Spatiotemporal dispersion of DENV-1 genotype V in Western Colombia

Abstract

Dengue virus (DENV) is a significant public health concern in Colombia, with increased transmission of DENV type 1 (DENV-1) in the departments of Risaralda and Valle del Cauca in the Central-West region of the country following a large outbreak in 2019. However, little is known about the source, genetic diversity, and evolution of circulating viruses. We obtained serum samples from individuals with acute DENV infection and analysed DENV-1 genetic diversity, phylodynamics, and phylogeography. We found that most viruses belonged to DENV-1 genotype V, and phylogenetic analysis revealed three distinct clades, each of which was most closely related to viruses from neighbouring departments of Colombia sampled over the last 5-10 years. Thus, the 2019 outbreak and subsequent DENV-1 circulation was not due to the introduction of a new lineage to the country but rather reflected local DENV-1 V dispersion and evolution. We identified amino acid positions under positive selection in structural proteins and NS1, which may have a role in immune evasion and pathogenesis. Overall, our analysis of DENV-1 V diversity, evolution, and spread within Colombia highlights the important role of genomic surveillance in understanding virus dynamics during endemic circulation and outbreaks.

Keywords: Colombia; DENV-1V; genetic diversity; phylogenetic analysis; spatiotemporal dispersion.

Figure 1.

ML phylogenetic analyses of 24 newly generated DENV-1V sequences compared to reference sequences. (a) The full-length coding regions for the 24 newly generated sequences in this study were aligned with 79 reference sequences representing each DENV-1 genotype, and underwent ML phylogenetic analysis. Red branches indicate the 24 newly generated sequences in this study. (b) The envelope coding regions for the 24 newly generated sequences in this study were aligned with 276 reference sequences that had been selected by genetic proximity (subsampled dataset 2 in ‘Methods’ section), and underwent ML phylogenetic analysis. Red branches indicate all sequences from Colombia. The 24 newly generated sequences in this study clustered in three distinct clades, Clade A (blue), Clade B (yellow), and Clade C (green). For both trees, black circles indicate nodes with an ultrafast bootstrap value greater than or equal to 95, and the internal tree scale represents the nucleotide substitutions per site.

Figure 2.

Temporal and geographical analysis of 24 newly generated DENV-1V envelope sequences. (a) The envelope coding regions for the 24 newly generated sequences in this study were aligned with 123 reference sequences from the Americas that had been selected by genetic proximity (subsampled dataset 3 in ‘Methods’ section) and underwent Bayesian analysis. On a time-scaled MCC tree, the 24 newly generated sequences in this study clustered in three clades, which are highlighted with red boxes. Black circles indicate nodes with a posterior probability of 90% or greater. Branches are coloured by location or inferred location, and pie charts indicate the posterior LP for each node of interest. Colombian sequences are coloured with department-level resolution; location names are Col_ followed by the department name. (b) Posterior probability of the node position, location, and date, including 95% highest posterior density (HPD), for the labelled nodes. (c) Most probable dispersion routes of clades identified in this study.

Figure 3.

Amino acid changes observed in 24 newly generated DENV-1V sequences, compared to the 2005 ancestral sequence. Upper rows indicate the protein region and specific amino acid position within the DENV polyprotein where each substitution occurred. The substitutions in black font are clade-specific, while those in green font are found in multiple clades. Dots represent conserved positions. The horizontal dashed line at the bottom separates the Risaralda sequence found in 2019 from those found in 2021.