Figure 4. Stabilization of the stem-loop structure in the cleavage site region of H5 HA segments of the A/goose/Guangdong/1/96 (H5N1) lineage of highly pathogenic viruses.

The GGN codon coding for the first Gly residue of the HA2 chain downstream of the cleavage site is shown by an asterisk. The codons inserted in the highly pathogenic H5 HA segments (b,c) are shown in magenta, structure-stabilizing mutations in red. The clades of the gsGD96 lineage are designated according to the accepted classification⁴¹. More detailed analysis of the stabilization of this structure in other clades is given in Fig. 5. Folding free energies ΔG°₃₇ (kcal/mol) are given for both positive sense RNA structures and corresponding negative-sense vRNA conformations. It should be noted that the deletion of one of the four extra codons in some of the gs/GD/96 clades (compare (c) and (b)) stabilizes the structure by only 0.1 kcal/mol. The structure predicted in a low pathogenic H5 HA segment (a) is given for comparison.