Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay

Abstract

Paraguay has been severely affected by emergent Zika and chikungunya viruses, and dengue virus is endemic. To learn more about the origins of genetic diversity and epidemiologic history of these viruses in Paraguay, we deployed portable sequencing technologies to strengthen genomic surveillance and determine the evolutionary and epidemic history of arthropod-borne viruses (arboviruses). Samples stored at the Paraguay National Central Laboratory were sequenced and subjected to phylogenetic analysis. Among 33 virus genomes generated, we identified 2 genotypes of chikungunya and 2 serotypes of dengue virus that circulated in Paraguay during 2014-2018; the main source of these virus lineages was estimated to be Brazil. The evolutionary history inferred by our analyses precisely matched the available travel history of the patients. The genomic surveillance approach used was valuable for describing the epidemiologic history of arboviruses and can be used to determine the origins and evolution of future arbovirus outbreaks.

Keywords: Paraguay; arboviruses; chikungunya virus; dengue virus; genomic surveillance; nanopore sequencing; vector-borne infections; viruses.

Figure 1

Geopolitical map of Paraguay showing locations of sampling for dengue virus (DENV) and chikungunya virus (CHIKV). Circle sizes are scaled to represent the number of genomes isolated in each municipality. Numbers inside triangles indicate sampled departments: 1, Amambay; 2, San Pedro; 3, Alto Paraná; 4, Itapúa; 5, Guairá; 6, Paraguarí; 7, Central; 8, Asunción. Callout map shows the Central and Asunción Departments of Paraguay; inset map shows the location of Paraguay in South America.

Figure 2

Chikungunya virus (CHIKV) outbreaks in Paraguay during 2014–2018 and the spatial–temporal history of virus diffusion. A) Total number of cases of CHIKV infection reported by epidemiologic week in the departments from which genome sequences were available. B) Location transitions to Paraguay inferred from the posterior distribution of phylogenetic trees by the Markov jump approach, and the time to most recent common ancestor for the CHIKV clusters detected in the country. Lines are colored according to the origin of the estimated transition toward Paraguay. Violin plots show 95% CIs with internal boxplots showing median and interquartile ranges. Brazil-N, Brazil North Region; Brazil-NE, Brazil Northeast Region; ECSA, East/Central/South African genotype.

Figure 3

Time-scaled phylogenetic trees of chikungunya virus (CHIKV) genomes isolated in the Americas. A) CHIKV Asian genotype; B) CHIKV East/Central/South African genotype from Brazil. Tips and internal branches are colored according to the most likely geographic location, and ancestral states were estimated by phylogeographic methods. Clusters relevant to the epidemic in Paraguay are shown in detail where the most likely ancestral state estimation is annotated. Asterisks indicate highly supported clusters (posterior probability >0.9).

Figure 4

Dengue virus (DENV) outbreaks in Paraguay during 2015–2018 and tMCRA of serotypes 1 and 4. A) Total cases of DENV infections reported by epidemiologic week in the departments from which genome sequences were available. The black bars in 2018 delimit the sampling time range for the DENV genomes. B) tMRCA for DENV-1 and DENV-4 in the same timescale as the number of cases reported. Violin plots show 95% CIs; internal boxplots show medians and interquartile ranges. tMCRA, time to most recent common ancestor.

Figure 5

Time-scaled phylogenetic trees of dengue virus (DENV) serotypes 1 and 4 genomes isolated in Paraguay and related sequences. A) DENV-1; B) DENV-4. Tips and internal branches are colored according to geographic location, and ancestral states were estimated by phylogeographic methods. Clusters relevant to the epidemic in Paraguay are shown in detail where the most likely ancestral state estimation is annotated. Asterisks indicate highly supported clusters (posterior probability >0.9).