Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance

被引：0

作者：

Ngwana-Joseph, Gabrielle C. ^{[1
]}

Phelan, Jody E. ^{[1
]}

Manko, Emilia ^{[1
]}

Dombrowski, Jamille G. ^{[1
,2
]}

Santos, Simone da Silva

Suarez-Mutis, Martha ^{[3
]}

Velez-Tobon, Gabriel ^{[4
]}

Tobon Castano, Alberto ^{[4
]}

Machado, Ricardo Luiz Dantas ^{[5
]}

Marinho, Claudio R. F. ^{[2
]}

Nolder, Debbie ^{[6
]}

Nosten, Francois ^{[7
,8
]}

Sutherland, Colin J. ^{[1
,6
]}

Campino, Susana ^{[1
]}

Clark, Taane G. ^{[1
,9
]}

机构：

[1] London Sch Hyg & Trop Med, Fac Infect & Trop Dis, Dept Infect Biol, London, England

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

[3] Oswaldo Cruz Fdn FIOCRUZ, Rio De Janeiro, Brazil

[4] Univ Antioquia, Fac Med, Grp Malaria, Antioquia, Colombia

[5] Univ Fed Fluminense, Ctr Invest Microrganismos CIM, Dept Microbiol & Parasitol, Niteroi, Brazil

[6] UK Hlth Secur Agcy, London Sch Hyg & Trop Med, Malaria Reference Lab, London, England

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

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

[9] London Sch Hyg & Trop Med, Fac Epidemiol & Populat Hlth, London, England

来源：

NATURE COMMUNICATIONS | 2024年 / 15卷 / 01期

基金：

巴西圣保罗研究基金会; 英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会; 英国惠康基金;

关键词：

SINGLE-NUCLEOTIDE POLYMORPHISMS; POSITIVE SELECTION; P; FALCIPARUM; R PACKAGE; EX-VIVO; CHLOROQUINE; PAPUA; ASSOCIATION; PIPERAQUINE; FRAMEWORK;

D O I：

10.1038/s41467-024-54964-x

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Increasing reports of chloroquine resistance (CQR) in Plasmodium vivax endemic regions have led to several countries, including Indonesia, to adopt dihydroarteminsin-piperaquine instead. However, the molecular drivers of CQR remain unclear. Using a genome-wide approach, we perform a genomic analysis of 1534 P. vivax isolates across 29 endemic countries, detailing population structure, patterns of relatedness, selection, and resistance profiling, providing insights into potential drivers of CQR. Selective sweeps in a locus proximal to pvmdr1, a putative marker for CQR, along with transcriptional regulation genes, distinguish isolates from Indonesia from those in regions where chloroquine remains highly effective. In 106 isolates from Indonesian Papua, the epicentre of CQR, we observe an increasing prevalence of novel SNPs in the candidate resistance gene pvmrp1 since the introduction of dihydroartemisinin-piperaquine. Overall, we provide novel markers for resistance surveillance, supported by evidence of regions under recent directional selection and temporal analysis in this continually evolving parasite.

引用

页数：13

共 81 条

[1] Accurate structure prediction of biomolecular interactions with AlphaFold 3 [J].

Abramson, Josh ;

Adler, Jonas ;

Dunger, Jack ;

Evans, Richard ;

Green, Tim ;

Pritzel, Alexander ;

Ronneberger, Olaf ;

Willmore, Lindsay ;

Ballard, Andrew J. ;

Bambrick, Joshua ;

Bodenstein, Sebastian W. ;

Evans, David A. ;

Hung, Chia-Chun ;

O'Neill, Michael ;

Reiman, David ;

Tunyasuvunakool, Kathryn ;

Wu, Zachary ;

Zemgulyte, Akvile ;

Arvaniti, Eirini ;

Beattie, Charles ;

Bertolli, Ottavia ;

Bridgland, Alex ;

Cherepanov, Alexey ;

Congreve, Miles ;

Cowen-Rivers, Alexander I. ;

Cowie, Andrew ;

Figurnov, Michael ;

Fuchs, Fabian B. ;

Gladman, Hannah ;

Jain, Rishub ;

Khan, Yousuf A. ;

Low, Caroline M. R. ;

Perlin, Kuba ;

Potapenko, Anna ;

Savy, Pascal ;

Singh, Sukhdeep ;

Stecula, Adrian ;

Thillaisundaram, Ashok ;

Tong, Catherine ;

Yakneen, Sergei ;

Zhong, Ellen D. ;

Zielinski, Michal ;

Zidek, Augustin ;

Bapst, Victor ;

Kohli, Pushmeet ;

Jaderberg, Max ;

Hassabis, Demis ;

Jumper, John M. .

NATURE, 2024, 630 (8016) :493-500

[2] Enhancements to the ADMIXTURE algorithm for individual ancestry estimation [J].

Alexander, David H. ;

Lange, Kenneth .

BMC BIOINFORMATICS, 2011, 12

[3] Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1 [J].

