P-values < 0.05 were considered statistically significant unless stated otherwise. Results Dengue virus serotypes and genetic diversity The sequence data investigated in this study represent genome-wide coding sequences of DENV (n = 260 isolates) from different countries. While samples of DENV serotype 1, 2 and 3 are derived from both Asian and American countries, the collections of serotype 4 are limited to AZD3965 molecular weight Central and South American countries (Additional file 1). The sequences of serotype 4 available
by the GRID project are only from Americas. Thus, serotype 1, 2 and 3 sequences represented geographically more diverse samples unlike the serotype 4 sequences. Accordingly, the genetic diversity observed within serotype 1, 2 or 3 samples was higher than that of serotype 4 samples. The 4-Hydroxytamoxifen purchase average number of nucleotide differences ranges from 168 to 492 among the samples. The nucleotide diversity (π) is ~ 0.04 among samples
belonging to serotype 1, 2 and 3 and 0.01 for serotype 4. The neighbor-joining phylogenetic tree analyses of the coding sequences also show that samples of serotype 1, 2 and 3 are associated with two groups corresponding to Asian and American DENV isolates whereas those of serotype 4 represent a monophyletic group (Figure 1). However, diversity within serotype 4 is also evident that corresponds to the Central and South American DENV isolates, respectively. More than 80% of the nucleotides in the coding sequences of
the DENV genome remain fixed. Although this suggests that these isolates Selleck GSK2118436 are genetically very similar, about 1500 to 2000 sites (15% – 18% of the total sites) reflect nucleotide substitutions among them across serotypes. Furthermore, the relative rate of transition versus transversion substitutions (Additional file 2) also suggests that the nucleotide substitution patterns are biased towards excess transitions over transversions among the samples in each serotype. Figure 1 Geographical structuring within dengue virus serotypes evident from phylogenetic (neighbor-joining tree) analysis. Asian isolates (red) and American isolates (green) are compared for serotypes 1, 2 and 3. For serotype 4, isolates from Central America (light green) are compared with isolates from South America (dark green). Florfenicol The unit of branch length is shown for each tree. Synonymous and non-synonymous substitutions The counts of synonymous and non-synonymous substitution sites are shown in Table 1, and indicate that nearly 80% of all the substitutions in the DENV genome are synonymous. The number of synonymous and non-synonymous changes at 1st, 2nd and 3rd codon positions of each serotype is also shown in Table 1. It shows that the number of silent changes at the 1st position of codons among the samples of serotypes 1, 2 and 3 are similar to that of serotype 4, in spite of differences in the overall nucleotide diversity among the serotypes.