Dengue virus genetic diversity in unvaccinated and vaccinated dengue-infected individuals: an observational analysis of the Butantan-DV phase 3 trial in Brazil.

Background: Dengue has emerged as a public health challenge in Brazil since the early 1980s, and it is currently one of the most affected regions and an epicenter of the disease. The country faced its worst dengue epidemic on record, with the co-circulation of different dengue virus (DENV) serotypes alongside genotypes and lineages. This scenario stresses the urgent need for a vaccination strategy that addresses the current burden by protecting against all four DENV serotypes and ensuring safety despite a history of dengue exposure, given the high seroprevalence of dengue in Brazil. Methods: In this study, we analyzed 365 DENV-1 and DENV-2 wild-type positive samples from unvaccinated and vaccinated (28 days post-vaccination) dengue-infected participants enrolled in the Butantan-dengue vaccine (Butantan-DV) phase 3 trial conducted in Brazil from 2016 to 2021. Genome sequences were obtained from 160 samples in order to analyze the genetic diversity of these strains through phylogenetic and genomic studies. Findings: The 365 participants (mean age: 16.6, range: 2-59; male: 52.3%, female: 47.7%) enrolled and tested positive for DENV-1 and DENV-2 from both groups (vaccinated and placebo) reflected the spatial and epidemic patterns recorded in the country during the study period. Despite the limited statistical power due to the low number of samples, we observed significantly lower RT-qPCR Ct values in the vaccinated group, particularly for the DENV-1 cases, suggesting that the vaccine could be reducing viral replication. Additionally, vaccine breakthrough infections were not linked with any specific DENV-1 or DENV-2 lineage. Genetic diversity analysis showed no differences in intra-host synonymous or non-synonymous mutation rates between the groups, combined with the absence of positive selection sites in the DENV-1 and DENV-2 coding regions. Interpretation: Our phylogenetic data demonstrate that Butantan-DV breakthrough infections is not linked to any unique DENV-1 or DENV-2 lineages. The circulating strains in both groups reflect typical transmission patterns of both viruses, highlighting instances of co-circulation and lineage replacement. Notably, the absence of positive selection sites and stable synonymous/non-synonymous mutation rates provides suggestive evidence that the vaccine does not promote vaccine-driven adaptive evolution. Funding: Instituto Butantan, National Institutes of Health, National Council for Science and Technology and Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Instituto Nacional de Ciência e Tecnologia em Dengue (INCT), INCT Viral Genomic Surveillance and One Health, São Paulo Research Foundation.