Multilocus genotyping reveals high heterogeneity and strong local population structure of the Plasmodium vivax population in the Peruvian Amazon

Abstract

Background: Peru is one of the Latin American countries with the highest malaria burden, mainly due to Plasmodium vivax infections. However, little is known about P. vivax transmission dynamics in the Peruvian Amazon, where most malaria cases occur. The genetic diversity and population structure of P. vivax isolates collected in different communities around Iquitos city, the capital of the Peruvian Amazon, was determined.

Methods: Plasmodium vivax population structure was determined by multilocus genotyping with 16 microsatellites on 159 P. vivax infected blood samples (mono-infections) collected in four sites around Iquitos city. The population characteristics were assessed only in samples with monoclonal infections (n = 94), and the genetic diversity was determined by calculating the expected heterozygosity and allelic richness. Both linkage disequilibrium and the genetic differentiation (theta) were estimated.

Results: The proportion of polyclonal infections varied substantially by site (11% - 70%), with the expected heterozygosity ranging between 0.44 and 0.69; no haplotypes were shared between the different populations. Linkage disequilibrium was present in all populations (IAS 0.14 - 0.61) but was higher in those with fewer polyclonal infections, suggesting inbreeding and a clonal population structure. Strong population differentiation (theta = 0.45) was found and the Bayesian inference cluster analysis identified six clusters based on distinctive allele frequencies.

Conclusion: The P. vivax populations circulating in the Peruvian Amazon basin are genetically diverse, strongly differentiated and they have a low effective recombination rate. These results are in line with the low and clustered pattern of malaria transmission observed in the region around Iquitos city.

Figure 1

Map of the study area (study sites mapped with GPS on Google maps) and number samples for each community (Total samples population = 159).

Figure 2

Estimated P. vivax population structure by STRUCTURE software. Panel A represents the STRUCTURE results for the whole dataset, showing two peaks at K = 3 and 6 (delta K = 6 and 8.8). Panel B contains the bar plot at K = 3 and K = 6 with each sample being represented by a single vertical line divided into K colors, where K is the number of populations assumed. Each color represents one population, and the length of the colored segment shows the estimated proportion of membership of that sample to each population. Sample number 1-31 belong to population C, 32-70 to population B, 71-85 to population A1, and 86-94 to population A2.