Figure 3

Lineage-specific conservation in the Dengue virus genome. (a) The phylogeny generated by the regions assigned to the most prevalent cactus was found to closely resemble previous findings [17]. Sequence from Dengue virus serotype 1 was used to root the tree. (b) In contrast, the phylogeny based on the most discordant cactus (cactus 5), groups the sequences of all viruses together with the exception of those representing the Thai Dengue virus strains. (c) Sequence conservation across the viral genome is plotted for all strains (grey) and after excluding strains from Thailand (black). While the highest level of conservation among all strains is located close to the 3’ end of the virus, the highest conservation peak after excluding the Thai strains coincides with the longest region assigned to cactus 5, indicating high levels of lineage-specific sequence conservation. Shown at the bottom are also all regions modelled by cactus 5 (dark pink).