Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012–2017)

Figure 1. Phylogenetic trees based on the ORF (open reading frame) nucleotide sequence of the (a) VP7 and (b) VP4 genes of G1P[8] strains circulating in Mozambique and global strains obtained from GenBank. The trees were constructed based on the maximum likelihood method implemented in MEGA X [29], applying the best-fit nucleotide substitution model Tamura-3-parameter (T92+G+I) for VP7 and General Time Reversible (GTR-G) for VP4, determined by JModelTest [30]. Bootstrap values (1000 replicates) ≥70% are shown with DS-1 serving as an out-group (not shown in the final tree). Scale bar indicates genetic distance expressed as the number of nucleotide substitutions per site. Pre-vaccine Mozambican strains are indicated by blue squares, post-vaccine by red circles, the Rotarix® vaccine strain by a green triangle and Mozambican strains from previous studies [14,19] are indicated by black triangles. Lineages are defined from I-VIII for VP7 and I-IV for VP4 [21,22,23,25,26,27,28].

Figure 2. Phylogenetic trees based on the ORF nucleotide sequences of the (a) VP1, (b) VP2, (c) VP3, (d) VP6, (e) NSP1, (f) NSP2, (g) NSP3, (h) NSP4 and (i) NSP5 genes of G1P[8] strains circulating in Mozambique and global strains obtained from GenBank. The trees were constructed based on the maximum likelihood method implemented in MEGA X [29], using the best-fit nucleotide substitution model General Time Reversible (GTR+G+I) for VP3, GTR+G for VP2, NSP2 and NSP3, Hasegawa Kishino Yano (HKY+G+I) for VP6 and NSP1, HKY+G for VP1, NSP4 and NSP5/6, determined by JModelTest [30]. Bootstrap values (1000 replicates) ≥70% are shown with DS-1 serving as an out-group (not shown in the final tree). Scale bar indicates genetic distance expressed as the number of nucleotide substitutions per site. Pre-vaccine Mozambican strains are indicated by blue squares, post-vaccine by red circles, the Rotarix® vaccine strain by a green triangle and Mozambican strains from a previous study [19] are indicated by black triangles.

Figure 3. The alignment of amino acids corresponding to three VP7 antigenic epitopes (7-1a, 7-1b and 7-2). The amino acid sequence of Rotarix® is the reference strain and the conserved residues between the Rotarix® to Mozambican strains are indicated by dots (.) and residues that differ are in bold.

Figure 4. The alignment of the amino acids corresponding to the VP4 antigenic epitopes (8-1, 8-2, 8-3, 8-4 for VP8* and 5-1, 5-2, 5-3, 5-4, 5-5 for VP5). The amino acid sequence of Rotarix® is the reference strain and the conserved residues between the Rotarix® to Mozambican strains are indicated by dots (.) and residues that differ are in bold.