhomogeneous Poisson processes, I study how immune selection pressures at the within-host level impact population-level evolutionary dynamics. The second problem involves the more general question of evolutionary dynamics when selection occurs antagonistically at two biological scales. In addition to host-pathogen systems, such situations arise naturally in the evolution of traits such as the production of a public good and the use of a common resource. I introduce a model for this general phenomenon that is intuitively visualized as a a stochastic ball-and-urn system and can be used to systematically obtain general properties of antagonistic multiscale evolution. Lastly, this ball-and-urn framework is in itself an interesting mathematical object which can studied as either a measure-valued process or an interacting particle system. In this mathematical context, I show that under different scalings, the measure-valued process can have either a propagation of chaos or Fleming-Viot limit.</p> / Dissertation

<p>Despite high vaccination rates and effective adaptive immune responses from the part of infected individuals, influenza A viruses cause significant morbidity and mortality annually. This is due to influenza's rapid antigenic evolution, whereby continual mutations occurring in epitope regions of the virus's hemagglutinin protein result in the diminishment of long-term antibody recognition, in a process that has been termed `antigenic drift'. Although it is clear that antigenic drift enables previously infected individuals to become reinfected, the mechanism that is responsible for influenza's antigenic drift is still under debate. As recently as 2009, a new hypothesis of antigenic drift was put forward that argues that binding avidity changes in the viral hemagglutinin result in antigenic drift as a side effect. This hypothesis stands in contrast to the traditionally accepted hypothesis that mutations in epitope regions are positively selected for their ability to evade immune recognition. This thesis focuses on the use of epidemiological models and empirical data analysis to explore different hypotheses of antigenic drift. </p><p>In the first chapter, I am asking what effects on antigenic drift rate would be produced under the new hypothesis. I mathematically formulate the hypothesis that antigenic drift is simply a side effect of cellular receptor binding avidity changes that occur as the virus is transmitted between individuals of different immune status levels. I then use this formulation to explore how influenza's rate of antigenic drift depends on different epidemiological factors, including host contact rate, host lifespan, and the duration of infection. Finally, I use the model to assess alternative vaccination strategies by the impact they have on rates of antigenic drift and therewith rates of disease incidence/</p><p>In the second chapter, I critically evaluate the binding avidity hypothesis by comparing predictions of the hypothesis against empirical data. I first use a `phylodynamic' extension of the model presented in the first chapter to determine whether the hypothesis is consistent with the ladderlike phylogeny of influenza's hemagglutinin protein. I then use viral sequence data and metadata to determine whether older aged individuals (with a higher number of previous infections) harbor viruses with higher binding avidity than younger aged individuals (with a lower number of previous infections), a prediction made by the binding avidity hypothesis. Finally, I perform a phylogenetic analysis to determine how rapidly binding avidity changes occur. From these analyses, I conclude that the binding avidity hypothesis is not well supported by empirical data.</p><p>In the third chapter, I develop an integrated viral life cycle model, in which viral replication depends on three viral phenotypes: receptor binding avidity, neuraminidase activity, and antigenicity. This integrated model recognizes that receptor binding avidity changes will influence viral replication, but also allows for antigenic evolution to be brought about directly by epitope changes. I first use this model to show how the evolutionary dynamics of these phenotypes are dependent on one another and how antigenic drift can be interpreted within this framework. I then return to some of the questions addressed in the first chapter to ask how different epidemiological factors impact influenza's rate of antigenic drift.</p><p>Together, these three chapters highlight the importance of viral phenotypes other than antigenicity in contributing to influenza's antigenic evolution, and, more generally, the importance of computational and mathematical research in understanding constraints on viral adaptation.</p> / Dissertation

An important characteristic of influenza A is its ability to escape host immunity through antigenic drift. A novel influenza A strain that causes a pandemic confers full immunity to infected individuals, yet because of antigenic drift, these individuals have decreased immunity to drifted strains. We compute the required decrease in immunity so that a recurrence is possible. Models for influenza A must make assumptions on the host contact structure on which the disease spreads. By computing the reproduction number, we show that the classical random mixing assumption predicts an unrealistically large decrease of immunity before a recurrence is possible. We improve over the classical random mixing assumption by incorporating a contact network structure. A complication of contact networks is correlations induced by the initial pandemic. Thus, we provide a novel analytic derivation of such correlations and show that contact networks may require a dramatically smaller drop in immunity before recurrence. Hence, the key new insight is that on contact networks the establishment of a new strain is possible for much higher immunity levels of previously infected individuals than predicted by the commonly used random mixing assumption. This suggests that stable contacts like classmates, coworkers and family members are a crucial path for the spread of influenza in human population. / Graduate

