Thailand was a hyper-endemic country for dengue with co-circulation of four serotypes and tens of thousands of infected cases annually. Taking into consideration the large number of local dengue virus (DENV) sequences available in GenBank, Thailand was the most ideal locality to study co-evolution of DENV. Therefore, we undertook a large-scale molecular epidemiological analysis of all DENV strains isolated in Thailand. In this study, we demonstrated that DENV strains of four serotypes post-1990 grouped into distinct clades, and that specific mutations in the envelope protein were first confirmed in these clades. Compared to the DENV1, DENV2 and DENV3 clades, the DENV4 clade evolved markedly more slowly (6·4 × 10−5 substitutions/site per year). Our results also showed that the genetic diversity of the predominant genotype of each serotype tended to slightly increase over time with fluctuating changes, followed by a stationary phase after 2000. This suggests that the four DENV clades became the predominant strains due to DENV possessing improved fitness after long-term selection.
