Evolution and molecular epidemiology of Classical swine fever virus during a multi-annual outbreak among European wild boar
Classical swine fever (CSF) is a viral disease of pigs with tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord Mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of CSFV strains over the years, and no impact of vaccination on mutation rates. However, substitution rates varied among protein genes and furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.