High Prevalence, Genetic Diversity and Temporal Differentiation of Plasmodium vivax in a Remote Hard-to-Reach Community from the Peruvian Amazon Region

Assessing parasite population genetic diversity and structure in remote areas is essential for understanding malaria transmission and guiding interventions toward elimination. This study monitored the genetic diversity and population structure of Plasmodium vivax as part of a longitudinal surveillance in Santa Emilia, a hard-to-reach community in Loreto, Peru. A total of 221 of 3,434 P. vivax samples collected through active and passive case detection between 2015 and 2016 were genotyped using 16 neutral microsatellites. Additionally, 139 genotyped samples from 2013, previously reported, were included for comparison. Malaria prevalence (microscopic and submicroscopic), genetic diversity, population differentiation, structure, bottleneck analysis, and relatedness between years were evaluated. We found 56% P. vivax prevalence by quantitative real-time polymerase chain reaction, with 44% submicroscopic infections in 2015 and 2016. Genetic diversity and population differentiation were high between 2013, 2015, and 2016. Parasites from 2015 to 2016 had a lower Jost D. In 2013 and 2015, more than 40% of infections were polyclonal infections, but only 29% were polyclonal infections in 2016. Moderate linkage disequilibrium was found over time. Four populations were detected in 2013, 2015, and 2016, with increasing admixture in 2015–2016. Genetically related parasites with clonal expansion suggest that there was no recent bottleneck. Santa Emilia has a persistent high genetic diversity and structured, temporally differentiated clonal populations over the time periods of the study. This analysis highlights the complexity of parasite dynamics in this remote area of malaria transmission, making it a challenging area for the malaria elimination plan in Peru.