Seasonal recurrence of cowpox virus outbreaks in captive cheetahs (Acinonyx jubatus)

Stagegaard, Julia; Kurth, Andreas; Stern, Daniel; Dabrowski, Piotr Wojciech; Pocknell, Ann; Nitsche, Andreas; Schrick, Livia

Viral genome sequencing and phylogenetic analysis. Furthermore, a whole genome sequence was reconstructed from one sample of each cluster (for selection of material see Table 2 , for contig length and accessions see S1 Table) , and phylogenetic analysis was performed. In the resulting tree (see Fig 3) , the five representative outbreak sequences from Ree Park clearly form a distinct clade, with intra-clade distances much lower than the distance of any of the outbreak sequences to any other known CPXV. However, the intra-clade distances are still larger than those observed within clades formed by other CPXV known to come from distinct outbreak events. Maximum likelihood tree based on stripped whole-genome alignment. The representative strains of the CPXV clusters from cheetah are highlighted in red. Groups of CPXV strains belonging to known outbreaks are colored in blue, same superscripts denote the same outbreak. The clustering between the sequences from the known outbreaks (blue) is much tighter than between the sequences from the outbreaks in cheetah (red). All branch supports (aLRT [26] ) are above 0.99.