Field-collected <i>Plasmodium vivax</i> isolates from Brazil with nuclear genomes newly sequenced in this study and summary of sequencing statistics.

<p>Field-collected <i>Plasmodium vivax</i> isolates from Brazil with nuclear genomes newly sequenced in this study and summary of sequencing statistics.</p

A neighbor-joining phylogenetic tree with 1,000 bootstrap pseudoreplicates obtained with genomic sequences of <i>P</i>. <i>vivax</i> isolates from Brazil (n = 11 isolates), Peru (n = 23), Colombia (= 31), and Mexico (n = 19).

<p>Branch tips were colored according to the geographic origin of samples, as shown in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005824#pntd.0005824.g001" target="_blank">Fig 1</a>. Grey circles indicate internal nodes with > 70% bootstrap support.</p

Principal component analysis of the population structure of <i>P</i>. <i>vivax</i> in the New World.

<p>Panel A shows results using the complete data set of 94,122 SNPs; panel B shows results obtained with a set of 37 segregating SNPs included in a previously described <i>P</i>. <i>vivax</i> barcode [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005824#pntd.0005824.ref049" target="_blank">49</a>]; and panel C shows results obtained with a hypothetical barcode comprising the 100 SNPs yielding the highest average Wright’s fixation index <i>F</i>_ST values in pairwise comparisons of New World <i>P</i>. <i>vivax</i> populations. The SNPs used in the analysis shown in panel C are listed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005824#pntd.0005824.s011" target="_blank">S5 Table</a>. Samples are colored according to their geographic origin as shown in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005824#pntd.0005824.g001" target="_blank">Fig 1</a>. The percentage contributions of each principal component (C1, C2, and C3) to overall variance were as follows: panel A, C1 = 22.27%, C2 = 14.15%, and C3 = 8.15%; panel B, C1 = 19.93%, C2 = 12.03%, and C3 = 11.42%; and panel C, C1 = 21.36%, C2 = 10.93%, and C3 = 9.33%.</p

Pairwise differentiation between populations, estimated using the Wright's fixation index <i>F</i>_ST averaged across all loci, in <i>Plasmodium vivax</i> populations from Brazil, Peru, Colombia, and Mexico.

<p>Pairwise differentiation between populations, estimated using the Wright's fixation index <i>F</i>_ST averaged across all loci, in <i>Plasmodium vivax</i> populations from Brazil, Peru, Colombia, and Mexico.</p

Map showing the sampling locations of the New World <i>P</i>. <i>vivax</i> isolates analyzed in this study, comprising Brazil, Peru, Colombia, and Mexico.

<p>The insert shows the study sites in northwestern Brazil (Acrelândia and Remansinho, 120 km apart), close to the border with Bolivia and Peru. Adapted from [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005824#pntd.0005824.ref015" target="_blank">15</a>] and <a href="https://commons.wikimedia.org/wiki/Atlas_of_the_world#/media/File:BlankMap-World6.svg" target="_blank">https://commons.wikimedia.org/wiki/Atlas_of_the_world#/media/File:BlankMap-World6.svg</a>.</p

Frequency distribution of Tajima’s <i>D</i> values calculated within 1-kb windows of genomic sequence in four New World populations of <i>P</i>. <i>vivax</i>.

<p>BRA = Brazil (n = 11 isolates), PER = Peru (n = 23), COL = Colombia (n = 31), and MEX = Mexico (n = 19).</p

Nonsynonymous single-nucleotide polymorphism (SNPs) detected in drug resistance genes by whole-genome sequencing in <i>Plasmodium vivax</i> isolates from Brazil, Peru, Colombia, and Mexico.

<p>Nonsynonymous single-nucleotide polymorphism (SNPs) detected in drug resistance genes by whole-genome sequencing in <i>Plasmodium vivax</i> isolates from Brazil, Peru, Colombia, and Mexico.</p

Linkage disequilibrium (LD) decay with increasing distance between SNPs on the same chromosome.

<p>Solid lines show median <i>r</i>² estimates for SNPs along the same chromosome plotted against the inter-marker physical distance for Brazil (pink), Peru (green), Colombia (blue), and Mexico (orange). Dotted lines show the background genome-wide LD (median <i>r</i>² estimates for unlinked SNPs—those mapping to different chromosomes).</p

Proportion of <i>P.vivax</i> infections diagnosed during 8 consecutive cross-sectional surveys in Remansinho, Brazil, that were symptomatic (black bar segments) and asymptomatic (white bar segments) according to parasite density estimated by quantitative PCR.

<p>The bar widths are proportional to the number of cases within each parasite density class. A total of 129 <i>P. vivax</i> infections were classified according to the presence of symptoms and parasite density.</p

Kaplan-Meier estimates of the proportion of <i>P. vivax</i>-infected (continuous black line) and uninfected (continuous red line) asymptomatic subjects who remained free of slide-confirmed clinical vivax malaria over the follow-up period.

<p>Dashed lines represent the respective 95% confidence intervals. The small vertical tick-marks indicate the occurrence of a slide positive case of <i>P.vivax</i>, corresponding to the right censoring of the individual survival time. A Cox proportional hazards model revealed no significant difference, between the two groups, in overall risk of vivax malaria episodes, after controlling for potential confounders (hazard ratio = 1.07; 95% CI, 0.52–2.22, <i>P</i> = 0.840).</p