Genomic analysis of local variation and recent evolution in Plasmodium vivax

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samp...

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Main Authors:	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, Hien, Tinh Tran, 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
Format:	Online
Language:	English
Published:	2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966634/

id	pubmed-4966634
recordtype	oai_dc
spelling	pubmed-49666342016-12-27 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 Hien, Tinh Tran 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 Article The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 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 novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination. 2016-06-27 2016-08 /pmc/articles/PMC4966634/ /pubmed/27348299 http://dx.doi.org/10.1038/ng.3599 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	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 Hien, Tinh Tran 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
spellingShingle	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 Hien, Tinh Tran 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
author_facet	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 Hien, Tinh Tran 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
author_sort	Pearson, Richard D
title	Genomic analysis of local variation and recent evolution in Plasmodium vivax
title_short	Genomic analysis of local variation and recent evolution in Plasmodium vivax
title_full	Genomic analysis of local variation and recent evolution in Plasmodium vivax
title_fullStr	Genomic analysis of local variation and recent evolution in Plasmodium vivax
title_full_unstemmed	Genomic analysis of local variation and recent evolution in Plasmodium vivax
title_sort	genomic analysis of local variation and recent evolution in plasmodium vivax
description	The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 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 novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination.
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966634/
_version_	1613617836312231936

Genomic analysis of local variation and recent evolution in Plasmodium vivax

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