A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

Detalhes bibliográficos
Autor(a) principal: Trimarsanto, Hidayat
Data de Publicação: 2022
Outros Autores: Amato, Roberto, Pearson, Richard D., Sutanto, Edwin, Noviyanti, Rintis, Trianty, Leily, Marfurt, Jutta, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia M., Tobón-Castaño, Alberto, Grigg, Matthew J., Barber, Bridget, William, Timothy, Anstey, Nicholas M., Getachew, Sisay, Petros, Beyene, Aseffa, Abraham, Assefa, Ashenafi, Rahim, Awab G., Chau, Nguyen H., Hien, Tran T., Alam, Mohammad S., Khan, Wasif A., Ley, Benedikt, Thriemer, Kamala, Wangchuck, Sonam, Hamedi, Yaghoob, Adam, Ishag, Liu, Yaobao, Gao, Qi, Sriprawat, Kanlaya, Ferreira, Marcelo U., Laman, Moses, Barry, Alyssa, Mueller, Ivo, Lacerda, Marcus V.G., Llanos-Cuentas, Alejandro, Krudsood, Srivicha, Lon, Chanthap, Mohammed, Rezika, Yilma, Daniel, Pereira, Dhelio B., Espino, Fe E.J., Chu, Cindy S., Vélez, Iván D., Namaik-larp, Chayadol, Villegas, Maria F., Green, Justin A.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/148961
Resumo: Funding Information: We would like to thank the patients who contributed their samples to the study, and the health workers and field teams who assisted with the sample collections. We also thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contributions. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research was funded in part by the Wellcome Trust (Senior Fellowship in Clinical Science awarded to R.N.P., 200909). The research was also funded in part by the Australian Department of Foreign Affairs and Trade (TDCRRI 72904), the Australian National Health and Medical Research Council (NHMRC) (APP2001083 awarded to S.A.), and the Bill and Melinda Gates Foundation (OPP1164105). H.T. was supported by a Charles Darwin University International PhD Scholarship (CDIPS). The patient sampling and metadata collection was funded by the Asia-Pacific Malaria Elimination Network (108-07), the Malaysian Ministry of Health (BP00500420), and the NHMRC (1037304 and 1045156; Fellowships to N.M.A. [1042072 and 1135820], B.E.B. [1088738] and M.J.G. [1074795]). M.J.G was also supported by a ‘Hot North’ Earth Career Fellowship (1131932). M.U.F is supported by a senior researcher scholarship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. The whole genome sequencing component of the study was supported by grants from the Medical Research Council and UK Department for International Development (M006212) and the Wellcome Trust (204911) awarded to D.P.K., and a Wellcome Trust grant (206194/Z/17/Z) awarded to D.P.K. and J.C.R. This work was supported by the Australian Centre for Research Excellence on Malaria Elimination (ACREME), funded by the NHMRC (APP 1134989). Publisher Copyright: © 2022, The Author(s).
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spelling A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malariaPlasmodium vivaxbarcodeMalaria/epidemiologySNPsRA0421 Public health. Hygiene. Preventive MedicineMedicine (miscellaneous)Biochemistry, Genetics and Molecular Biology(all)Agricultural and Biological Sciences(all)EpidemiologySDG 3 - Good Health and Well-beingSDG 1 - No PovertySDG 6 - Clean Water and SanitationFunding Information: We would like to thank the patients who contributed their samples to the study, and the health workers and field teams who assisted with the sample collections. We also thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contributions. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research was funded in part by the Wellcome Trust (Senior Fellowship in Clinical Science awarded to R.N.P., 200909). The research was also funded in part by the Australian Department of Foreign Affairs and Trade (TDCRRI 72904), the Australian National Health and Medical Research Council (NHMRC) (APP2001083 awarded to S.A.), and the Bill and Melinda Gates Foundation (OPP1164105). H.T. was supported by a Charles Darwin University International PhD Scholarship (CDIPS). The patient sampling and metadata collection was funded by the Asia-Pacific Malaria Elimination Network (108-07), the Malaysian Ministry of Health (BP00500420), and the NHMRC (1037304 and 1045156; Fellowships to N.M.A. [1042072 and 1135820], B.E.B. [1088738] and M.J.G. [1074795]). M.J.G