Reassessing the dengue virus type 4 in Brazil: Genomic sequencing and dispersion dynamics, 2011–2017

Orthoflavivirus denguei (Dengue virus) type 4; (DENV-4) has emerged as a significant public health concern in Brazil, particularly following its reintroduction in the early 21st century. This study provides a comprehensive analysis of DENV-4's genetic characterization and its spatiotemporal dynamics reassessment within Brazil, with a focus on the period between 2010 and 2017. We performed direct genomic sequencing on 24 human samples obtained from various Brazilian states using a multiplex sequencing approach on the Ion Torrent platform. Phylogenetic analysis revealed that the new isolates belong exclusively to the genotype 4II, lineage 4II_B.1.1, with no detection of genotype 4I, which was previously identified in Brazil. This absence of genotype 4I in our findings suggests a potential decline, not adaptation to mosquito host, sub endemic circulation or displacement of this genotype in the country. The phylogeographic analysis indicates multiple introduction events of genotype 4II into Brazil, with significant dispersion across different regions, including the North, Northeast, Midwest, and Southeast. The temporal analysis confirmed a robust evolutionary signal, supporting the observed phylogenetic clustering. Eighteen of the 24 genomes in this study had unique nonsynonymous mutations across the entire coding sequences and seven genomes showed mutations that altered the biochemical property of the amino acids at E, NS1, NS2B, NS3,and NS5 genes compared with genotype 4I. Our findings underscore the ongoing spread of DENV-4 within Brazil, and in the Americas driven by complex networks of viral dispersion, and highlight the dynamic nature of DENV-4 genotype distribution. This study emphasizes the importance of advanced direct genomic sequencing tools in understanding the DENV-4 dynamics and spreading, providing critical insights for public health strategies on genomic surveillance to control further dengue outbreaks.