Genomic analysis of local variation and recent evolution in Plasmodium vivax
© 2016 Nature America, Inc. All rights reserved. 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 perfo...
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th-mahidol.429472019-03-14T15:03:59Z 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 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 Wellcome Trust Sanger Institute Wellcome Trust Centre for Human Genetics Menzies School of Health Research Mahidol University National Institute of Allergy and Infectious Diseases National Centre for Parasitology, Entomology and Malaria Control Sampov Meas Referral Hospital Eijkman Institute for Molecular Biology Queen Elizabeth Hospital Oxford University Clinical Research Unit Papua New Guinea Institute of Medical Research Divine Word University Walter and Eliza Hall Institute of Medical Research University of Melbourne Universidade de Sao Paulo - USP University of Colombo Faculty of Medicine Institut Pasteur de Madagascar Ministry of Health of People's Republic of China Nuffield Department of Clinical Medicine Biochemistry, Genetics and Molecular Biology © 2016 Nature America, Inc. All rights reserved. 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. 2018-12-11T02:11:34Z 2019-03-14T08:03:59Z 2018-12-11T02:11:34Z 2019-03-14T08:03:59Z 2016-08-01 Article Nature Genetics. Vol.48, No.8 (2016), 959-964 10.1038/ng.3599 15461718 10614036 2-s2.0-84971401229 https://repository.li.mahidol.ac.th/handle/123456789/42947 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84971401229&origin=inward |
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Biochemistry, Genetics and Molecular Biology 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 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 Genomic analysis of local variation and recent evolution in Plasmodium vivax |
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© 2016 Nature America, Inc. All rights reserved. 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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Wellcome Trust Sanger Institute |
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Wellcome Trust Sanger Institute 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 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 |
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Article |
author |
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 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 |
author_sort |
Richard D. Pearson |
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 |
publishDate |
2018 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/42947 |
_version_ |
1763494322651529216 |