Fig. 4: Protein sequence and structural analysis of FCoV-23 spike.

a, Analysis of the different domains of FCoV-23 S. D0 shows high similarity to CB/05 pCCoV with a prominent, variable deletion between amino acids (AA) 11–265 resembling the deletion previously observed in TGEV and PRCV S. Multisequence alignment mirroring sequences used for computational analysis previously²⁶ is shown. Amino acids with side-chain type changes against FCoV-2s, and changes at position 546, where a leucine is more predominant in the FIPV rather than the FECV sequences, are shown. Colours were assigned according to the RasMol amino acid scheme. Amino acid changes that could potentially be associated with biotype change are highlighted in bold. The schematic of spike was created using BioRender. b, D0 S deletions in 57 cats (8 full length) are shown from the beginning of S to amino acid 267. Sequences are ordered by the shortest N-terminal sequence. Identical deletions are highlighted in shades of green. All deletions are in-frame. c, Structural modelling of the full-length or long S version, represented by sample G8, and the ΔD0 or short version, represented by sample C10. The samples were modelled against CCoV-HuPN-2018, experimentally determined S in the swung-out confirmation 7usa.1.A⁴⁰. The proximal confirmation and comparisons are shown in Extended Data Fig. 8. Colours indicate the confidence, with blue highlighting strong and red highlighting weak confidence. d, Modelling of amino acid changes on a structural prediction of the FCoV-23 RBD against CCoV-HuPN-2018 7u8I.1.B. Side-chain type amino acid changes as identified in a are highlighted; side chains are shown in blue for variations in FCoV-2s that are distant from the RBD, red for variations that are close to the RBD, orange for the variations at amino acid 546, similar to FIPV-2, and olive for variation differing both from FCoV-2 and pCCoV. A comparison showing a confidence model of the FCoV-23 RBD structure prediction paired with the CCoV-HuPN-2018-canine aminopeptidase N (APN) is shown for orientation and binding visualization at the top right.