Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

Zuleima Pava; Rintis Noviyanti; Irene Handayuni; Hidayat Trimarsanto; Leily Trianty; Faustina H. Burdam; Enny Kenangalem; Retno A. S Utami; Yusrifar K. Tirta; Farah Coutrier; Jeanne R. Poespoprodjo; Ric N. Price; Jutta Marfurt; Sarah Auburn

doi:10.1371/journal.pone.0177445

Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

Zuleima Pava, Rintis Noviyanti, Irene Handayuni, Hidayat Trimarsanto, Leily Trianty, Faustina H. Burdam, Enny Kenangalem, Retno A. S Utami, Yusrifar K. Tirta, Farah Coutrier, Jeanne R. Poespoprodjo, Ric N. Price, Jutta Marfurt, Sarah Auburn

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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 (H_E = 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.

Original language	English
Article number	e0177445
Pages (from-to)	1-13
Number of pages	13
Journal	PLoS One
Volume	12
Issue number	5
DOIs	https://doi.org/10.1371/journal.pone.0177445
Publication status	Published - 1 May 2017

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Pava, Z., Noviyanti, R., Handayuni, I., Trimarsanto, H., Trianty, L., Burdam, F. H., Kenangalem, E., Utami, R. A. S., Tirta, Y. K., Coutrier, F., Poespoprodjo, J. R., Price, R. N., Marfurt, J., & Auburn, S. (2017). Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections. PLoS One, 12(5), 1-13. [e0177445]. https://doi.org/10.1371/journal.pone.0177445

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title = "Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections",

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.",

author = "Zuleima Pava and Rintis Noviyanti and Irene Handayuni and Hidayat Trimarsanto and Leily Trianty and Burdam, {Faustina H.} and Enny Kenangalem and Utami, {Retno A. S} and Tirta, {Yusrifar K.} and Farah Coutrier and Poespoprodjo, {Jeanne R.} and Price, {Ric N.} and Jutta Marfurt and Sarah Auburn",

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Pava, Z, Noviyanti, R, Handayuni, I, Trimarsanto, H, Trianty, L, Burdam, FH, Kenangalem, E, Utami, RAS, Tirta, YK, Coutrier, F, Poespoprodjo, JR, Price, RN, Marfurt, J & Auburn, S 2017, 'Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections', PLoS One, vol. 12, no. 5, e0177445, pp. 1-13. https://doi.org/10.1371/journal.pone.0177445

TY - JOUR

T1 - Genetic micro-epidemiology of malaria in Papua Indonesia

T2 - Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

AU - Pava, Zuleima

AU - Noviyanti, Rintis

AU - Handayuni, Irene

AU - Trimarsanto, Hidayat

AU - Trianty, Leily

AU - Burdam, Faustina H.

AU - Kenangalem, Enny

AU - Utami, Retno A. S

AU - Tirta, Yusrifar K.

AU - Coutrier, Farah

AU - Poespoprodjo, Jeanne R.

AU - Price, Ric N.

AU - Marfurt, Jutta

AU - Auburn, Sarah

PY - 2017/5/1

Y1 - 2017/5/1

N2 - 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.

AB - 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.

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SN - 1932-6203

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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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