Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam

Abstract

Background: The burden of malaria in Vietnam has drastically reduced, prompting the National Malaria Control Program to officially engage in elimination efforts. Plasmodium vivax is becoming increasingly prevalent, remaining a major problem in the country's central and southern provinces. A better understanding of P. vivax genetic diversity and structure of local parasite populations will provide baseline data for the evaluation and improvement of current efforts for control and elimination. The aim of this study was to examine the population genetics and structure of P. vivax isolates from four communities in Tra Leng commune, Nam Tra My district in Quang Nam, Central Vietnam.

Methodology/principal findings: P. vivax mono infections collected from 234 individuals between April 2009 and December 2010 were successfully analyzed using a panel of 14 microsatellite markers. Isolates displayed moderate genetic diversity (He = 0.68), with no significant differences between study communities. Polyclonal infections were frequent (71.4%) with a mean multiplicity of infection of 1.91 isolates/person. Low but significant genetic differentiation (FST value from -0.05 to 0.18) was observed between the community across the river and the other communities. Strong linkage disequilibrium ([Formula: see text] = 0.113, p < 0.001) was detected across all communities, suggesting gene flow within and among them. Using multiple approaches, 101 haplotypes were grouped into two genetic clusters, while 60.4% of haplotypes were admixed.

Conclusions/significance: In this area of Central Vietnam, where malaria transmission has decreased significantly over the past decade, there was moderate genetic diversity and high occurrence of polyclonal infections. Local human populations have frequent social and economic interactions that facilitate gene flow and inbreeding among parasite populations, while decreasing population structure. Findings provide important information on parasites populations circulating in the study area and are relevant to current malaria elimination efforts.

Fig 1. Study area in Nam Tra My district, Quang Nam, Vietnam.

Fig 2. Allele frequency distribution in four communities in Quang Nam (n = 234).

Predominant allele database and all loci combined are included.

Fig 3. Pair-wise loci linkage disequilibrium analysis (N = 234).

Significant association between alleles at pairs of loci in each sample was tested using FSTAT. Green color denotes LD at 5% based on 36400 permutations. Markers within the same contig are: MS4-MS5, MS7-MS8, MS12-MS15.

Fig 4. Genetic clustering analysis by STRUCTURE.

The graph represent the clustering model when the parasite population was grouped into 2 clusters (K = 2). In the bar plot, each isolate is represented by a single vertical line divided into K colors.

Fig 5. Phylogenetic relationship of 101 unique P. vivax haplotypes using PHYLOViZ.

Haplotypes relationships by (A) community, and (B) clustering K = 2. Each colored figure represents a unique haplotype and grey lines indicate shared alleles among individual haplotypes.