was also supported by a ‘Hot North’ Earth Career Fellowship (1131932). M.U.F is supported by a senior researcher scholarship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. The whole genome sequencing component of the study was supported by grants from the Medical Research Council and UK Department for International Development (M006212) and the Wellcome Trust (204911) awarded to D.P.K., and a Wellcome Trust grant (206194/Z/17/Z) awarded to D.P.K. and J.C.R. This work was supported by the Australian Centre for Research Excellence on Malaria Elimination (ACREME), funded by the NHMRC (APP 1134989). Publisher Copyright: © 2022, The Author(s).Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection’s country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.Individual Health Care (IHC)Global Health and Tropical Medicine (GHTM)Universidade NOVA de LisboaInstituto de Higiene e Medicina Tropical (IHMT)RUNTrimarsanto, HidayatAmato, RobertoPearson, Richard D.Sutanto, EdwinNoviyanti, RintisTrianty, LeilyMarfurt, JuttaPava, ZuleimaEcheverry, Diego F.Lopera-Mesa, Tatiana M.Montenegro, Lidia M.Tobón-Castaño, AlbertoGrigg, Matthew J.Barber, BridgetWilliam, TimothyAnstey, Nicholas M.Getachew, SisayPetros, BeyeneAseffa, AbrahamAssefa, AshenafiRahim, Awab G.Chau, Nguyen H.Hien, Tran T.Alam, Mohammad S.Khan, Wasif A.Ley, BenediktThriemer, KamalaWangchuck, SonamHamedi, YaghoobAdam, IshagLiu, YaobaoGao, QiSriprawat, KanlayaFerreira, Marcelo U.Laman, MosesBarry, AlyssaMueller, IvoLacerda, Marcus V.G.Llanos-Cuentas, AlejandroKrudsood, SrivichaLon, ChanthapMohammed, RezikaYilma, DanielPereira, Dhelio B.Espino, Fe E.J.Chu, Cindy S.Vélez, Iván D.Namaik-larp, ChayadolVillegas, Maria F.Green, Justin A.2023-02-09T22:21:50Z2022-122022-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/148961eng2399-3642PURE: 50149914https://doi.org/10.1038/s42003-022-04352-2info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:30:43Zoai:run.unl.pt:10362/148961Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:53:34.027318Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
title A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
spellingShingle A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
Trimarsanto, Hidayat
Plasmodium vivax
barcode
Malaria/epidemiology
SNPs
RA0421 Public health. Hygiene. Preventive Medicine
Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Epidemiology
SDG 3 - Good Health and Well-being
SDG 1 - No Poverty
SDG 6 - Clean Water and Sanitation
title_short A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
title_full A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
title_fullStr A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
title_full_unstemmed A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
title_sort A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
author Trimarsanto, Hidayat
author_facet Trimarsanto, Hidayat
Amato, Roberto
Pearson, Richard D.
Sutanto, Edwin
Noviyanti, Rintis
Trianty, Leily
Marfurt, Jutta
Pava, Zuleima
Echeverry, Diego F.
Lopera-Mesa, Tatiana M.
Montenegro, Lidia M.
Tobón-Castaño, Alberto
Grigg, Matthew J.
Barber, Bridget
William, Timothy
Anstey, Nicholas M.
Getachew, Sisay
Petros, Beyene
Aseffa, Abraham
Assefa, Ashenafi
Rahim, Awab G.
Chau, Nguyen H.
Hien, Tran T.
Alam, Mohammad S.
Khan, Wasif A.
Ley, Benedikt
Thriemer, Kamala
Wangchuck, Sonam
Hamedi, Yaghoob
Adam, Ishag
Liu, Yaobao
Gao, Qi
Sriprawat, Kanlaya
Ferreira, Marcelo U.
Laman, Moses
Barry, Alyssa
Mueller, Ivo
Lacerda, Marcus V.G.
Llanos-Cuentas, Alejandro
Krudsood, Srivicha
Lon, Chanthap
Mohammed, Rezika
Yilma, Daniel
Pereira, Dhelio B.
Espino, Fe E.J.
Chu, Cindy S.
Vélez, Iván D.
Namaik-larp, Chayadol
Villegas, Maria F.
Green, Justin A.
author_role author
author2 Amato, Roberto
Pearson, Richard D.
Sutanto, Edwin
Noviyanti, Rintis
Trianty, Leily
Marfurt, Jutta
Pava, Zuleima
Echeverry, Diego F.
Lopera-Mesa, Tatiana M.
Montenegro, Lidia M.
Tobón-Castaño, Alberto
Grigg, Matthew J.
Barber, Bridget
William, Timothy
Anstey, Nicholas M.
Getachew, Sisay
Petros, Beyene
Aseffa, Abraham
Assefa, Ashenafi
Rahim, Awab G.
Chau, Nguyen H.
Hien, Tran T.
Alam, Mohammad S.
Khan, Wasif A.
Ley, Benedikt
Thriemer, Kamala
Wangchuck, Sonam
Hamedi, Yaghoob
Adam, Ishag
Liu, Yaobao
Gao, Qi
Sriprawat, Kanlaya
Ferreira, Marcelo U.