La influenza es una enfermedad altamente infectocontagiosa de la cual se tienen registros históricos descriptivos desde la época griega y de certeza etiológica tan solo hace casi ocho décadas atras. Su agente causal es el virus del influenza de los que se conoce exiten tres grandes tipos: A B y C. El tipo A tiene la propiedad de circular por diversos reservorios biológicos, tales como el hombre, los cerdos y las aves, entre otros. Representa además una elevada variabilidad genética lo que le permite continuos cambios o derivas antigénicas menores responsables de la influenza humanas epidémicas y a veces reordenamientos amplios con cambios antigénicos mayores los que originan la temida influenza pandémica. En un mundo cada vez mas globalizado, con una población superior a los seis mil millones de personas, marcado por grandes inequidades sociales y con cambios climáticos evidentes, los virus de la influenza serán un riesgo permanente para la seguridad de la humanidad. La clínica de los diversos subtipos virales pueden balancearce desde las formas inaparentes hasta las formas graves de gripe o influenza, dependiendo de la virulencia del subtipo viral infectante y del huesped. Aunque nuestra tecnología diagnóstica y de inmunización ha avanzado sorprendentemente, la preparación y disposición de los nuevos kits diagnósticos suelen tardar al principio y en el caso de las vacunas estas no están disponibles para el un nuevo subtipo viral pandémico en el momento que se las necesita. El desarrollo de antivirales contra la gripe no es notorio, contándose aprobados para uso humano los amadantanes como la amantadina y la rimantadina y los inhibidores de la neuraminidasa como oseltamivir y sanamivir principalmente. Claramente los más vulnerables en este contexto son los países en vías de desarrollo y en especial aquellos mas pobres, hecho que nos debería llamar a una profunda reflexión. / Influenza is a highly contagious disease. There are some historical descriptions of this condition by ancient Greek physicians, and the etiological agents have been known only for the last eight decades. The causative agent is the influenza virus, which has three main types: A, B, and C. Type A is capable of circulating within many different biological reservoirs, including humans, swine, and birds. It also has high genetic variability, which allows it to have minor antigenic drifts or mutations which are responsible of epidemics in humans. Sometimes changes are quite marked, leading to pandemics. In a globalized world, with more than 6 billion inhabitants, with many social inequities and evident climate changes, influenza viruses are a permanent risk for mankind. Clinical features for the different viral subtypes may vary from subtle infections to full blown and severe, life-threatening forms. Event with the great advances in diagnostics and immunization, the manufacture and distribution of new diagnostic kits may take some time, and new vaccines are not always readily available. Specific therapies against influenza are not well developed. There are two groups of drugs, the so called adamantane derivatives, such as amantadine and rimantadine, and the neuraminidase inhibitors, such as oseltamivir and zanamivir. Most vulnerable areas for the new flu pandemics include developing countries, particularly the poorest ones, so that the greatest effort must be made for helping these areas.

Emerging influenza viruses continue to challenge public health. The problem is public health science professionals have been battling emerging human influenza diseases with tactile and reactionary methods because there is a lack of knowledge and data at the human-animal interface. This research was a baseline study of the proportion of influenza A virus (IAV) in urban and rural communities in California. The population was artificial recirculating water ponds in the geographic locations of rural and urban Californian communities. Surface water samples [N = 182] were collected from artificial recirculating ponds in California. Positivity for IAV was verified by real time RT-PCR, MDCK cells for virus infectivity, nucleotide sequencing of the RNA genome, and phylogenic analysis of IAV H5N1 strains. The proportion of IAV in rural and urban ponds favored the greater burden of IAV in urban ponds over rural ponds. The presence of waterfowl and IAV M gene sequence positivity were found not to be significantly related. The geochemical properties--pH, salinity, and water temperature at time of collection--were not predictors of IAV infectivity. This baseline research study validated these water ponds as resource sites for IAV surveillance and monitoring. The social change implications of this study can be recognized at the national and international levels, to the population level, and to the individual level by providing geospatial analysis and spatial-temporal data for IAV surveillance, initiating biosecurity measures to protect poultry industries in the United States and Brazil, and contributing to the current IAV strain library. Contributions to the IAV strain library may be used to develop vaccines against human pandemics.

