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Yi B, Zhang L, Yin J, Zhou S, Xia Z. 1-3-7 surveillance and response approach in malaria elimination: China's practice and global adaptions. Malar J 2023; 22:152. [PMID: 37161379 PMCID: PMC10169118 DOI: 10.1186/s12936-023-04580-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/28/2023] [Indexed: 05/11/2023] Open
Abstract
There has been a significant reduction in malaria morbidity and mortality worldwide from 2000 to 2019. However, the incidence and mortality increased again in 2020 due to the disruption to services during the COVID-19 pandemic. Surveillance to reduce the burden of malaria, eliminate the disease and prevent its retransmission is, therefore, crucial. The 1-3-7 approach proposed by China has played an important role in eliminating malaria, which has been internationally popularized and adopted in some countries to help eliminate malaria. This review summarizes the experience and lessons of 1-3-7 approach in China and its application in other malaria-endemic countries, so as to provide references for its role in eliminating malaria and preventing retransmission. This approach needs to be tailored and adapted according to the region condition, considering the completion, timeliness and limitation of case-based reactive surveillance and response. It is very important to popularize malaria knowledge, train staff, improve the capacity of health centres and monitor high-risk groups to improve the performance in eliminating settings. After all, remaining vigilance in detecting malaria cases and optimizing surveillance and response systems are critical to achieving and sustaining malaria elimination.
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Affiliation(s)
- Boyu Yi
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Li Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Jianhai Yin
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Shuisen Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Zhigui Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China.
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Hubbard A, Hemming-Schroeder E, Machani MG, Afrane Y, Yan G, Lo E, Janies D. Implementing landscape genetics in molecular epidemiology to determine drivers of vector-borne disease: A malaria case study. Mol Ecol 2023; 32:1848-1859. [PMID: 36645165 PMCID: PMC10694861 DOI: 10.1111/mec.16846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
This study employs landscape genetics to investigate the environmental drivers of a deadly vector-borne disease, malaria caused by Plasmodium falciparum, in a more spatially comprehensive manner than any previous work. With 1804 samples from 44 sites collected in western Kenya in 2012 and 2013, we performed resistance surface analysis to show that Lake Victoria acts as a barrier to transmission between areas north and south of the Winam Gulf. In addition, Mantel correlograms clearly showed significant correlations between genetic and geographic distance over short distances (less than 70 km). In both cases, we used an identity-by-state measure of relatedness tailored to find highly related individual parasites in order to focus on recent gene flow that is more relevant to disease transmission. To supplement these results, we performed conventional population genetics analyses, including Bayesian clustering methods and spatial ordination techniques. These analyses revealed some differentiation on the basis of geography and elevation and a cluster of genetic similarity in the lowlands north of the Winam Gulf of Lake Victoria. Taken as a whole, these results indicate low overall genetic differentiation in the Lake Victoria region, but with some separation of parasite populations north and south of the Winam Gulf that is explained by the presence of the lake as a geographic barrier to gene flow. We recommend similar landscape genetics analyses in future molecular epidemiology studies of vector-borne diseases to extend and contextualize the results of traditional population genetics.
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Affiliation(s)
- Alfred Hubbard
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina, Charlotte, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Elizabeth Hemming-Schroeder
- Department of Microbiology, Center for Vector-borne Infectious Diseases (CVID), Colorado State University, Fort Collins, Colorado, USA
| | | | - Yaw Afrane
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, USA
| | - Eugenia Lo
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina, Charlotte, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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Duan M, Bai Y, Deng S, Ruan Y, Zeng W, Li X, Wang X, Zhao W, Zhao H, Sun K, Zhu W, Wu Y, Miao J, Kyaw MP, Yang Z, Cui L. Different In Vitro Drug Susceptibility Profile of Plasmodium falciparum Isolates from Two Adjacent Areas of Northeast Myanmar and Molecular Markers for Drug Resistance. Trop Med Infect Dis 2022; 7:tropicalmed7120442. [PMID: 36548697 PMCID: PMC9782301 DOI: 10.3390/tropicalmed7120442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The Greater Mekong Subregion (GMS) is the epicenter of antimalarial drug resistance. We determined in vitro susceptibilities to 11 drugs of culture-adapted Plasmodium falciparum isolates from adjacent areas (Laiza and Muse) along the China−Myanmar border. Parasites from this region were highly resistant to chloroquine and pyrimethamine but relatively sensitive to other antimalarial drugs. Consistently, the Dd2-like pfcrt mutations were fixed or almost fixed in both parasite populations, and new mutations mediating piperaquine resistance were not identified. Similarly, several mutations related to pfdhfr and pfdhps were also highly prevalent. Despite their geographical proximity, malaria parasites from Laiza showed significantly higher in vitro resistance to artemisinin derivatives, naphthoquine, pyronaridine, lumefantrine, and pyrimethamine than parasites from Muse. Likewise, the pfdhfr N51I, pfdhps A581G, pfmrp1 H785N, and pfk13 F446I mutations were significantly more frequent in Laiza than in Muse (p < 0.05). For the pfmdr1 mutations, Y184F was found only in Laiza (70%), whereas F1226Y was identified only in Muse (31.8%). Parasite isolates from Laiza showed a median RSA value of 5.0%, significantly higher than the 2.4% in Muse. Altogether, P. falciparum parasite populations from neighboring regions in the GMS may diverge substantially in their resistance to several antimalarial drugs. This information about different parasite populations will guide antimalarial treatment policies to effectively manage drug resistance during malaria elimination.
