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Get Free AccessTraditionally, 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.
Hidayat Trimarsanto, Roberto Amato, Richard D. Pearson, Edwin Sutanto, Rintis Noviyanti, Leily Trianty, Jutta Marfurt, Zuleima Pava, Diego F. Echeverry, Tatiana M. Lopera-Mesa, Lidia Madeline Montenegro, Alberto Tobón-Castaño, Matthew J. Grigg, Bridget E. Barber, Timothy William, Nicholas M. Anstey, Sisay Getachew, Beyene Petros, Abraham Aseffa, Ashenafi Assefa, Ghulam Rahim Awab, Nguyen Hoang Chau, Tran Tinh Hien, Mohammad Shafiul Alam, Wasif Ali Khan, Benedikt Ley, Kamala Thriemer, Sonam Wangchuck, Yaghoob Hamedi, Ishag Adam, Yaobao Liu, Qi Gao, Kanlaya Sriprawat, Marcelo U. Ferreira, Moses Laman, Alyssa E. Barry, Ivo Müeller, Marcus Lacerda, Alejandro Llanos‐Cuentas, Srivicha Krudsood, Chanthap Lon, Rezika Mohammed, Daniel Yilma, Dhélio B. Pereira, Fe Esperanza Espino, Cindy S. Chu, Iván Darío Vélez, Chayadol Namaik-larp, María Fernanda Villegas, Justin A. Green, Gavin Koh, Julian C. Rayner, Eleanor Drury, Sónia Gonçalves, Victoria J. Simpson, Olivo Miotto, Alistair Miles, Sir Nicholas White, François Nosten, Dominic Kwiatkowski, Ric N. Price, Sarah Auburn (2022). A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria. Communications Biology, 5(1), DOI: 10.1038/s42003-022-04352-2.
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Type
Article
Year
2022
Authors
62
Datasets
0
Total Files
0
Language
English
Journal
Communications Biology
DOI
10.1038/s42003-022-04352-2
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