Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of ,10.700 nucleotides with a single open readingframe that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5)proteins. It possesses four antigenically distinct serotypes (DENV 1–4). Many phylogenetic studies address particularities ofthe different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urbansetting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in Sa˜o Jose´ do Rio Preto, Brazil, during2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-NPCRusing primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures andsequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences werealigned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion.The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor(TMRCA) were estimated...