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Affiliation(s)
- Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Yao Bai
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Shuang Deng
- Department of Pathology, Kunming Medical University, Kunming 650500, China
| | - Yonghua Ruan
- Department of Pathology, Kunming Medical University, Kunming 650500, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Wei Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Kemin Sun
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Wenya Zhu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Yiman Wu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL 33612, USA
| | | | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming 650500, China
- Correspondence: (Z.Y.); (L.C.); Tel.: +86-871-68225541 (Z.Y.); +1-(813)-974-9606 (L.C.)
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL 33612, USA
- Correspondence: (Z.Y.); (L.C.); Tel.: +86-871-68225541 (Z.Y.); +1-(813)-974-9606 (L.C.)
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PvMSP-3α and PvMSP-3β genotyping reveals higher genetic diversity in Plasmodium vivax parasites from migrant workers than residents at the China-Myanmar border. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105387. [PMID: 36403920 DOI: 10.1016/j.meegid.2022.105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The genetic diversity of malaria parasites traces the origin and spread of new variants and can be used to evaluate the effectiveness of malaria control measures. Therefore, this study aims to improve the understanding of the molecular epidemiology of Plasmodium vivax malaria at the China-Myanmar border by genotyping the PvMSP-3α and PvMSP-3β genes. METHODS Blood samples were collected from P. vivax malaria patients along the China-Myanmar border. The PvMSP-3α and PvMSP-3β genes were amplified by polymerase chain reaction (PCR) and the genetic polymorphism and haplotype of the two genes were analyzed. RESULTS A total of 422 blood samples were used for this study, of which 224 were analyzed at PvMSP-3α and 126 at PvMSP-3β. Samples mainly were from young adults aged 18-45 years, although local patients were significantly younger than migrant laborers crossing the border at Tengchong (P < 0.0001). Molecular evolutionary analysis revealed that PvMSP-3α and PvMSP-3β underwent diversifying natural selection, and intragenic recombination contributed to the diversity of the isolates. Based on the length of the genes, we identified three types of PvMSP-3α [1.9-2.0 kb (Type-A), 1.4-1.5 kb (Type-B), and 1.1-1.3 kb (Type-C)] and two types of PvMSP-3β [1.7-2.2 kb (Type-A) and 1.4-1.5 kb (Type-B)]. Migrant laborers returning to China through Tengchong bore P. vivax infections displaying significantly higher genetic diversity than local residents. CONCLUSIONS Both PvMSP-3 paralogs were subjected to diversifying selection in each sample population. Clustering of alleles supports ephemeral endemic differentiation of alleles, but the broader phylogeny suggests that alleles transit the globe, perhaps accelerated by movements of migrants such as those transiting Tengchong.
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Cui L, Sattabongkot J, Aung PL, Brashear A, Cao Y, Kaewkungwal J, Khamsiriwatchara A, Kyaw MP, Lawpoolsri S, Menezes L, Miao J, Nguitragool W, Parker D, Phuanukoonnon S, Roobsoong W, Siddiqui F, Soe MT, Sriwichai P, Yang Z, Zhao Y, Zhong D. Multidisciplinary Investigations of Sustained Malaria Transmission in the Greater Mekong Subregion. Am J Trop Med Hyg 2022; 107:138-151. [PMID: 36228909 DOI: 10.4269/ajtmh.21-1267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/28/2022] [Indexed: 11/07/2022] Open
Abstract
In the course of malaria elimination in the Greater Mekong Subregion (GMS), malaria epidemiology has experienced drastic spatiotemporal changes with residual transmission concentrated along international borders and the rising predominance of Plasmodium vivax. The emergence of Plasmodium falciparum parasites resistant to artemisinin and partner drugs renders artemisinin-based combination therapies less effective while the potential spread of multidrug-resistant parasites elicits concern. Vector behavioral changes and insecticide resistance have reduced the effectiveness of core vector control measures. In recognition of these problems, the Southeast Asian International Center of Excellence for Malaria Research (ICEMR) has been conducting multidisciplinary research to determine how human migration, antimalarial drug resistance, vector behavior, and insecticide resistance sustain malaria transmission at international borders. These efforts allow us to comprehensively understand the ecology of border malaria transmission and develop population genomics tools to identify and track parasite introduction. In addition to employing in vivo, in vitro, and molecular approaches to monitor the emergence and spread of drug-resistant parasites, we also use genomic and genetic methods to reveal novel mechanisms of antimalarial drug resistance of parasites. We also use omics and population genetics approaches to study insecticide resistance in malaria vectors and identify changes in mosquito community structure, vectorial potential, and seasonal dynamics. Collectively, the scientific findings from the ICEMR research activities offer a systematic view of the factors sustaining residual malaria transmission and identify potential solutions to these problems to accelerate malaria elimination in the GMS.
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Affiliation(s)
- Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | | | | | - Awtum Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Yaming Cao
- Department of Immunology, China Medical University, Shenyang, China
| | | | | | | | | | - Lynette Menezes
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Mahidol University, Bangkok, Thailand
| | - Daniel Parker
- Department of Epidemiology, University of California at Irvine, Irvine, California
| | | | | | - Faiza Siddiqui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon, Myanmar
| | - Patchara Sriwichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, China Medical University, Shenyang, China
| | - Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, California
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6
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Sattabongkot J, Cui L, Bantuchai S, Chotirat S, Kaewkungwal J, Khamsiriwatchara A, Kiattibutr K, Kyaw MP, Lawpoolsri S, Linn NYY, Menezes L, Miao J, Nguitragool W, Parker D, Prikchoo P, Roobsoong W, Sa-Angchai P, Samung Y, Sirichaisinthop J, Sriwichai P, Suk-Uam K, Thammapalo S, Wang B, Zhong D. Malaria Research for Tailored Control and Elimination Strategies in the Greater Mekong Subregion. Am J Trop Med Hyg 2022; 107:152-159. [PMID: 36228914 DOI: 10.4269/ajtmh.21-1268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/28/2022] [Indexed: 11/07/2022] Open
Abstract
The malaria landscape in the Greater Mekong Subregion has experienced drastic changes with the ramp-up of the control efforts, revealing formidable challenges that slowed down the progress toward malaria elimination. Problems such as border malaria and cross-border malaria introduction, multidrug resistance in Plasmodium falciparum, the persistence of Plasmodium vivax, the asymptomatic parasite reservoirs, and insecticide resistance in primary vectors require integrated strategies tailored for individual nations in the region. In recognition of these challenges and the need for research, the Southeast Asian International Center of Excellence for Malaria Research has established a network of researchers and stakeholders and conducted basic and translational research to identify existing and emerging problems and develop new countermeasures. The installation of a comprehensive disease and vector surveillance system at sentinel sites in border areas with the implementation of passive/active case detection and cross-sectional surveys allowed timely detection and management of malaria cases, provided updated knowledge for effective vector control measures, and facilitated the efficacy studies of antimalarials. Incorporating sensitive molecular diagnosis to expose the significance of asymptomatic parasite reservoirs for sustaining transmission helped establish the necessary evidence to guide targeted control to eliminate residual transmission. In addition, this program has developed point-of-care diagnostics to monitor the quality of artemisinin combination therapies, delivering the needed information to the drug regulatory authorities to take measures against falsified and substandard antimalarials. To accelerate malaria elimination, this program has actively engaged with stakeholders of all levels, fostered vertical and horizontal collaborations, and enabled the effective dissemination of research findings.
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Affiliation(s)
- Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | | | - Sadudee Chotirat
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | | | - Kirakorn Kiattibutr
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | | | - Nay Yi Yi Linn
- Department of Public Health, Ministry of Health, Nay Pyi Taw, Myanmar
| | - Lynette Menezes
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Daniel Parker
- Department of Epidemiology, University of California at Irvine, Irvine, California
| | - Pathomporn Prikchoo
- Office of Disease Prevention and Control 12, Ministry of Public Health, Songkla, Thailand
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Yudthana Samung
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jeeraphat Sirichaisinthop
- Vector-Borne Disease Control Center, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Patchara Sriwichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kritsana Suk-Uam
- Vector Borne Disease Control Center 2.3, Ministry of Public Health, Tak, Thailand
| | - Suwich Thammapalo
- Vector-Borne Disease Control Center, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Baomin Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, California
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Githure JI, Yewhalaw D, Atieli H, Hemming-Schroeder E, Lee MC, Wang X, Zhou G, Zhong D, King CL, Dent A, Mukabana WR, Degefa T, Hsu K, Githeko AK, Okomo G, Dayo L, Tushune K, Omondi CO, Taffese HS, Kazura JW, Yan G. Enhancing Malaria Research, Surveillance, and Control in Endemic Areas of Kenya and Ethiopia. Am J Trop Med Hyg 2022; 107:14-20. [PMID: 36228905 PMCID: PMC9662210 DOI: 10.4269/ajtmh.21-1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/18/2022] [Indexed: 01/27/2023] Open
Abstract
Malaria control programs in Africa encounter daunting challenges that hinder progressive steps toward elimination of the disease. These challenges include widespread insecticide resistance in mosquito vectors, increasing outdoor malaria transmission, lack of vector surveillance and control tools suitable for outdoor biting vectors, weakness in malaria surveillance, and an inadequate number of skilled healthcare personnel. Ecological and epidemiological changes induced by environmental modifications resulting from water resource development projects pose additional barriers to malaria control. Cognizant of these challenges, our International Center of Excellence for Malaria Research (ICEMR) works in close collaboration with relevant government ministries and agencies to align its research efforts with the objectives and strategies of the national malaria control and elimination programs for the benefit of local communities. Our overall goal is to assess the impact of water resource development projects, shifting agricultural practices, and vector interventions on Plasmodium falciparum and P. vivax malaria in Kenya and Ethiopia. From 2017 to date, the ICEMR has advanced knowledge of malaria epidemiology, transmission, immunology, and pathogenesis, and developed tools to enhance vector surveillance and control, improved clinical malaria surveillance and diagnostic methods, and strengthened the capacity of local healthcare providers. Research findings from the ICEMR will inform health policy and strategic planning by ministries of health in their quest to sustain malaria control and achieve elimination goals.
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Affiliation(s)
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia;,Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Harrysone Atieli
- School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | | | - Ming-Chieh Lee
- Program in Public Health, University of California at Irvine, Irvine, California
| | - Xiaoming Wang
- Program in Public Health, University of California at Irvine, Irvine, California
| | - Guofa Zhou
- Program in Public Health, University of California at Irvine, Irvine, California
| | - Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, California
| | - Christopher L. King
- Center for Global Health & Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Arlene Dent
- Center for Global Health & Diseases, Case Western Reserve University, Cleveland, Ohio
| | | | - Teshome Degefa
- Department of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Kuolin Hsu
- Center for Hydrometeorology and Remote Sensing, Department of Civil and Environmental Engineering, University of California at Irvine, Irvine, California
| | - Andrew K. Githeko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Gordon Okomo
- Ministry of Health, Homa Bay County, Homa Bay, Kenya
| | - Lilyana Dayo
- Ministry of Health, Kisumu County, Kisumu, Kenya
| | - Kora Tushune
- Department of Health Management and Policy, Faculty of Public Health, Jimma University, Jimma, Ethiopia
| | | | - Hiwot S. Taffese
- National Malaria Program, Federal Ministry of Health, Addis Ababa, Ethiopia
| | - James W. Kazura
- Center for Global Health & Diseases, Case Western Reserve University, Cleveland, Ohio;,Address correspondence to Guiyun Yan, Program in Public Health, University of California at Irvine, Irvine, CA, E-mail: or James Kazura, Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH, E-mail:
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, Irvine, California;,Address correspondence to Guiyun Yan, Program in Public Health, University of California at Irvine, Irvine, CA, E-mail: or James Kazura, Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH, E-mail:
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8
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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9
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Shi TQ, Shen HM, Chen SB, Kassegne K, Cui YB, Xu B, Chen JH, Zheng B, Wang Y. Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China. Front Microbiol 2021; 12:758061. [PMID: 34912313 PMCID: PMC8667024 DOI: 10.3389/fmicb.2021.758061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/12/2021] [Indexed: 11/15/2022] Open
Abstract
Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.
