Multilocus haplotypes reveal variable levels of diversity and population structure of Plasmodium falciparum in Papua New Guinea, a region of intense perennial transmission

Abstract

BackgroundThe South West Pacific nation of Papua New Guinea has intense year round transmission of Plasmodium falciparum on the coast and in the low-lying inland areas. Local heterogeneity in the epidemiology of malaria suggests that parasites from multiple locations will need to be surveyed to define the population biology of P. falciparum in the region. This study describes the population genetics of P. falciparum in thirteen villages spread over four distinct catchment areas of Papua New Guinea.MethodsTen microsatellite loci were genotyped in 318 P. falciparum isolates from the parasite populations of two inland catchment areas, namely Wosera (number of villages (n) = 7) and Utu (n = 1) and; and two coastal catchments, Malala (n = 3) and Mugil (n = 3). Analysis of the resultant multilocus haplotypes was done at different spatial scales (2-336 km) to define the genetic diversity (allelic richness and expected heterozygosity), linkage disequilibrium and population structure throughout the study area.ResultsAlthough genetic diversity was high in all parasite populations, it was also variable with a lower allelic richness and expected heterozygosity for inland populations compared to those from the more accessible coast. This variability was not correlated with two proxy measures of transmission intensity, the infection prevalence and the proportion multiple infections. Random associations among the microsatellite loci were observed in all four catchments showing that a substantial degree of out-crossing occurs in the region. Moderate to very high levels of population structure were found but the amount of genetic differentiation (FST) did not correlate with geographic distance suggesting that parasite populations are fragmented. Population structure was also identified between villages within the Malala area, with the haplotypes of one parasite population clustering with the neighbouring catchment of Mugil.ConclusionThe observed population genetics of P. falciparum in this region is likely to be a consequence of the high transmission intensity combined with the isolation of human and vector populations, especially those located inland and migration of parasites via human movement into coastal populations. The variable genetic diversity and population structure of P. falciparum has important implications for malaria control strategies and warrants further fine scale sampling throughout Papua New Guinea.

High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

“…However, surveys of the same populations using a panel of 10 microsatellite markers have demonstrated that the catchments and even some villages within the same catchment are genetically isolated from each other, suggesting that there is a limit to the influx of alleles from distant and even nearby populations. 18 Diversity as measured by these putatively neutral markers was also high and there was no correlation with the infection prevalence. 18 It may be that the reduction of transmission in the dry season and by the recent distribution of LLINs in the Wosera has created a situation in which diverse populations have become isolated.…”

“…18 Diversity as measured by these putatively neutral markers was also high and there was no correlation with the infection prevalence. 18 It may be that the reduction of transmission in the dry season and by the recent distribution of LLINs in the Wosera has created a situation in which diverse populations have become isolated. To confirm this, it will be important to later compare the data to that for the rainy season and pre-LLIN distributions.…”

“…18 Utu, the Mugil village of Karkum, and Wosera villages of Gwinyingi and Kitikum had the highest values of R s , and the Wosera village of Patigo the lowest. There was a limited variability of He among the villages, with all showing very high levels of diversity (H e = 0.90-0.96).…”

“…The msp2 diversity data were then compared with that previously published for microsatellite haplotypes. 18 Microsatellite haplotype diversity (R s ) was much lower than that for msp2 (Supplemental Figure S2). In this study a higher resolution marker, such as msp2 was necessary to allow the distinction between clones within samples.…”

“…Diversity was not associated with the P. falciparum infection prevalence, but lower levels of diversity were found in the more isolated inland populations. 18 Since 2003, efforts to control malaria in PNG have been significantly intensified with support from the Global Fund to Combat AIDS, Tuberculosis, and Malaria. The strategies being used have included the extensive distribution of long-lasting insecticide-treated nets (LLINs) and more recently, policy change to ensure better diagnosis of infections and the treatment of clinical cases with artemisinin combination therapy.…”