Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda

Figures

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  Figure 1. Maximum likelihood phylogram revealing the genetic relatedness of the concatenated, whole-gene ORF sequences (17,492 base pairs) for the 25 post-vaccine G1P[8] and 10 pre-vaccine G1P[8] RVA study strains characterized by whole-gene analysis. The strain-specific genotype constellations are included to the right of each strain and were identified using the assembled ORF sequences. Black circle denotes post-vaccine strains, while red squares denotes pre-vaccine strains. Bootstrap values ≥ 70% are indicated at branch nodes where applicable and the scale bar indicates the number of nucleotide substitutions per site. On the table, colored in yellow and sky blue are lineage 2 pre- and post-vaccine strains belonging in sub-lineage 2a and sub-lineage 2b, respectively. Colored in green and brown are lineage 1 pre- and post-vaccine strains belonging in sub-lineage 1a and sub-lineage 1b, respectively.

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  Figure 2. (A)–(K) Phylogenetic relatedness of rotavirus group A species base on (A) VP7, (B) VP4, (C) VP6, (D) VP1, (E) VP2, (F) VP3, (G) NSP1, (H) NSP2, (I) NSP3, (J) NSP4 and (K) NSP5 of the study strains from Rwanda with representatives of known human and animal rotavirus genotypes. Pre- and post-vaccine strains are indicated with a red squares and black circles, respectively. Bootstrap values ≥ 70% are indicated at each branch node. Scale bars represents substitutions per nucleotide site.

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  Figure 3. (A) The alignment of the G1 component of Rotarix and RotaTeq vaccines and Rwandan wildtypes circulating from 2011- 2016 RVA seasons, based on the three VP7 antigenic residues (7-1a, 7-1b, and 7-2). Amino acids residues at positions 97 and 147 differ between Rotarix and RotaTeq and are indicated in boldface. Study strains amino acid residues highlighted in sky blue differs from both Rotarix and RotaTeq, while the green and brown colored residues are different from Rotarix and RotaTeq, respectively. The black dot indicates changes in the residues associated with escape neutralization with monoclonal antibodies. Post-vaccine and pre-vaccine G1P[8] study strains are bolded in black and red, respectively. (B) Location of surface-exposed amino acids differences between VP7 protein of RotaTeq G1 vaccine component versus a G1 wild-type strain from Rwanda (indicated in red). Antigenic epitopes in 3B are colored in yellow (7-1a), green (7-1b), and blue (7-2).

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  Figure 4. Alignment of antigenic residues in T-cell antigen epitopes of the G1 vaccine component contained in Rotarix and RotaTeq compared to Rwanda G1 wild type strains circulating from 2011–2016 RVA seasons. Amino acid changes are highlighted in sky blue.

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  Figure 5. (A) The alignment of the P[8] component of Rotarix and RotaTeq vaccines and wild type P[8] strains circulating in Rwanda from 2011–2016 RVA seasons, based on the antigenic residues in VP4. VP4 is divided into two regions VP8* (antigenic epitope 8-1, 8-2, 8-3, and 8-4) and VP5* (antigenic epitope 5-1, 5-2, 5-3, 5-4, and 5-5). The black dot indicates changes in the residues associated with escape neutralization with monoclonal antibodies. Amino acids differences between Rotarix and RotaTeq are shown at positions 195 (antigenic epitope 8-1), 125, 131 and 135 (antigenic epitope 8-3) and are indicated in boldface. Study strains amino acid residues highlighted in green and brown are residues that are different from Rotarix and RotaTeq, respectively. Also, amino acids differences between study strains and Rotarix and RotaTeq are highlighted in sky blue. Post-vaccine and pre-vaccine G1P[8] study strains are bolded in black and red, respectively. (B) Location of surface-exposed amino acids differences between VP8* protein of RotaTeq P[8] vaccine component versus a wild-type P[8] strain from Rwanda (indicated in red). Antigenic epitopes in (B) are colored in yellow (8-1), green (8-2), blue…