Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Abstract

BackgroundThe ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized.ResultsWe examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.ConclusionThese findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.See commentary: http://www.biomedcentral.com/1741-7007/8/90

Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

“…Sixty-five (7.4%) of the 883 P. vivax isolates analyzed worldwide had the FF haplotype, but they originated from only three countries: Brazil (Paragominas and Granada), 14,26 Honduras, 24 and Papua New Guinea. 9 More extensive genotyping at and surrounding the pvmdr-1 locus might indicate whether these haplotypes share a common ancestor.…”

“…We analyzed newly obtained SNP data for 13 isolates collected in Acrelâ ndia, 21 in Plácido de Castro and 46 in Remansinho, and data previously obtained with the same typing strategy, for 37 isolates from Plá cido de Castro and 111 from Granada. 14 Of five SNPs assayed, two were monomorphic in the Western Amazon Basin of Brazil: all 228 isolates examined had the amino acid replacements (relative to the pvmdr-1 sequence of Sal-1 strain, which is defined as wild type) N89S and M908L (Table 1). Although these changes are not putatively associated with CQ resistance, they can be useful in tracing the geographic origin of pvmdr-1 haplotypes carrying mutations Y976F and F1076L, which in turn might underlie CQ resistance.…”

“…13 Thus, we cannot interpret detection of the first mutation (F1076L) as an early warning of the imminent emergence of CQ resistance. 14 Copy number variation of the mdr-1 gene in P. vivax isolates from northwestern Brazil. Of 217 samples from northwestern Brazil available for analysis, we obtained a pvmdr-1 copy number estimate for 215 isolates (10 collected in Acrelâ ndia, 54 in Plácido de Castro, 97 in Granada, and 54 in Remansinho); only two samples (both from Granada) yielded no amplification.…”

“…3,[10][11][12] Interestingly, the Y976F change has been reported to be rare in alleles that do not carry the F1076L (TTT!CTT) change, consistent with a two-step mutation pathway (F1076L followed by Y976F) putatively leading to CQ resistance. 13,14 Similar to P. falciparum, 15 susceptibility to CQ in P. vivax appears to be also modulated by pvmdr-1 copy number. Amplification of the pvmdr-1 gene correlates with increased susceptibility to CQ and decreased susceptibility to amodiaquine, artesunate and mefloquine in vitro.…”

High Genetic Diversity of Plasmodium vivax on the North Coast of Papua New Guinea

“…WGA, a method that has been used in similar molecular epidemiological studies, [25][26][27][28] was performed prior to genotyping to increase the amount of P. vivax DNA for analysis. The multiple displacement amplification (MDA) method used in this study has been shown to result in a higher yield of non-artifact DNA template and reduced amplification bias compared with PCR-based WGA methods.…”