Retrospective and Contemporary Genomic Surveillance Reveals Genotype-Specific Dengue Lineage Dynamics in Rio de Janeiro

Dengue virus (DENV) transmission in Brazil is characterized by recurrent epidemics involving the introduction, persistence, and replacement of viral lineages. However, temporal gaps in genomic surveillance limit our understanding of how these processes shape successive epidemics in Rio de Janeiro. Here, in a retrospective observational molecular epidemiology study, we combined archived genomic data with publicly available sequences and epidemiological surveillance data to investigate the temporal dynamics of DENV serotypes and lineages in Rio de Janeiro. Archived DENV-positive samples were curated and subjected to whole-genome amplicon sequencing, and the resulting consensus sequences were analyzed together with publicly available sequences using time-scaled phylogenetic reconstruction and epidemiological data. We recovered 35 DENV genomes from samples collected in 2013, 2018, 2020, and 2021, including DENV-1 genotype V, DENV-2 genotypes II and III, and DENV-4 genotype II. Analysis of the combined datasets identified multiple Rio de Janeiro-associated clades with distinct temporal patterns. Publicly available sequences supported the broader clade structure and long-term temporal patterns independently of most genomes generated here. The newly generated genomes made genotype-specific contributions: the five DENV-1 genotype V genomes placed archived 2020–2021 samples within previously represented Rio de Janeiro-associated groups, while the single DENV-2 genotype II genome provided phylogenetic placement of a travel-associated 2018 case. In contrast, the 20 DENV-2 genotype III genomes identified a Rio de Janeiro-associated cluster not represented among the public sequences, and the nine DENV-4 genotype II genomes increased representation of the 2013 epidemic. Thus, the principal contribution of retrospective sequencing was to fill specific temporal and geographic gaps rather than to redefine the broader historical phylogenetic structure of all genotypes.