Molecular typing based on full-length VP1 sequences.

<p>Molecular typing based on full-length VP1 sequences.</p

Phylograms depicting the relationships between the studied HEV-C in different genomic regions.

<p>The percentage of bootstrap replicates is indicated at nodes if higher than 70%. The length of branches is proportional to the number of nucleotide changes (percent divergence). The sequences of CV-A10 and EV-19 (members of HEV species A and B, respectively) were introduced for correct rooting of the tree. Triangles indicate the prototype strains, circles the field strains; the VDPV strain MAD004 is labelled with open circles. Each color corresponds to a given HEV-C serotype. Below each tree, the region taken in consideration for alignment is highlighted in red in the schematic diagram of the genome.</p

Phylogenetic relationships between Madagascan HEV-C field isolates collected in 2002 and other isolates for which sequences are available in GenBank, based on full-length VP1 sequences.

<p>The length of the branches is proportional to the number of nucleotide changes (percent divergence). The percentage of bootstrap replicates is indicated for the main nodes. Each area of grey shading corresponds to a serotype. The field strains isolated in Madagascar in 2002 are indicated by circles; the isolates whose full-length genome was subsequently sequenced are indicated in bold. For the other isolates, the location and year of isolation are indicated in the tree. Triangles indicate the prototype strains.</p

Phylogenetic relationships between Madagascan CV-A13 field strains and other CV-A13 isolates for which sequences are available in GenBank, based on 3′ one-third of the VP1 region (∼300 nt).

<p>The length of the branches is proportional to the number of nucleotide changes (percent divergence). The percentage of bootstrap replicates is indicated if higher than 70%. The field strains isolated in Madagascar are indicated by full circles if isolated in 2002, by open circles if isolated in other years. For the other isolates, the location and year of isolation are indicated in the tree. Triangles indicate the prototype strains. The CV-A11 G9 sequence was introduced for correct rooting of the tree.</p

Additional file 2 of Enterovirus detection in different regions of Madagascar reveals a higher abundance of enteroviruses of species C in areas where several outbreaks of vaccine-derived polioviruses occurred

Additional file 2: Figure S1. Detection of NPEVs on RD and HEp-2c cells

Additional file 3 of Enterovirus detection in different regions of Madagascar reveals a higher abundance of enteroviruses of species C in areas where several outbreaks of vaccine-derived polioviruses occurred

Additional file 3: Figure S2. Phylogenetic trees of Madagascan EV-Cs based on the 5′UTR, the VP1- and the 3D-encoding sequences. The isolates are colour-coded according to their respective type; triangles indicate isolates from this study, circles isolates from previous works

Additional file 1 of Enterovirus detection in different regions of Madagascar reveals a higher abundance of enteroviruses of species C in areas where several outbreaks of vaccine-derived polioviruses occurred

Additional file 1: Table S1. Accession numbers of the sequences used to draw the tree displayed in Fig. 7

Phylogenetic relationships between EV-A71 full-length VP1 sequences inferred using the Neighbor-Joining method.

<p>The evolutionary distances were computed using the Kimura 2-parameter method. The length of the branches is proportional to the number of nt divergence. The percent of bootstrap replicates is indicated for the main nodes.</p

Similarity within the EV-A71 genogroups through comparison of the full-length VP1 gene sequences.

<p>Similarity within the EV-A71 genogroups through comparison of the full-length VP1 gene sequences.</p

Molecular differentiation of the EV-A71 genogroups.

<p>The percentages of nucleotide and amino acid divergences were calculated in pairwise comparisons of 59 sequences selected as representative of the EV-A71 genogroups and subgenogroups. A scatter plot was produced with the divergence values to determine a threshold between intra-and inter-genogroup differences.</p