Origin and evolution of dengue virus type 3 in Brazil

Abstract

The incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 (DENV-3) at the early 2000s. Despite the major public health concerns, there have been very few studies of the molecular epidemiology and time-scale of this DENV lineage in Brazil. In this study, we investigated the origin and dispersion dynamics of DENV-3 genotype III in Brazil by examining a large number (n=107) of E gene sequences sampled between 2001 and 2009 from diverse Brazilian regions. These Brazilian sequences were combined with 457 DENV-3 genotype III E gene sequences from 29 countries around the world. Our phylogenetic analysis reveals that there have been at least four introductions of the DENV-3 genotype III in Brazil, as signified by the presence of four phylogenetically distinct lineages. Three lineages (BR-I, BR-II, and BR-III) were probably imported from the Lesser Antilles (Caribbean), while the fourth one (BR-IV) was probably introduced from Colombia or Venezuela. While lineages BR-I and BR-II succeeded in getting established and disseminated in Brazil and other countries from the Southern Cone, lineages BR-III and BR-IV were only detected in one single individual each from the North region. The phylogeographic analysis indicates that DENV-3 lineages BR-I and BR-II were most likely introduced into Brazil through the Southeast and North regions around 1999 (95% HPD: 1998-2000) and 2001 (95% HPD: 2000-2002), respectively. These findings show that importation of DENV-3 lineages from the Caribbean islands into Brazil seems to be relatively frequent. Our study further suggests that the North and Southeast Brazilian regions were the most important hubs of introduction and spread of DENV-3 lineages and deserve an intense epidemiological surveillance.

Figure 1. ML tree of 564 DENV-3 genotype III E gene sequences circulating globally.

Brackets indicate clades comprised of sequences sampled from Asia, Africa and the Americas. Taxon labels include reference to country of isolation, year of isolation, and GenBank accession number. Country represented are American Samoa (AS), Bangladesh (BD), Bhutan (BT), China (CH), Honduras (HN), India (IN), Malaysia (MY), Mexico (MX), Nicaragua (NI), Panama (PA), Saudi Arabia (SA), Singapore (SG), Somalia (SO), Sri Lanka (LK), Taiwan (TW). For visual clarity, supported clades comprised of sequences sampled from Caribbean/South America (see Fig. 2), Bhutan and Singapore has been collapsed. Only aLTR support values >80 are shown. All horizontal branch lengths are drawn to a scale of nucleotide substitutions per site. The tree was rooted using DENV-3 genotype I strains. UP (Unidentified Place).

Figure 2. Sub-trees corresponding to the Caribbean/South America clades I (a), II (b) and III (c).

The color of a tip branch represents the geographic region from where the strain originated, according to the legend given in the figure. Numbers in the legend represent the sampling date of sequences. For visual clarity, some clades composed by sequences from the same country/region are schematically represented by triangles. All horizontal branch lengths are drawn to a scale of nucleotide substitutions per site. *Caribbean: Martinique, Trinidad and Tobago, Saint Lucia and Anguilla.

Figure 3. This map identifies the regions and states that make up Brazil.

Legend described the color code and the number of sequences analyzed from each Brazilian region.

Figure 4. Majority-rule Bayesian consensus tree representing the global diversity of DENV-3 genotype III.

The color of a tip branch represents the geographic region from where the strain originated, according to the legend given in the figure. Brackets indicate major region-specific genotype III clades and discrete Brazilian lineages (indicative of separate introductions). Broken boxes highlight subclades of Brazilian sequences circulating in Rio de Janeiro (RJ) and Sao Paulo (SP) states. Taxon labels include reference to country of isolation, year of isolation, and GenBank accession number or strain designation. Country represented are: Anguilla (AI), Argentina (AR), Bolivia (BO), Brazil (BR), Cuba (CU), Colombia (CO), Ecuador (EC), Guyana (GY), Honduras (HN), Martinique (MQ), Mexico (MX), Nicaragua (NI), Panama (PA), Peru (PE), Puerto Rico (PR), Paraguay (PY), Saint Lucia (SL), Somalia (SO), Sri Lanka (LK), Trinidad and Tobago (TT), and Venezuela (VE). PP values are shown for relevant nodes. All horizontal branch lengths are drawn to a scale of nucleotide substitutions per site. The tree was rooted using DENV-3 genotype I strains. UP (Unidentified Place).

Figure 5. Time-scaled Bayesian Maximum Clade Credibility tree for the DENV-3 Caribbean/South America III lineage.

Terminal branches of the tree are colored according to the sampled location of the taxon at the tip. Internal branches are colored according to the most probable location of their parental node. The age (with 95% HPD in parentheses) and the posterior probabilities for the geographic locations of parental nodes of the Caribbean/South America III, BR-I and BR-II lineages are shown. Branch lengths of the trees correspond to length of time (see the time scale bar). The tree is automatically rooted under the assumption of a relaxed molecular clock.