Revisiting Key Entry Routes of Human Epidemic Arboviruses into the Mainland Americas through Large-Scale Phylogenomics

Abstract

The rapid worldwide spread of chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses have raised great international concern. Knowledge about the entry routes and geographic expansion of these arboviruses to the mainland Americas remain incomplete and controversial. Epidemics caused by arboviruses continue to cause socioeconomic burden globally, particularly in countries where vector control is difficult due to climatic or infrastructure factors. Understanding how the virus circulates and moves from one country to another is of paramount importance to assist government and health officials in anticipating future epidemics, as well as to take steps to help control or mitigate the spread of the virus. Through the analyses of the sequences of arbovirus genomes collected at different locations over time, we identified patterns of accumulated mutations, being able to trace routes of dispersion of these viruses. Here, we applied robust phylogenomic methods to trace the evolutionary dynamics of these arboviruses with special focus on Brazil, the epicenter of these triple epidemics. Our results show that CHIKV, DENV-1-4, and ZIKV followed a similar path prior to their first introductions into the mainland Americas, underscoring the need for systematic arboviral surveillance at major entry points of human population movement between countries such as airports and seaports.

Figure 1

Phylogenetic reconstructions of CHIKV whole genome sequences. Bayesian MCC tree enforcing a strict molecular clock. The values along the tree branches represent the posterior distribution. The horizontal bars show phylogenetic uncertainty. The branches in blue and red represent Central/East African and Asian CHIKV genotypes, respectively. Abbreviation: CAR = Central African Republic.

Figure 2

Bayesian maximum clade credibility (MCC) phylogenetic tree of DENVs' whole genomes. MCC trees were used to represent population dynamics over time of different genotypes of DENV-1 (a), DENV-2 (b), DENV-3 (c), and DENV-4 (d). The branch length is scaled in time enforcing strict (DENV-1 and DENV-4) and relaxed (DENV-2 and DENV-3) molecular clocks. The colors highlighted in the MCC trees represent different groups of countries and the horizontal blue bars represent phylogenetic uncertainty. DENV genotypes and lineages are indicated in each panel by roman numerals. One asterisk represents ≥86% and two ≥99% of posterior probability values. In (c) (DENV-3), the naming of Brazilian genotypes BR-I and BR-II as South America I (SA-I) and South America II (SA-II) is suggested to better represent the geographic locations of the isolates. Country abbreviations: ARG: Argentina; BRA: Brazil; BVI_Tortola = British Virgin Island, Tortola; COL: Colombia; DOM: Dominican Republic; IND: India; JAM: Jamaica; KHM: Cambodia; PRI: Puerto Rico; PRY: Paraguay; TTO: PER: Peru; PHL: Philippines; Trinidad and Tobago; USA: United States of America; VEN: Venezuela.

Figure 3

Bayesian reconstruction of the spatiotemporal spread pattern of ZIKV. The transmission networks during ZIKV outbreaks as well as its origin and spread are exhibited by the minimum spanning tree (MST) analysis. Countries and nodes were colored following the continent legend (a). DensiTree analysis shows the frequency of clades and nodes from the Bayesian approach. Well-supported branches are indicated by solid colors. The sequences in bold indicate ZIKV-associated microcephaly and those in italics indicate that ZIKV was imported from Venezuela to China (b). Time-scaled Bayesian MCC phylogenetic tree of ZIKV full-length genome sequences enforcing a relaxed molecular clock. The blue and yellow rectangles show two well-supported monophyletic clades that help to elucidate the dynamics and dissemination of ZIKV to different countries. Roman numerals in front of the yellow rectangles represent our hypothesis for different ZIKV variants that are currently circulating in South America. The horizontal blue bars in the tree indicate the phylogenetic uncertainty and the asterisks the posterior probability values greater than or equal to 98% (c).

Figure 4

Route map of arboviruses assessed in the study. The colors and arrows highlight the entry routes of DENV, CHIKV, and ZIKV into mainland South America. On the bottom left, there is a summary of routes traced in the study. Abbreviations: ARG: Argentina; BRA: Brazil; BVI = British Virgin Island; CHI: CACIs: Central America and Caribbean islands; China; COL: Colombia; DOM: Dominican Republic; FSM: Federated States of Micronesia; HTI: Haiti; IND: India; KHM: Cambodia; MTQ: Martinique; PIs: Pacific Islands; PER: Peru; PHL: Philippines; PRI: Puerto Rico; PRY: Paraguay; PYF: French Polynesia; SA: South America; THA: Thailand; TTO: Trinidad and Tobago; VEN: Venezuela.