Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Figure 1. Maximum likelihood phylogenetic tree based on the full-length nucleotide sequences of genome segment 9 encoding the VP7 protein. The T92 + G evolutionary model was used for phylogenetic inference. South African pre-vaccine G1 strains are highlighted in bold-face while post-vaccine strains are highlighted in bold-red. Adjacent to some sequences is indicated a plus (+) sign followed by the number of identical sequences (S3). The number in brackets denotes the number of compressed strains. Lineages are indicated in roman numerals. Only bootstrap values ≥70% are shown adjacent to each branch node. Scale bar indicates the number of nucleotide substitutions per site.

Figure 2. Maximum likelihood phylogenetic tree based on the full-length nucleotide sequences of genome segment 4 encoding VP4 protein. The GTR+G+I evolutionary model was used for phylogenetic inference. African pre-vaccine P[8] strains are highlighted in bold-face while post-vaccine strains are highlighted in bold-red. Adjacent to some sequences is indicated a plus (+) sign followed by the number of identical sequences (S3). The number in brackets denotes the number of compressed strains. Lineages are indicated in roman numerals. Only bootstrap values ≥ 70% are shown adjacent to each branch node. Scale bar indicates the number of nucleotide substitutions per site.

Figure 3. Structure models showing the mutation sites N147D (A) and T242A (B), respectively, that were only present in post-vaccine G1P[8] strains when superposed with VP7 of Rotarix®. The structure of the study strain is in green, while the Rotarix® structure is in deep-teal. The amino acid residues are represented in dark gray and red to examine whether the replacing amino acid alters the conformation of the protein structure. The amino acid residue highlighted in dark gray represents the study strain while that in firebrick red represents the Rotarix® strain. RMSD is the superposition value where the value of zero indicates absolute similarity. The stability of the protein after mutation was measured in kcal/mol, whereby free energy change of ±0.5 kcal/moL was regarded as significant for the stabilizing/destabilizing effect.

Figure 4. VP4 structure models showing mutations at sites T88I (A) and N89S (B), respectively, that were only seen in some post-vaccine strains when superposed with VP4 of Rotarix®. The structure of the study strain is in green while the Rotarix® structure is in deep-teal. The amino acid residues are represented in dark gray and red to examine whether the replacing amino acid alters the conformation of the protein structure. The amino acid residue highlighted in dark gray represents the study strain while the firebrick red represents the Rotarix® strain. The stability of the protein after mutation was measured in kcal/mol, whereby the folding energy change of ±0.5 kcal/mol is regarded as statistically significant for either stabilizing (−)/destabilizing (+) effect.