Genomic analysis of local variation and recent evolution in Plasmodium vivax

被引：141

作者：

Pearson, Richard D. ^{[1
,2
]}

Amato, Roberto ^{[1
,2
]}

Auburn, Sarah ^{[3
,4
]}

Miotto, Olivo ^{[1
,2
,5
]}

Almagro-Garcia, Jacob ^{[2
]}

Amaratunga, Chanaki ^{[6
]}

Suon, Seila ^{[7
]}

Mao, Sivanna ^{[8
]}

Noviyanti, Rintis ^{[9
]}

Trimarsanto, Hidayat ^{[9
]}

Marfurt, Jutta ^{[3
,4
]}

Anstey, Nicholas M. ^{[3
]}

William, Timothy ^{[10
,11
]}

Boni, Maciej F. ^{[12
]}

Dolecek, Christiane ^{[12
]}

Hien Tinh Tran ^{[12
]}

White, Nicholas J. ^{[5
]}

Michon, Pascal ^{[13
,14
]}

Siba, Peter ^{[13
]}

Tavul, Livingstone ^{[13
]}

Harrison, Gabrielle ^{[15
,16
]}

Barry, Alyssa ^{[15
,16
]}

Mueller, Ivo ^{[15
,16
]}

Ferreira, Marcelo U. ^{[17
]}

Karunaweera, Nadira ^{[18
]}

Randrianarivelojosia, Milijaona ^{[19
]}

Gao, Qi ^{[20
]}

Hubbart, Christina ^{[2
]}

Hart, Lee ^{[2
]}

Jeffery, Ben ^{[2
]}

Drury, Eleanor ^{[1
]}

Mead, Daniel ^{[1
]}

Kekre, Mihir ^{[1
]}

Campino, Susana ^{[1
]}

Manske, Magnus ^{[1
]}

Cornelius, Victoria J. ^{[1
,2
]}

MacInnis, Bronwyn ^{[1
]}

Rockett, Kirk A. ^{[1
,2
]}

Miles, Alistair ^{[1
,2
]}

Rayner, Julian C. ^{[1
]}

Fairhurst, Rick M.

Nosten, Francois ^{[21
,22
]}

Price, Ric N. ^{[3
,4
,22
]}

Kwiatkowski, Dominic P. ^{[1
,2
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge, England

[2] Wellcome Trust Ctr Human Genet, MRC Ctr Genom & Global Hlth, Oxford, England

[3] Menzies Sch Hlth Res, Global & Trop Hlth Div, Darwin, NT, Australia

[4] Charles Darwin Univ, Darwin, NT, Australia

[5] Mahidol Univ, Mahidol Oxford Trop Med Res Unit, Bangkok, Thailand

[6] NIAID, NIH, Rockville, MD USA

[7] Natl Ctr Parasitol Entomol & Malaria Control, Phnom Penh, Cambodia

[8] Sampov Meas Referral Hosp, Pursat, Cambodia

[9] Eijkman Inst Mol Biol, Jakarta, Indonesia

[10] Sabah Menzies Sch Hlth Res, Clin Res Unit, Infect Dis Soc, Kota Kinabalu, Sabah, Malaysia

[11] Queen Elizabeth Hosp, Clin Res Ctr, Kota Kinabalu, Sabah, Malaysia

[12] Univ Oxford, Clin Res Unit, Ho Chi Minh City, Vietnam

[13] Papua New Guinea Inst Med Res, Madang, Papua N Guinea

[14] Divine Word Univ, Fac Med & Hlth Sci, Madang, Papua N Guinea

[15] Walter & Eliza Hall Inst Med Res, Div Populat Hlth & Immun, Parkville, Vic, Australia

[16] Univ Melbourne, Dept Med Biol, Parkville, Vic, Australia

[17] Univ Sao Paulo, Inst Biomed Sci, Dept Parasitol, Sao Paulo, Brazil

[18] Univ Colombo, Fac Med, Dept Parasitol, Colombo, Sri Lanka

[19] Inst Pasteur Madagascar, Antananarivo, Madagascar

[20] Minist Hlth, Jiangsu Inst Parasit Dis, Key Lab Parasit Dis Control & Prevent, Prov Key Lab Parasite Mol Biol, Wuxi, Jiangsu, Peoples R China

[21] Mahidol Univ, Mahidol Oxford Trop Med Res Unit, Shoklo Malaria Res Unit, Fac Trop Med, Mae Sot, Thailand

[22] Univ Oxford, Nuffield Dept Med, Ctr Trop Med & Global Hlth, Oxford, England

来源：

NATURE GENETICS | 2016年 / 48卷 / 08期

基金：

英国医学研究理事会; 英国惠康基金; 美国国家卫生研究院;

关键词：

DRUG-RESISTANCE GENES; DNA-SEQUENCING DATA; DUFFY-BLOOD-GROUP; MALARIA; FALCIPARUM; DIVERSITY; CHLOROQUINE; INFECTIONS; REVEALS; POLYMORPHISMS;

D O I：

10.1038/ng.3599

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：959 / 964

页数：6

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