Amino acid changes observed within and between influenza B virus lineages (A). Arrow colours in (A) correspond to inter- (B) or intra- (C) lineage amino acid changes, based on previously resolved crystal structure (PDB:4FQM). Amino acids in red represent differences between the two lineages that were retained over all sampling years; yellow represents differences that are newly observed in 2012 compared to 2002; and magenta represents changes lost in 2012 compared to 2002. Amino acids in blue and green represent changes that occurred in Victoria and Yamagata viruses between 2002 and 2012, respectively; whereas cyan represents difference between 2002 and 2012 shared between both lineages. These amino acid changes occur in regions that cluster around 21, 29, and 37 Å distant from the RBP (C). Structural differences in RBP among recent Victoria (B/Brisbane/60/2008) and Yamagata (B/Florida/4/2006) strains with a human-like α-2,6 host receptor analogue (magenta) modeled within the viral RBP (D). D was based on crystal structures PDB:4FQM and PDB:4FQJ with side-chains minimized after addition of ligand from PDB:2RFU through superposition. Regions differing in backbone conformation are shown in orange for Victoria and cyan for Yamagata, while conserved regions are shown in gray. Residues with conserved backbone structure but different amino acid side-chains are shown in red for Victoria and blue for Yamagata. Side-chains are shown only for residues within 5 Å of the receptor ligand and differing between the lineages. Structural view of receptor binding pocket with α-2,6- (green) and α-2,3-linked (red) host receptor and glycans (blue) (E). E was based on crystal structure PDB:4FQM, with the addition of ligands from PDB:2RFU and PDB:2RFT through superposition and no minimization. The presence of a glycan on site 212 allows binding only to 2,6-linked receptors, while loss of the glycan allows binding to both α-2,3- and α-2,6-linked receptors. Brown arrows (B and C) indicate relative position of receptor binding pocket (RBP), whereas black arrow heads (C and D) point to site of known antigenic cluster transition (Koel et al., 2013).