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 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

Research output: Contribution to journalArticle

61 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 languageEnglish (US)
Pages (from-to)959-964
Number of pages6
JournalNature Genetics
Volume48
Issue number8
DOIs
StatePublished - Aug 1 2016

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Plasmodium vivax
Malaria
Parasites
Genome
Population
High-Throughput Nucleotide Sequencing
Inbreeding
Genetic Structures
Infection
Drug Resistance
Single Nucleotide Polymorphism
Clone Cells
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Pearson, R. D., Amato, R., Auburn, S., Miotto, O., Almagro-Garcia, J., Amaratunga, C., ... 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
Pearson, Richard D. ; Amato, Roberto ; Auburn, Sarah ; Miotto, Olivo ; Almagro-Garcia, Jacob ; Amaratunga, Chanaki ; Suon, Seila ; Mao, Sivanna ; Noviyanti, Rintis ; Trimarsanto, Hidayat ; Marfurt, Jutta ; Anstey, Nicholas M. ; William, Timothy ; Boni, MacIej F. ; Dolecek, Christiane ; Tran, Hien Tinh ; White, Nicholas J. ; Michon, Pascal ; Siba, Peter ; Tavul, Livingstone ; Harrison, Gabrielle ; Barry, Alyssa ; Mueller, Ivo ; Ferreira, Marcelo U. ; Karunaweera, Nadira ; Randrianarivelojosia, Milijaona ; Gao, Qi ; Hubbart, Christina ; Hart, Lee ; Jeffery, Ben ; Drury, Eleanor ; Mead, Daniel ; Kekre, Mihir ; Campino, Susana ; Manske, Magnus ; Cornelius, Victoria J. ; MacInnis, Bronwyn ; Rockett, Kirk A. ; Miles, Alistair ; Rayner, Julian C. ; Fairhurst, Rick M. ; Nosten, Francois ; Price, Ric N. ; Kwiatkowski, Dominic P. / Genomic analysis of local variation and recent evolution in Plasmodium vivax. In: Nature Genetics. 2016 ; Vol. 48, No. 8. pp. 959-964.
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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, A, 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

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

In: Nature Genetics, Vol. 48, No. 8, 01.08.2016, p. 959-964.

Research output: Contribution to journalArticle

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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.

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AU - White, Nicholas J.

AU - Michon, Pascal

AU - Siba, Peter

AU - Tavul, Livingstone

AU - Harrison, Gabrielle

AU - Barry, Alyssa

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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Pearson RD, Amato R, Auburn S, Miotto O, Almagro-Garcia J, Amaratunga C et al. Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nature Genetics. 2016 Aug 1;48(8):959-964. https://doi.org/10.1038/ng.3599