Comparative analysis of pentavalent rotavirus vaccine strains and G8 rotaviruses identified during vaccine trial in Africa

Abstract

RotaTeqTM is a pentavalent rotavirus vaccine based on a bovine rotavirus genetic backbone in vitro reassorted with human outer capsid genes. During clinical trials of RotaTeqTM in Sub-Saharan Africa, the vaccine efficacy over a 2-year follow-up was lower against the genotypes contained in the vaccine than against the heterotypic G8P[6] and G8P[1] rotavirus strains of which the former is highly prevalent in Africa. Complete genome analyses of 43 complete rotavirus genomes collected during phase III clinical trials of RotaTeqTM in Sub-Saharan Africa, were conducted to gain insight into the high level of cross-protection afforded by RotaTeqTM against these G8 strains. Phylogenetic analysis revealed the presence of a high number of bovine rotavirus gene segments in these human G8 strains. In addition, we performed an in depth analysis on the individual amino acid level which showed that G8 rotaviruses were more similar to the RotaTeqTM vaccine than non-G8 strains. Because RotaTeqTM possesses a bovine genetic backbone, the high vaccine efficacy against G8 strains might be partially explained by the fact that all these strains contain a complete or partial bovine-like backbone. Altogether, this study supports the hypothesis that gene segments other than VP7 and VP4 play a role in vaccine-induced immunity.

Figure 1. Genomic constellations of the reassortant RVA strains of RV5 and the G8 RVA strains analysed in this study.

Gene segments of typical human DS-1-like RVA origin are coloured red, the human P[6] VP4 genotype is coloured yellow, and different shades of blue are used to indicate gene segments of distinct animal (most likely bovine or similar) origin.

Figure 2. Phylogenetic dendrograms based on the nucleotide sequences of the outer capsid proteins VP4 and VP7.

Bootstrap values (500 replicates) above 70 are shown. G8 RVA strains analysed in this study are indicated with a triangle (colour code according to Fig. 1), selected non-G8 strains were indicated with a black triangle, viruses present in RV5 are indicated with a diamond.

Figure 3. Phylogenetic dendrograms based on the nucleotide sequences of VP6, VP1, VP3 and NSP2.

Bootstrap values (500 replicates) above 70 are shown. G8 RVA strains analysed in this study are indicated with a triangle (colour code according to Fig. 1), selected non-G8 strains were indicated with a black triangle, viruses present in RV5 are indicated with a diamond.

Figure 4. Phylogenetic dendrograms based on the nucleotide sequences of NSP1 and NSP3.

Bootstrap values (500 replicates) above 70 are shown. G8 RVA strains analysed in this study are indicated with a triangle (colour code according to Fig. 1), selected non-G8 strains were indicated with a black triangle, viruses present in RV5 are indicated with a diamond.

Figure 5. Phylogenetic dendrograms based on the nucleotide sequences of VP2, NSP4 and NSP5.

Bootstrap values (500 replicates) above 70 are shown. G8 RVA strains analysed in this study are indicated with a triangle (colour code according to Fig. 1), selected non-G8 strains were indicated with a black triangle, viruses present in RV5 are indicated with a diamond.

Figure 6. Linear plot showing the percentage of amino acid differences between gene segments of wild-type RVAs and RV5 vaccine strains.

G8 strains from Ghana, Mali and Kenya are indicated by red dots, squares and triangles respectively. Non-G8 DS-1-like strains are visualized by blue dots (Ghana) or squares (Mali).

Figure 7. Comparison of the similarity of the G8 strains to RV5 and the non-G8 strains to RV5 per amino acid position.

Each amino acid position with a score different from zero was indicated with a dot, color-coded ranging from red (1) to blue (–1). Positive similarity scores represent positions for which G8 strains were more similar to RV5 than non-G8 strains. Negative scores indicate amino acids positions were non-G8 strains are more similar to RV5 strains than G8 strains.