Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax

Abstract

Background: The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.

Methods: We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19).

Principal findings/conclusions: We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data.

Fig 1. Map showing the sampling locations of the New World P. vivax isolates analyzed in this study, comprising Brazil, Peru, Colombia, and Mexico.

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 [15] and https://commons.wikimedia.org/wiki/Atlas_of_the_world#/media/File:BlankMap-World6.svg.

Fig 2. Venn diagram showing the number of SNPs shared by P. vivax samples from Brazil (n = 11 isolates), Peru (n = 23), Colombia (n = 31), and Mexico (n = 19).

Fig 3. Frequency distribution of Tajima’s D values calculated within 1-kb windows of genomic sequence in four New World populations of P. vivax.

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

Fig 4. Principal component analysis of the population structure of P. vivax in the New World.

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 P. vivax barcode [49]; and panel C shows results obtained with a hypothetical barcode comprising the 100 SNPs yielding the highest average Wright’s fixation index F_ST values in pairwise comparisons of New World P. vivax populations. The SNPs used in the analysis shown in panel C are listed in S5 Table. Samples are colored according to their geographic origin as shown in Fig 1. 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%.

Fig 5. A neighbor-joining phylogenetic tree with 1,000 bootstrap pseudoreplicates obtained with genomic sequences of P. vivax isolates from Brazil (n = 11 isolates), Peru (n = 23), Colombia (= 31), and Mexico (n = 19).

Branch tips were colored according to the geographic origin of samples, as shown in Fig 1. Grey circles indicate internal nodes with > 70% bootstrap support.

Fig 6. Linkage disequilibrium (LD) decay with increasing distance between SNPs on the same chromosome.

Solid lines show median r² 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 r² estimates for unlinked SNPs—those mapping to different chromosomes).