Das murine Norovirus ist ein neu entdecktes Mitglied der Familie Caliciviridae. Bislang wurden vier Virusstämme beschrieben und charakterisiert (MNV1-4). In dieser Arbeit wurde erstmals die Prävalenz von MNV bei Labormäusen in Deutschland untersucht. Daraufhin wurden die neu detektierten Virusstämme anhand ihrer morphologischen, phylogenetischen und pathogenen Eigenschaften charakterisiert. In 55% der untersuchten 82 Kotproben wurde mittels real-time PCR die Ausscheidung von MNV nachgewiesen. Morphologische Untersuchungen bestätigten das Vorhandensein intakter Viruspartikel in den Proben, die auch genetisch als MNVs charakterisiert wurden. Phylogenetisch wurden die Viren in vier genetische Cluster eingruppiert, die sich sowohl untereinander als auch von den Stämmen MNV1-4 deutlich unterscheiden. Die Relevanz der Subklassifizierung von MNV wurde durch unterschiedliche Wachstumskinetiken und IFN-beta-Sensitivitäten divergenter Stämme funktional bekräftigt. Zudem konnten, basierend auf Sequenzdaten aus zwei subgenomischen Bereichen, rekombinante Virusstämme identifiziert werden. Durch Kokultivierung von MNV-Isolaten wurde homologe Rekombination von Noroviren erstmals in vitro simuliert. Beobachtungen von natürlich und experimentell infizierten Mäusen zeigten, dass der Stamm MNV-M21 in den Tieren eine persistierende Infektion induziert. Serologische Untersuchungen verdeutlichten, dass die Persistenz unabhängig von einer intakten und protektiven Immunantwort stattfand. Bestimmungen der ORF2-Sequenzen zu unterschiedlichen Zeitpunkten der Infektion gaben Hinweise auf Antigendrift der hypervariablen P2-Domäne. Innerhalb dieser Domäne ist eine zwischen murinen und humanen Noroviren konservierte Proteinsequenz lokalisiert. Die antigenen Eigenschaften dieses Peptids wurden genauer untersucht. Generierte Antiseren zeigten Kreuzreaktivitäten gegenüber verschiedenen Norovirus-Kapsidproteinen. Zudem waren Peptidantikörper in der Lage eine MNV-Infektion in vitro zu neutralisieren. / The murine norovirus is a newly discovered member of the familiy Caliciviridae. So far, four strains have been described and characterised (MNV1-4). This is the first study on the prevalence of MNV among laboratory mice in Germany. Thereupon the detected new strains have been characterised considering morphologic, phylogenetic and pathogenic properties. Using real-time PCR, shedding of MNV has been found in 55% of 82 investigated faeces samples. Morphologic investigations confirmed the presence of intact virus particles within the samples, which genetically also have been characterised as MNVs. Phylogenetically these viruses have been grouped into four genetic clusters, which could be distinguished from each other and from strains MNV1-4. Relevance of MNV subtyping has been functionally corroborated through different growth kinetics and Interferon-beta sensitivities of divergent strains. Based on subtyping in two different subgenomic regions, recombinant strains have been identified. By cocultivation of MNV isolates, homologous recombination of noroviruses in vitro has been simulated for the first time. Studies of naturally and experimentally infected mice showed that strain MNV-M21 induce a persistent infection. Serological testings confirmed that the persistence occured independently of an intact and protective immune response. Determination of ORF2 sequences at different time points of infection indicated antigenic drift of the hypervariable P2 domain. A protein sequence stretch, which is conserved between murine and human noroviruses, is located within this domain. The antigenic features of this stretch have been investigated. Generated antisera against this peptide were crossreactive with different norovirus capsid proteins and were able to neutralize MNV infection in vitro.

No description available.