Regions of sampling countries^a.

<p>Regions of sampling countries<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006670#t001fn001" target="_blank">^a</a>.</p

Phylodynamics of CHIKV Asian genotype epidemics.

<p>Time-scaled maximum clade credibility (MCC) tree of the CHIKV Asian genotype was inferred by Bayesian analysis. Sequences from different regions are colored as described in the key. The Caribbean outbreak (CO) clade is supported by Bayesian posterior probabilities (BPP) as 1 in BMCMC analysis and bootstrap values 96% in the maximum likelihood phylogeny. Subclades CO1 and CO2, supported by BPP over 0.98, are also marked in the tree. A small group of Nicaraguan sequences that are relatively distinct from other Nicaraguan sequences are highlighted by a red hash symbol (#). The major ancestral geographic states (state probabilities over 0.5) at the backbone of phylogenetic tree are colored by region and labeled in the tree. The nodes with state probabilities greater than 0.9 are marked by asterisks. The mean and 95% highest posterior density (HPD) of the most recent common ancestor (tMRCA) of the entire Asian genotype and tMRCAs of virus movement between regions are also indicated. The scale bar represents chronological time (in years).</p

Maximum likelihood tree of CHIKV Asian genotype.

<p>The major nodes with bootstrap values above 70% are indicated. The CO clade, supported by bootstrap value 96.6%, is colored in red. Amino acid substitutions that contribute to clade diversity are mapped to the branches of the tree. CO-clade-specific amino acid substitutions are marked in red. Monophyletic groups within CO clade and associated amino acid changes are marked in blue. The scale bar represents genetic distance.</p

Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic

<div><p>Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited understanding of the molecular evolution of CHIKV in the Americas during this epidemic. We sequenced 185 complete CHIKV genomes collected mainly from Nicaragua in Central America and Florida in the United States during the 2014–2015 Caribbean/Americas epidemic. Our comprehensive phylogenetic analyses estimated the epidemic history of the Asian genotype and the recent Caribbean outbreak (CO) clade, revealed considerable genetic diversity within the CO clade, and described different epidemiological dynamics of CHIKV in the Americas. Specifically, we identified multiple introductions in both Nicaragua and Florida, with rapid local spread of viruses in Nicaragua but limited autochthonous transmission in Florida in the US. Our phylogenetic analysis also showed phylogeographic clustering of the CO clade. In addition, we identified the significant amino acid substitutions that were observed across the entire Asian genotype during its evolution and examined amino acid changes that were specific to the CO clade. Deep sequencing analysis identified specific minor variants present in clinical specimens below-consensus levels. Finally, we investigated the association between viral phylogeny and geographic/clinical metadata in Nicaragua. To date, this study represents the largest single collection of CHIKV complete genomes during the Caribbean/Americas epidemic and significantly expands our understanding of the emergence and evolution of CHIKV CO clade in the Americas.</p></div

Significant residue diversity between CO clades.

<p>Significant residue diversity between CO clades.</p

Maximum likelihood phylogenetic tree of complete coding nucleotide sequences of CHIKV.

<p>Well-supported nodes by bootstrap values over 70% are marked in the tree. Three genotypes (West African, ECSA, and Asian) and clades (Indian Ocean and Caribbean outbreaks) are described in the trees. New sequences sampled from the Americas are colored in red. The phylogenetic tree is midpoint-rooted, and the scale bar represents the number of nucleotide substitutions per site. Arrows indicate known recent travel of the human hosts to Africa or Asia in the ECSA genotype.</p

Phylogeographic clustering of Caribbean/Americas epidemic CHIKV strains.

<p>The Bayesian maximum clade credibility (MCC) tree of CHIKV Asian genotype was annotated to reflect the geographic origin of samples collected in the Americas. The CO clade was split into three parts, magnified, and indicated by gray shading: subclade CO1 (right side of the tree), subclade CO2 (left middle panel), and non-CO1/CO2 strains (left lower panel). Sequences from different regions are colored in branches as described in the key. The original countries of infections (either indigenous or travel-related) are depicted with colored ovals next to the complete strain names and described in the key as well.</p

Relationship between MIC and MAC Chromosomes

<p>The top horizontal bar shows a small portion of one of the five pairs of MIC chromosomes. MAC-destined sequences are shown in alternating shades of gray. MIC-specific IESs (internally eliminated sequences) are shown as blue rectangles, and sites of the 15-bp Cbs are shown as red bars (not to scale). Below the top bar are shown macronuclear chromosomes derived from the above region of the MIC by deletion of IESs, site-specific cleavage at Cbs sites, and amplification. Telomeres are added to the newly generated ends (green bars). Most of the MAC chromosomes are amplified to approximately 45 copies (only three shown). Through the process of phenotypic assortment, initially heterozygous loci generally become homozygous in each lineage within approximately 100 vegetative fissions. Polymorphisms located on the same MAC chromosome tend to co-assort.</p

Scaffold Sizes

<div><p>(A) Scaffold sizes versus MAC chromosome size. Blue diamonds represent scaffolds capped by telomeres on both ends. Red squares and green triangles represent incomplete scaffolds capped by telomeres at one or neither end, respectively.</p> <p>(B) Size distribution of scaffolds capped by telomeres on both ends.</p></div

Depth of Coverage versus Scaffold Size

<p>Black diamonds indicate all scaffolds; red diamonds, scaffolds capped with telomeres on both ends.</p