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. 2017 May 12;12(5):e0177445.
doi: 10.1371/journal.pone.0177445. eCollection 2017.

Genetic Micro-Epidemiology of Malaria in Papua Indonesia: Extensive P. Vivax Diversity and a Distinct Subpopulation of Asymptomatic P. Falciparum Infections

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Free PMC article

Genetic Micro-Epidemiology of Malaria in Papua Indonesia: Extensive P. Vivax Diversity and a Distinct Subpopulation of Asymptomatic P. Falciparum Infections

Zuleima Pava et al. PLoS One. .
Free PMC article

Abstract

Background: Genetic analyses of Plasmodium have potential to inform on transmission dynamics, but few studies have evaluated this on a local spatial scale. We used microsatellite genotyping to characterise the micro-epidemiology of P. vivax and P. falciparum diversity to inform malaria control strategies in Timika, Papua Indonesia.

Methods: Genotyping was undertaken on 713 sympatric P. falciparum and P. vivax isolates from a cross-sectional household survey and clinical studies conducted in Timika. Standard population genetic measures were applied, and the data was compared to published data from Kalimantan, Bangka, Sumba and West Timor.

Results: Higher diversity (HE = 0.847 vs 0.625; p = 0.017) and polyclonality (46.2% vs 16.5%, p<0.001) were observed in P. vivax versus P. falciparum. Distinct P. falciparum substructure was observed, with two subpopulations, K1 and K2. K1 was comprised solely of asymptomatic infections and displayed greater relatedness to isolates from Sumba than to K2, possibly reflecting imported infections.

Conclusions: The results demonstrate the greater refractoriness of P. vivax versus P. falciparum to control measures, and risk of distinct parasite subpopulations persisting in the community undetected by passive surveillance. These findings highlight the need for complimentary new surveillance strategies to identify transmission patterns that cannot be detected with traditional malariometric methods.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Neighbour-joining and STRUCTURE plots illustrating the genetic diversity and structure in the P. vivax and P. falciparum populations in Timika.
Panels A) and B) present unrooted neighbour-joining trees illustrating the genetic relatedness amongst P. vivax and P. falciparum isolates, respectively. Panel C) presents a bar plot illustrating the substructure in the P. falciparum population at K = 2. Each vertical bar represents an individual sample and each colour represents one of the K clusters (sub-populations) defined by STRUCTURE.
Fig 2
Fig 2. Principal coordinate analysis (PCoA) and STRUCTURE plots illustrating the genetic differentiation between P. falciparum isolates from Timika relative to Kalimantan, Bangka, Sumba and West Timor.
Panels A) and B) present PCoA and STRUCTURE bar plots, respectively, illustrating the similarity between the Timika K1 subpopulation and the other four islands. The STRUCTURE bar plot presents the results for K = 2. Panels C) and D) present PCoA and STRUCTURE bar plots, respectively, for all five P. falciparum populations, with the exclusion of the Timika K2 subpopulation, illustrating the greater relatedness between K1 and Sumba relative to the other islands. The STRUCTURE bar plot presents the results for K = 2, separating K1, Sumba and West Timor in the east from Kalimantan and Bangka in the west.

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Grant support

The study was supported by the Wellcome Trust (a Senior Fellowship in Clinical Science awarded to RNP - 200909) and Fellowships to: JRP (Wellcome Trust - 099875) and ZP (Instituto Colombiano para el Desarrollo de la Ciencia y la Tecnología Francisco José de Caldas, Colciencias - 512-2010). The Timika Research Facility and Papuan Health and Community Development Foundation were supported by DFAT (Australian Department of Foreign Affairs and Trade) and the NHMRC (Program Grant 1037304). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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