Amambua-Ngwa, Alfred ;

Button-Simons, Katrina A. A. ;

Li, Xue ;

Kumar, Sudhir ;

Brenneman, Katelyn Vendrely ;

Ferrari, Marco ;

Checkley, Lisa A. A. ;

Haile, Meseret T. T. ;

Shoue, Douglas A. A. ;

McDew-White, Marina ;

Tindall, Sarah M. M. ;

Reyes, Ann ;

Delgado, Elizabeth ;

Dalhoff, Haley ;

Larbalestier, James K. K. ;

Amato, Roberto ;

Pearson, Richard D. D. ;

Taylor, Alexander B. B. ;

Nosten, Francois H. ;

D'Alessandro, Umberto ;

Kwiatkowski, Dominic ;

Cheeseman, Ian H. H. ;

Kappe, Stefan H. I. ;

Avery, Simon V. V. ;

Conway, David J. J. ;

Vaughan, Ashley M. M. ;

Ferdig, Michael T. T. ;

Anderson, Timothy J. C. .

NATURE MICROBIOLOGY, 2023, 8 (07) :1213-+

[4] Efficacy and safety of dihydroartemisinin-piperaquine for the treatment of uncomplicated Plasmodium falciparum and Plasmodium vivax malaria in Papua and Sumatra, Indonesia [J].

Asih, Puji B. S. ;

Rozi, Ismail E. ;

Dewayanti, Farahana K. ;

Wangsamuda, Suradi ;

Zulfah, Syarifah ;

Robaha, Marthen ;

Hutahaean, Jonny ;

Anggraeni, Nancy D. ;

Kusumaningsih, Marti ;

Mulyani, Pranti S. ;

Sariwati, Elvieda ;

Basri, Herdiana H. ;

Bustos, Maria Dorina G. ;

Syafruddin, Din .

MALARIA JOURNAL, 2022, 21 (01)

[5] Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics [J].

Auburn, Sarah ;

Benavente, Ernest D. ;

Miotto, Olivo ;

Pearson, Richard D. ;

Amato, Roberto ;

Grigg, Matthew J. ;

Barber, Bridget E. ;

William, Timothy ;

Handayuni, Irene ;

Marfurt, Jutta ;

Trimarsanto, Hidayat ;

Noviyanti, Rintis ;

Sriprawat, Kanlaya ;

Nosten, Francois ;

Campino, Susana ;

Clark, Taane G. ;

Anstey, Nicholas M. ;

Kwiatkowski, Dominic P. ;

Price, Ric N. .

NATURE COMMUNICATIONS, 2018, 9

[6]

Auburn Sarah, 2016, Wellcome Open Res, V1, P4, DOI 10.12688/wellcomeopenres.9876.1

[7] PlasmoDB: a functional genomic database for malaria parasites [J].

Aurrecoechea, Cristina ;

Brestelli, John ;

Brunk, Brian P. ;

Dommer, Jennifer ;

Fischer, Steve ;

Gajria, Bindu ;

Gao, Xin ;

Gingle, Alan ;

Grant, Greg ;

Harb, Omar S. ;

Heiges, Mark ;

Innamorato, Frank ;

Iodice, John ;

Kissinger, Jessica C. ;

Kraemer, Eileen ;

Li, Wei ;

Miller, John A. ;

Nayak, Vishal ;

Pennington, Cary ;

Pinney, Deborah F. ;

Roos, David S. ;

Ross, Chris ;

Stoeckert, Christian J., Jr. ;

Treatman, Charles ;

Wang, Haiming .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D539-D543

[8] Dihydroartemisinin-piperaquine versus chloroquine to treat vivax malaria in Afghanistan: an open randomized, non-inferiority, trial [J].

Awab, Ghulam Rahim ;

Pukrittayakamee, Sasithon ;

Imwong, Mallika ;

Dondorp, Arjen M. ;

Woodrow, Charles J. ;

Lee, Sue Jean ;

Day, Nicholas P. J. ;

Singhasivanon, Pratap ;

White, Nicholas J. ;

Kaker, Faizullah .

MALARIA JOURNAL, 2010, 9

[9] Longitudinal surveillance of drug resistance in Plasmodium falciparum isolates from the China-Myanmar border reveals persistent circulation of multidrug resistant parasites [J].

Bai, Yao ;

Zhang, Jiaqi ;

Geng, Jinting ;

Xu, Shiling ;

Deng, Shuang ;

Zeng, Weilin ;

Wang, Zenglei ;

Mbenda, Huguette Gaelle Ngassa ;

Zhang, Jie ;

Li, Na ;

Wu, Yanrui ;

Li, Cuiying ;

Liu, Huae ;

Ruan, Yonghua ;

Cao, Yaming ;

Yang, Zhaoqing ;

Cui, Liwang .

INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE, 2018, 8 (02) :320-328

[10] Plasmodium vivax Resistance to Chloroquine in Madagascar: Clinical Efficacy and Polymorphisms in pvmdr1 and pvcrt-o Genes [J].

Barnadas, Celine ;

Ratsimbasoa, Arsene ;

Tichit, Magali ;

Bouchier, Christiane ;

Jahevitra, Martial ;

Picot, Stephane ;

Menard, Didier .

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2008, 52 (12) :4233-4240

← 1 2 3 4 5 6 7 8 9 →