Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health.

Autor:	Aranda-Díaz A; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA.; Chan Zuckerberg Biohub, San Francisco, California, USA., Vickers EN; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Murie K; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Palmer B; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Hathaway N; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Gerlovina I; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Boene S; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique., Garcia-Ulloa M; ISGlobal, Barcelona, Spain., Cisteró P; ISGlobal, Barcelona, Spain., Katairo T; Infectious Diseases Research Collaboration, Kampala, Uganda., Semakuba FD; Infectious Diseases Research Collaboration, Kampala, Uganda., Nsengimaana B; Infectious Diseases Research Collaboration, Kampala, Uganda., Gwarinda H; Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre of Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa., García-Fernández C; ISGlobal, Barcelona, Spain., Da Silva C; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique., Datta D; ISGlobal, Barcelona, Spain., Kiyaga S; Infectious Diseases Research Collaboration, Kampala, Uganda.; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda., Wiringilimaana I; Infectious Diseases Research Collaboration, Kampala, Uganda., Fekele SM; Ethiopian Public Health Institute, Addis Ababa, Ethiopia.; Department of Environment and Genetics, La Trobe University, Melbourne, Australia., Parr JB; Division of Infectious Diseases, University of North Carolina at Chapel Hill, North Carolina, USA., Conrad M; Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Raman J; Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre of Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.; Wits Research Institute for Malaria, University of Witwatersrand, Johannesburg, South Africa.; University of Pretoria Institute for Sustainable Malaria Control (UPISMC), University of Pretoria, Pretoria, South Africa., Tukwasibwe S; Infectious Diseases Research Collaboration, Kampala, Uganda., Ssewanyana I; Infectious Diseases Research Collaboration, Kampala, Uganda., Rovira-Vallbona E; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique., Tato CM; Chan Zuckerberg Biohub, San Francisco, California, USA., Briggs J; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA., Mayor A; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.; ISGlobal, Barcelona, Spain.; Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain.; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique., Greenhouse B; EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 25. Date of Electronic Publication: 2024 Aug 25.
DOI:	10.1101/2024.08.22.609145
Abstrakt:	Targeted amplicon sequencing is a powerful and efficient tool to interrogate the P. falciparum genome and generate actionable data from infections to complement traditional malaria epidemiology. For maximum impact, genomic tools should be multi-purpose, robust, sensitive and reproducible. We developed, characterized, and implemented MAD 4 HatTeR, an amplicon sequencing panel based on Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing, along with a bioinformatic pipeline for data analysis. MAD 4 HatTeR targets 165 highly diverse loci, focusing on multiallelic microhaplotypes; key markers for drug and diagnostic resistance, including duplications and deletions; and csp and potential vaccine targets. In addition, it can detect non- falciparum Plasmodium species. We used laboratory control and field sample data to demonstrate the high sensitivity and robustness of the panel. The successful implementation of this method in five laboratories, including three in malaria-endemic African countries, showcases its feasibility in generating reproducible data across laboratories. Finally, we introduce an analytical approach to detect gene duplications and deletions from amplicon sequencing data. MAD 4 HatTeR is thus a powerful research tool and a robust resource for malaria public health surveillance and control. Competing Interests: J.B.P. reports research support from Gilead Sciences, non-financial Support from Abbott Laboratories, and consulting for Zymeron Corporation, all outside the scope of the current work. All other authors report no potential conflicts of interest.
Databáze:	MEDLINE
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