Laman, Moses
Barry, Alyssa
Mueller, Ivo
Lacerda, Marcus V.G.
Llanos-Cuentas, Alejandro
Krudsood, Srivicha
Lon, Chanthap
Mohammed, Rezika
Yilma, Daniel
Pereira, Dhelio B.
Espino, Fe E.J.
Chu, Cindy S.
Vélez, Iván D.
Namaik-larp, Chayadol
Villegas, Maria F.
Green, Justin A.
author2_role author
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author
author
author
author
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author
author
author
author
author
author
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dc.contributor.none.fl_str_mv Individual Health Care (IHC)
Global Health and Tropical Medicine (GHTM)
Universidade NOVA de Lisboa
Instituto de Higiene e Medicina Tropical (IHMT)
RUN
dc.contributor.author.fl_str_mv Trimarsanto, Hidayat
Amato, Roberto
Pearson, Richard D.
Sutanto, Edwin
Noviyanti, Rintis
Trianty, Leily
Marfurt, Jutta
Pava, Zuleima
Echeverry, Diego F.
Lopera-Mesa, Tatiana M.
Montenegro, Lidia M.
Tobón-Castaño, Alberto
Grigg, Matthew J.
Barber, Bridget
William, Timothy
Anstey, Nicholas M.
Getachew, Sisay
Petros, Beyene
Aseffa, Abraham
Assefa, Ashenafi
Rahim, Awab G.
Chau, Nguyen H.
Hien, Tran T.
Alam, Mohammad S.
Khan, Wasif A.
Ley, Benedikt
Thriemer, Kamala
Wangchuck, Sonam
Hamedi, Yaghoob
Adam, Ishag
Liu, Yaobao
Gao, Qi
Sriprawat, Kanlaya
Ferreira, Marcelo U.
Laman, Moses
Barry, Alyssa
Mueller, Ivo
Lacerda, Marcus V.G.
Llanos-Cuentas, Alejandro
Krudsood, Srivicha
Lon, Chanthap
Mohammed, Rezika
Yilma, Daniel
Pereira, Dhelio B.
Espino, Fe E.J.
Chu, Cindy S.
Vélez, Iván D.
Namaik-larp, Chayadol
Villegas, Maria F.
Green, Justin A.
dc.subject.por.fl_str_mv Plasmodium vivax
barcode
Malaria/epidemiology
SNPs
RA0421 Public health. Hygiene. Preventive Medicine
Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Epidemiology
SDG 3 - Good Health and Well-being
SDG 1 - No Poverty
SDG 6 - Clean Water and Sanitation
topic Plasmodium vivax
barcode
Malaria/epidemiology
SNPs
RA0421 Public health. Hygiene. Preventive Medicine
Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Epidemiology
SDG 3 - Good Health and Well-being
SDG 1 - No Poverty
SDG 6 - Clean Water and Sanitation
description Funding Information: We would like to thank the patients who contributed their samples to the study, and the health workers and field teams who assisted with the sample collections. We also thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contributions. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research was funded in part by the Wellcome Trust (Senior Fellowship in Clinical Science awarded to R.N.P., 200909). The research was also funded in part by the Australian Department of Foreign Affairs and Trade (TDCRRI 72904), the Australian National Health and Medical Research Council (NHMRC) (APP2001083 awarded to S.A.), and the Bill and Melinda Gates Foundation (OPP1164105). H.T. was supported by a Charles Darwin University International PhD Scholarship (CDIPS). The patient sampling and metadata collection was funded by the Asia-Pacific Malaria Elimination Network (108-07), the Malaysian Ministry of Health (BP00500420), and the NHMRC (1037304 and 1045156; Fellowships to N.M.A. [1042072 and 1135820], B.E.B. [1088738] and M.J.G. [1074795]). M.J.G was also supported by a ‘Hot North’ Earth Career Fellowship (1131932). M.U.F is supported by a senior researcher scholarship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. The whole genome sequencing component of the study was supported by grants from the Medical Research Council and UK Department for International Development (M006212) and the Wellcome Trust (204911) awarded to D.P.K., and a Wellcome Trust grant (206194/Z/17/Z) awarded to D.P.K. and J.C.R. This work was supported by the Australian Centre for Research Excellence on Malaria Elimination (ACREME), funded by the NHMRC (APP 1134989). Publisher Copyright: © 2022, The Author(s).
publishDate 2022
dc.date.none.fl_str_mv 2022-12
2022-12-01T00:00:00Z
2023-02-09T22:21:50Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
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format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/148961
url http://hdl.handle.net/10362/148961
dc.language.iso.fl_str_mv eng
language eng
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PURE: 50149914
https://doi.org/10.1038/s42003-022-04352-2
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