Figure 5.

Bootstrap phylogenetic tree of spike (S) gene sequences. The evolutionary history was inferred using the Minimum Evolution (ME) method [55]. The optimal tree is shown. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches (values below 60 are not displayed) [56]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Jukes–Cantor method and are in the units of the number of base substitutions per site. The ME tree was searched using the Close Neighbor Interchange (CNI) algorithm [57] at a search level of one. The Neighbor Joining algorithm [58] was used to generate the initial tree. This analysis involved 86 nucleotide sequences. All ambiguous positions were removed for each sequence pair (pairwise deletion option). In total, there were 155 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [53]. Each sequenced FCoV strain is defined by the cat ID (T: treated FIP cat; C: companion cat), the compartment from which it has been isolated (feces, blood, effusion), and day of treatment (D#). Three prototype FCoV sequences from Genbank have been used in the tree: an enteric FCoV pathotype (FECV420, Accession no.: JQ304373) and an FIP virus pathotype (FIPV907, Accession no.: JQ304512) from the study [46], and an FIP virus pathotype isolated from the jejunum of an FIP cat (FCoV C1Je, Accession no.: DQ848678).