Fig. 3: Recombination analysis.

a, Visualizations of a recombination analysis carried out on the assembled FCoV-23 genome 2-C11 Re 10276 (PQ133182) and representative genomes of FCoV-1 (blue), FCoV-2 (black) and pCCoV (yellow). The section highlighted in yellow shows the likely recombination break region, with a red vertical line showing the likely breakpoint. The first panel shows the results of the bootscan analysis; the second panel shows the sequence distance; and the third panel shows the RDP pairwise identity analysis. All three panels show good support for the recombination between FCoV-1 and pCCoV. These results are further supported by a high statistical likelihood of recombination shown in Supplementary Table 21. Recombination analysis of a representative ΔD0 FCoV-23 is shown in Extended Data Figs. 3 and 4. b, Schematic of the major recombinations observed in FCoV and CCoV. A common-ancestral-origin virus is thought to have given rise to the original FCoV-1 and CCoV-1 types with further evolution in CCoVs yielding CCoV-2 and CCoV-1/2 serotypes. FCoVs are thought to have recombined with CCoV-2 to form FCoV-2. FCoV-2 and CCoV-2 recombinations have been shown to have different recombination points as highlighted by the different colorations (reviewed previously²³). The Cypriot FCoV strain, termed FCoV-23, is a recombinant between an FCoV-1 strain and a S recombination with a pantropic CCoV-2, pCCoV. Furthermore, deletion variants are observed in the majority of sequenced cases (white box; Fig. 4). The diagram in b was created using BioRender.