Genomic analysis of local variation and recent evolution in Plasmodium vivax

Richard D Pearson; Roberto Amato; Sarah Auburn; Olivo Miotto; Jacob Almagro-Garcia; Chanaki Amaratunga; Seila Suon; Sivanna Mao; Rintis Noviyanti; Hidayat Trimarsanto; Jutta Marfurt; Nicholas M. Anstey; Timothy WILLIAM; MacIej F. Boni; Christiane Dolecek; Hien Tinh Tran; Nicholas J White; Pascal Michon; Peter Siba; Livingstone Tavul; Gabrielle Harrison; Alyssa E. Barry; Ivo Mueller; Marcelo U. Ferreira; Nadira Karunaweera; Milijaona Randrianarivelojosia; Qi Gao; Christina Hubbart; Lee Hart; Ben Jeffery; Eleanor Drury; Daniel Mead; Mihir Kekre; Susana Campino; Magnus Manske; Victoria J. Cornelius; Bronwyn MacInnis; Kirk A. Rockett; Alistair Miles; Julian C. Rayner; Rick M. Fairhurst; Francois Nosten; Ric N. Price; Dominic P. Kwiatkowski

doi:10.1038/ng.3599

Genomic analysis of local variation and recent evolution in Plasmodium vivax

Richard D Pearson, Roberto Amato, Sarah Auburn, Olivo Miotto, Jacob Almagro-Garcia, Chanaki Amaratunga, Seila Suon, Sivanna Mao, Rintis Noviyanti, Hidayat Trimarsanto, Jutta Marfurt, Nicholas M. Anstey, Timothy WILLIAM, MacIej F. Boni, Christiane Dolecek, Hien Tinh Tran, Nicholas J White, Pascal Michon, Peter Siba, Livingstone TavulGabrielle Harrison, Alyssa E. Barry, Ivo Mueller, Marcelo U. Ferreira, Nadira Karunaweera, Milijaona Randrianarivelojosia, Qi Gao, Christina Hubbart, Lee Hart, Ben Jeffery, Eleanor Drury, Daniel Mead, Mihir Kekre, Susana Campino, Magnus Manske, Victoria J. Cornelius, Bronwyn MacInnis, Kirk A. Rockett, Alistair Miles, Julian C. Rayner, Rick M. Fairhurst, Francois Nosten, Ric N. Price, Dominic P. Kwiatkowski

Global and Tropical Health

Research output: Contribution to journal › Article › peer-review

140 Citations (Scopus)

Abstract

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

Original language	English
Pages (from-to)	959-964
Number of pages	6
Journal	Nature Genetics
Volume	48
Issue number	8
DOIs	https://doi.org/10.1038/ng.3599
Publication status	Published - 1 Aug 2016

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Pearson, R. D., Amato, R., Auburn, S., Miotto, O., Almagro-Garcia, J., Amaratunga, C., Suon, S., Mao, S., Noviyanti, R., Trimarsanto, H., Marfurt, J., Anstey, N. M., WILLIAM, T., Boni, M. F., Dolecek, C., Tran, H. T., White, N. J., Michon, P., Siba, P., ... Kwiatkowski, D. P. (2016). Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nature Genetics, 48(8), 959-964. https://doi.org/10.1038/ng.3599

@article{43ba2bf9a5794c0d8cf9ee77049fd133,

title = "Genomic analysis of local variation and recent evolution in Plasmodium vivax",

abstract = "The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.",

author = "Pearson, {Richard D} and Roberto Amato and Sarah Auburn and Olivo Miotto and Jacob Almagro-Garcia and Chanaki Amaratunga and Seila Suon and Sivanna Mao and Rintis Noviyanti and Hidayat Trimarsanto and Jutta Marfurt and Anstey, {Nicholas M.} and Timothy WILLIAM and Boni, {MacIej F.} and Christiane Dolecek and Tran, {Hien Tinh} and White, {Nicholas J} and Pascal Michon and Peter Siba and Livingstone Tavul and Gabrielle Harrison and Barry, {Alyssa E.} and Ivo Mueller and Ferreira, {Marcelo U.} and Nadira Karunaweera and Milijaona Randrianarivelojosia and Qi Gao and Christina Hubbart and Lee Hart and Ben Jeffery and Eleanor Drury and Daniel Mead and Mihir Kekre and Susana Campino and Magnus Manske and Cornelius, {Victoria J.} and Bronwyn MacInnis and Rockett, {Kirk A.} and Alistair Miles and Rayner, {Julian C.} and Fairhurst, {Rick M.} and Francois Nosten and Price, {Ric N.} and Kwiatkowski, {Dominic P.}",

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doi = "10.1038/ng.3599",

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Pearson, RD, Amato, R, Auburn, S, Miotto, O, Almagro-Garcia, J, Amaratunga, C, Suon, S, Mao, S, Noviyanti, R, Trimarsanto, H, Marfurt, J, Anstey, NM, WILLIAM, T, Boni, MF, Dolecek, C, Tran, HT, White, NJ, Michon, P, Siba, P, Tavul, L, Harrison, G, Barry, AE, Mueller, I, Ferreira, MU, Karunaweera, N, Randrianarivelojosia, M, Gao, Q, Hubbart, C, Hart, L, Jeffery, B, Drury, E, Mead, D, Kekre, M, Campino, S, Manske, M, Cornelius, VJ, MacInnis, B, Rockett, KA, Miles, A, Rayner, JC, Fairhurst, RM, Nosten, F, Price, RN & Kwiatkowski, DP 2016, 'Genomic analysis of local variation and recent evolution in Plasmodium vivax', Nature Genetics, vol. 48, no. 8, pp. 959-964. https://doi.org/10.1038/ng.3599

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AU - Pearson, Richard D

AU - Amato, Roberto

AU - Auburn, Sarah

AU - Miotto, Olivo

AU - Almagro-Garcia, Jacob

AU - Amaratunga, Chanaki

AU - Suon, Seila

AU - Mao, Sivanna

AU - Noviyanti, Rintis

AU - Trimarsanto, Hidayat

AU - Marfurt, Jutta

AU - Anstey, Nicholas M.

AU - WILLIAM, Timothy

AU - Boni, MacIej F.

AU - Dolecek, Christiane

AU - Tran, Hien Tinh

AU - White, Nicholas J

AU - Michon, Pascal

AU - Siba, Peter

AU - Tavul, Livingstone

AU - Harrison, Gabrielle

AU - Barry, Alyssa E.

AU - Mueller, Ivo

AU - Ferreira, Marcelo U.

AU - Karunaweera, Nadira

AU - Randrianarivelojosia, Milijaona

AU - Gao, Qi

AU - Hubbart, Christina

AU - Hart, Lee

AU - Jeffery, Ben

AU - Drury, Eleanor

AU - Mead, Daniel

AU - Kekre, Mihir

AU - Campino, Susana

AU - Manske, Magnus

AU - Cornelius, Victoria J.

AU - MacInnis, Bronwyn

AU - Rockett, Kirk A.

AU - Miles, Alistair

AU - Rayner, Julian C.

AU - Fairhurst, Rick M.

AU - Nosten, Francois

AU - Price, Ric N.

AU - Kwiatkowski, Dominic P.

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AB - The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

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DO - 10.1038/ng.3599

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SN - 1061-4036

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SP - 959

EP - 964

JO - Nature Genetics

JF - Nature Genetics

IS - 8

ER -

Genomic analysis of local variation and recent evolution in Plasmodium vivax

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