Figure 2

Lateral (A) and upper (B) view of the quaternary structure of the IBV spike protein. The full spike protein is reported for one monomer only (dark gray). The S1 region is shown for the two remaining monomers, which have been edited to highlight different selective pressure features. In the color-coded monomer, the scaled dN-dS difference between pre- and post-vaccination, calculated using FUBAR, is reported on the protein surface ranging from purple (higher pressure in the post-vaccination period) to light blue (higher pressure in the pre-vaccination period). In the white-colored monomer, sites under episodic diversifying or directional selection in the post-vaccination period are reported in red and green, respectively. The region demonstrating the higher cumulative dN-dS score (AA 300–400) is highlighted in yellow. The ribbon visualization of relevant protein domains is reported as inserts. Lower insert reports S1 NTD RBM and the partial ceiling over it (coded in light blue). Sites of the nearby monomer under episodic diversifying and directional selection in the post-vaccination period are reported in red and green, respectively. Right insert displays the S1 C-terminal domain (CTD) region. Two monomers are represented: one depicting the region with the highest cumulative score in dN-dS difference between vaccination periods (in yellow) and the other highlighting the corresponding extended putative RBM loops (in green). A more detailed representation of the overall protein structure is reported as Additional file 4.