Fig. 2: Genomic sequence analysis of Cypriot and UK-import FCoV cases.
From: Feline infectious peritonitis epizootic caused by a recombinant coronavirus
Sequences from three different genomic regions (orf1b, S and orf3c/E/M), as indicated by the grey regions marked on the overview of the genome, were obtained through Nanopore sequencing of 45, 63 and 42 Cypriot and UK-import samples, respectively. After initial BLAST analysis, maximum-likelihood trees were generated including other FCoV and CCoV strains to assess the genetic similarity of each region. CCoV-2 genomes are highlighted in blue with pCCoV-2 genomes within this region displayed in a darker blue. FCoV-1 genomes are highlighted in pink and FCoV-2 genomes are shown in purple. Samples from Cyprus (green) and one UK-imported Cypriot cat (dark green) can be seen clustered with FCoV-1 sequences in the orf1b and orf3c/E/M regions. However, the S gene clusters with CCoV-2, most closely with pCCoV-2. Different numbers of sequences are present in each tree due to missing sequence or poor sequence quality and/or alignments in genomes downloaded from NCBI, and due to not all regions being sequenced in all individuals from our samples. Silhouettes representing cats, dogs and foxes were created using BioRender.
