Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005-2010: Potential for Molecular Surveillance of New Outbreaks.

Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005-2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs

Sexual reproduction in Phytophthora infestans

Potato late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating plant diseases worldwide. It is becoming increasingly difficult to control the disease in Sweden, leading to an ever more intensified use of fungicides in the potato production. This unsustainable development could be caused by changes in the pathogen due to the introduction of sexual reproduction. These changes could result in an enhanced capability of the pathogen to adapt to different factors, e. g. weather, cultivar resistance, chemical control or other cultivation measures. This might manifest itself in earlier infections and a late blight that spreads faster in the potato fields requiring increasing efforts to control. Different approaches were taken to clarify the role of sexual reproduction in P. infestans in the epidemiology of potato late blight. The formation of sexually formed oospores and their ability to serve as primary inoculum was studied, both as field observations and by determining within-field genotypic diversity. To further estimate the importance of reproduction on a large spatial scale a population study based on molecular and phenotypic markers was performed on P. infestans isolates from the whole Nordic region. The variation in the aggressiveness of Nordic populations of P. infestans was studied by determining different components of aggressiveness, e.g. sporulation capacity, lesion growth and infection efficacy. The aggressiveness study was combined with an analysis of the phenotypic structure of the Nordic population of P. infestans. The results clearly indicate that the Swedish populations of P. infestans are influenced by sexual reproduction. The facts that both mating types are found all over the country in near 1:1 proportions and that oospores are commonly formed in field crops and serve as inoculum under field conditions support this. Studies of the genetic diversity also indicate that sexual reproduction has an effect on the population structure of P. infestans in Sweden and the Nordic region as a whole

Networks and the epidemiology of infectious disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape