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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Zhao H, Pi L, Zhao L, Qin Y, Zeng W, Xiang Z, Yang Q, Pan M, Li X, Zou C, Chen X, Zhao W, Lu Y, Wu Y, Duan M, Wang X, Li X, Mazier D, Huang Y, Yang Z. First Detection in West Africa of a Mutation That May Contribute to Artemisinin Resistance Plasmodium falciparum. Front Genet 2021; 12:701750. [PMID: 34691144 PMCID: PMC8531651 DOI: 10.3389/fgene.2021.701750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The spread of drug resistance has seriously impacted the effective treatment of infection with the malaria parasite, Plasmodium falciparum. Continuous monitoring of molecular marker polymorphisms associated with drug resistance in parasites is essential for malaria control and elimination efforts. Our study describes mutations observed in the resistance genes Pfkelch13, Pfcrt, and Pfmdr1 in imported malaria and identifies additional potential drug resistance-associated molecular markers. Methods: Chinese patients infected in Africa with P. falciparum were treated with intravenous (IV) injections of artesunate 240–360 mg for 3–5 days while hospitalized and treated with oral dihydroartemisinin-piperaquine (DHP) for 3 days after hospital discharge. Blood samples were collected and PCR sequencing performed on genes Pfkelch13, Pfcrt, and Pfmdr1 from all isolates. Results: We analyzed a total of 225 patients from Guangxi, China with P. falciparum malaria acquired in Africa between 2016 and 2018. All patients were cured completely after treatment. The F446I mutation of the Pfkelch13 gene was detected for the first time from samples of West African P. falciparum, with a frequency of 1.0%. Five haplotypes of Pfcrt that encode residues 72–76 were found, with the wild-type CVMNK sequence predominating (80.8% of samples), suggesting that the parasites might be chloroquine sensitive. For Pfmdr1, N86Y (13.1%) and Y184F (58.8%) were the most prevalent, suggesting that artemether-lumefantrine may not, in general, be a suitable treatment for the group. Conclusions: For the first time, this study detected the F446I mutation of the Pfkelch13 gene from Africa parasites that lacked clinical evidence of resistance. This study provides the latest data for molecular marker surveillance related to antimalarial drug resistance genes Pfkelch13, Pfcrt, and Pfmdr1 imported from Africa, in Guangxi, China from Chinese migrate workers. Clinical Trial Registration: ChiCTROPC17013106.
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Affiliation(s)
- Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liang Pi
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Luyi Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yucheng Qin
- Shanglin County People's Hospital, Guangxi, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Maohua Pan
- Shanglin County People's Hospital, Guangxi, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Chunyan Zou
- Guangxi Zhuang Autonomous Region People's Hospital, Nanning, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Wei Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yuxin Lu
- Shanglin County People's Hospital, Guangxi, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Dominique Mazier
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, CIMI, Paris, France
| | - Yaming Huang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
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