Fig. 6

The location of the positive selection amino acid sites in spike protein. (A) The selection sites were showed in the schematic structure of S gene. The spike protein contains S1 subunit and S2 subunit. S1-NTD, N-terminal domain of S1. S1-CTD, C-terminal domain of S1. RBD, receptor binding domain. CH-N and CH-C, central helices N and C. FP, fusion peptide. HR-N and HR-C, heptad repeats N and C. (B) Cartoon representation of the spike homotrimer. The blue spheres indicate the selected amino acid sites and most of them are distributed on the surface. (C) The selected sites (purple spheres) were displayed on the structure of PDCoV S monomer using PyMOL software. The residue sites (62, 123, 136, 137, 149, 169, and 183) are in the S1-NTD. The site 397 is located in the RBD. The residue 630 and 642 are in the CH-N region and the residue 698 is the FP region. The residues 40, 44, and 46 are not resolved in the known crystallographic structure. The raw data of positive selection analysis across the spike gene was provided in supplementary file 3