Genomic mosaicism in two strains of dengue virus type 3

•We documented the first evidence of recombination between DENV-3 viruses.•Two viruses represent recombination between viruses from different genotypes.•We identified multiple breakpoints sites in the recombinant viruses.•Multiple strand switching may be linked with the genomic mosaicism.

Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.