Al virussen, host evolutie (KB-12-005.01-029)

An important limitation of the genetic dataset obtained during an outbreak is the characterisation of only one virus sequence per farm, whereas each farm (and each individual host within this farm) may contain a wide variety of closely related virus variants. Our genetic data could be considered a reliable tool to elucidate the transmission pathways of the HPAI H7N7 between farms if it can be assumed that the virus genotype obtained for each farm represents the dominant strain in the pooled sample and that this dominant strain is the one most likely to be transmitted to other farms. In influenza research little is known about intra-host genetic diversity and thus it remains for instance unknown whether multiple genetically distinct viruses exist or co-circulate within an individual host (Nelson and Holmes (2007).  Also in poultry there is little or no information on the influenza virus evolution within individual chickens and thus within a flock of chickens. The same is true for other poultry types. The aim of this project is to study the genetic evolution within a host, chicken, duck, and within a flock. The evolution will be studied without or under selective pressures.