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Nevertheless, the flow of viruses from domestic to wild species was not negligible and should be considered as a threat to biodiversity. A dominant flux of viral strains was observed from wild to domestic populations, highlighting the directionality of viral transmission and the risk associated with the capturing and trade of wild birds. A good correlation was found between viral migration rate and the intensity of animal trade between regions over time. The results allowed us to reconstruct the variation of viral population size and demonstrated the effect of enforced international bans on these dynamics.
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With this in mind, a phylodynamic and phylogeographic analysis has been performed on a database of more than 400 replication‐associated protein (Rep) gene (ORF1) sequences downloaded from Genbank including some recently generated sequences from fifteen samples collected in Namibia. Understanding the epidemiology, dynamics, viral migration rate, interaction between wild and domestic animals and the effect of implemented control strategies, is fundamental in controlling the spread of the disease. In addition to having an impact on the health and welfare of domesticated birds, BFDV represents a significant threat to wild endangered species. bovis in the badger population in the South-West of France.īeak and feather disease virus (BFDV) infects domestic and wild psittacine species and is able to cause progressive beak, claw and feather malformation and necrosis. Thus, while we could not confirm badgers as possible intermediaries in farm-to-farm transmission, badger-to-cattle transition rate was high and we confirmed long-term presence of M. Our model enabled us to infer inter-species transitions but not intra-population transmission as in previous epidemiological studies, where relevant units were farms and badger social groups. In addition, we calculated a median of 64 transition events from badger-to-cattle (IQR: 10–91) and a median of zero transition event from cattle-to-badger (IQR: 0–3). Using the maximum clade credibility tree, we identified that over 75% of the lineages from 1989 to 2000 were present in badgers. We estimated a badger-to-cattle transition rate (median: 2.2 transitions/lineage/year) 52 times superior to the cattle-to-badger rate (median: 0.042 transitions/lineage/year). We selected a HKY model and a strict molecular clock.
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We included 167 SB0821 strains (21 isolated from badgers and 146 from cattle) and identified 171 single nucleotide polymorphisms. In order to account for sampling bias, sub-population structure was inferred using the marginal approximation of the structured coalescent (Mascot) implemented in BEAST2. We used a Bayesian evolutionary model, to infer phylogenetic trees and migration rates between two pathogen populations defined by their host-species.
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Using whole genome sequencing, the aim of our study was to clarify badger contribution to bTB transmission in this area. In two “départements” in the South-West of France, bovine tuberculosis (bTB) outbreaks due to Mycobacterium bovis spoligotype SB0821 have been identified in cattle since 2002 and in wildlife since 2013.