Nueva Publicación de nuestro investigador Alejandro Llanos

Revista:Communications Biology SJR:2.26  Q:1

Año:2022

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

Hidayat Trimarsanto 1 2Roberto Amato 3Richard D Pearson 3Edwin Sutanto 2 4Rintis Noviyanti 2Leily Trianty 2Jutta Marfurt 1Zuleima Pava 1Diego F Echeverry 5 6 7Tatiana M Lopera-Mesa 8Lidia M Montenegro 8Alberto Tobón-Castaño 8Matthew J Grigg 1 9Bridget Barber 1 9Timothy William 9 10Nicholas M Anstey 1Sisay Getachew 11 12Beyene Petros 11Abraham Aseffa 12Ashenafi Assefa 13Awab G Rahim 14 15Nguyen H Chau 16Tran T Hien 16Mohammad S Alam 17Wasif A Khan 17Benedikt Ley 1Kamala Thriemer 1Sonam Wangchuck 18Yaghoob Hamedi 19Ishag Adam 20Yaobao Liu 21 22Qi Gao 21Kanlaya Sriprawat 23Marcelo U Ferreira 24 25Moses Laman 26Alyssa Barry 27 28 29Ivo Mueller 28 30Marcus V G Lacerda 31 32Alejandro Llanos-Cuentas 33Srivicha Krudsood 34Chanthap Lon 35Rezika Mohammed 36Daniel Yilma 37Dhelio B Pereira 38Fe E J Espino 39Cindy S Chu 14 23Iván D Vélez 8Chayadol Namaik-Larp 40Maria F Villegas 41Justin A Green 42Gavin Koh 42Julian C Rayner 3 43Eleanor Drury 3Sónia Gonçalves 3Victoria Simpson 3Olivo Miotto 3 14Alistair Miles 3Nicholas J White 14 44Francois Nosten 23 44Dominic P Kwiatkowski 3Ric N Price 1 14 44Sarah Auburn 45 46 47

Affiliations

  1. Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
  2. Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
  3. Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
  4. Exeins Health Initiative, Jakarta, Indonesia.
  5. International Training and Medical Research Center (CIDEIM), Cali, Colombia.
  6. Departamento de Microbiología, Universidad del Valle, Cali, Colombia.
  7. Universidad Icesi, Cali, Colombia.
  8. Malaria Group, Universidad de Antioquia, Medellin, Colombia.
  9. Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia.
  10. Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia.
  11. College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
  12. Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
  13. Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
  14. Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
  15. Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan.
  16. Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
  17. Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh.
  18. Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan.
  19. Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran.
  20. Faculty of Medicine, University of Khartoum, Khartoum, Sudan.
  21. National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.
  22. School of Public Health, Nanjing Medical University, Nanjing, China.
  23. Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
  24. Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
  25. Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal.
  26. Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea.
  27. Deakin University, Victoria, Australia.
  28. Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.
  29. Department of Medical Biology, The University of Melbourne, Victoria, Australia.
  30. Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.
  31. Fundação de Medicina Tropical, Manaus, Brazil.
  32. Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil.
  33. Universidad Peruana Cayetano Heredia, Lima, Peru.
  34. Mahidol University, Bangkok, Thailand.
  35. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
  36. 36University of Gondar, Gondar, Ethiopia.
  37. Jimma University, Jimma, Ethiopia.
  38. Centro de Pesquisa em Medicina Tropical, Porto Velho, Brazil.
  39. Research Institute for Tropical Medicine, Manilla, Philippines.
  40. Umphang Hospital, Tak, Thailand.
  41. Centro de Investigaciones Clinicas, Cali, Colombia.
  42. GlaxoSmithKline, Brentford, UK.
  43. Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
  44. Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  45. Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia. Esta dirección de correo electrónico está siendo protegida contra los robots de spam. Necesita tener JavaScript habilitado para poder verlo..
  46. Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand. Esta dirección de correo electrónico está siendo protegida contra los robots de spam. Necesita tener JavaScript habilitado para poder verlo..
  47. Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK. Esta dirección de correo electrónico está siendo protegida contra los robots de spam. Necesita tener JavaScript habilitado para poder verlo..

PMID: 36564617   PMCID: PMC9789135   DOI: 10.1038/s42003-022-04352-2

Abstract

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.

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Fig. 1. Overview of the sample processing and marker selection approaches. 

Hexagons reflect datasets, rectangles reflect processes, triangles reflect SNP sets, ovals reflect results, and the diamond reflects the web-based classifier application. The BR38 Broad barcode reflects 38 assayable SNPs of the 42 Broad SNPs. The GEO33 set reflects the high-performance SNPs derived from the HFST approach with FST threshold of 0.9. The GEO50 set reflects the high-performance SNPs from the HFST approach with threshold FST of 0.95. The GEO55 set reflects the SNPs selected by the Decision Tree approach.