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Affiliation(s)
- Tian-Qi Shi
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Kokouvi Kassegne
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Zheng
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China.,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Wang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Institute of Parasitic Diseases, Hangzhou, China
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10
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A retrospective analysis of malaria epidemiological characteristics in Yingjiang County on the China-Myanmar border. Sci Rep 2021; 11:14129. [PMID: 34239003 PMCID: PMC8266812 DOI: 10.1038/s41598-021-93734-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/15/2021] [Indexed: 11/08/2022] Open
Abstract
Yingjiang County, which is on the China–Myanmar border, is the main focus for malaria elimination in China. The epidemiological characteristics of malaria in Yingjiang County were analysed in a retrospective analysis. A total of 895 malaria cases were reported in Yingjiang County between 2013 and 2019. The majority of cases occurred in males (70.7%) and individuals aged 19–59 years (77.3%). Plasmodium vivax was the predominant species (96.6%). The number of indigenous cases decreased gradually and since 2017, no indigenous cases have been reported. Malaria cases were mainly distributed in the southern and southwestern areas of the county; 55.6% of the indigenous cases were reported in Nabang Township, which also had the highest risk of imported malaria. The “1–3–7” approach has been implemented effectively, with 100% of cases reported within 24 h, 88.9% cases investigated and confirmed within 3 days and 98.5% of foci responded to within 7 days. Although malaria elimination has been achieved in Yingjiang County, sustaining elimination and preventing the re-establishment of malaria require the continued strengthening of case detection, surveillance and response systems targeting the migrant population in border areas.
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11
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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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12
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Hemming-Schroeder E, Zhong D, Machani M, Nguyen H, Thong S, Kahindi S, Mbogo C, Atieli H, Githeko A, Lehmann T, Kazura JW, Yan G. Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis. Sci Rep 2020; 10:19946. [PMID: 33203917 PMCID: PMC7673128 DOI: 10.1038/s41598-020-76248-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022] Open
Abstract
Anopheles gambiae and An. arabiensis are major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity of An. gambiae and An. arabiensis across Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity in An. gambiae, but not in An. arabiensis as compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow of An. gambiae and An. arabiensis was tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.
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Affiliation(s)
- Elizabeth Hemming-Schroeder
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA.,Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daibin Zhong
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Maxwell Machani
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Hoan Nguyen
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Sarah Thong
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Samuel Kahindi
- School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Charles Mbogo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harrysone Atieli
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya.,School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - Andrew Githeko
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Tovi Lehmann
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Guiyun Yan
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA.
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13
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Ford A, Kepple D, Abagero BR, Connors J, Pearson R, Auburn S, Getachew S, Ford C, Gunalan K, Miller LH, Janies DA, Rayner JC, Yan G, Yewhalaw D, Lo E. Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes. PLoS Negl Trop Dis 2020; 14:e0008234. [PMID: 33044985 PMCID: PMC7581005 DOI: 10.1371/journal.pntd.0008234] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 10/22/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale. Plasmodium vivax is the most geographically widespread parasite species that causes malaria in humans. Although it occurs in Africa as a member of a mix of Plasmodium species, P. vivax is dominant in other parts of the world outside of Africa (e.g., Brazil). It was previously thought that most African populations were immune to P. vivax infections due to the absence of Duffy antigen chemokine receptor (DARC) gene expression required for erythrocyte invasion. However, several recent reports have indicated the emergence and potential spread of P. vivax across human populations in Africa. Compared to Southeast Asia and South America where P. vivax is highly endemic, data on polymorphisms in erythrocyte binding gene candidates of P. vivax from Africa is limited. Filling this knowlege gap is critical for identifying functional genes in erythrocyte invasion, biomarkers for tracking the P. vivax isolates from Africa, as well as potential gene targets for vaccine development. This paper examined the level of genetic polymorphisms in a panel of 43 potential erythrocyte binding protein genes based on whole genome sequences and described transmission patterns of P. vivax infections from different study sites in Ethiopia based on the genetic variants. Our analyses showed that chromosomes 9 and 10 of the P. vivax genomes isolated in Ethiopia had the most high-quality genetic polymorphisms. Among all erythrocyte binding protein gene candidates, the merozoite surface proteins 1 and merozoite surface protein 3 showed high levels of polymorphism. MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. The expansion of the Duffy binding protein and merozoite surface protein 3 gene copies was an independent process among the P. vivax lineages in Ethiopia. Various levels of gene flow were observed even at a smaller geographical scale. Our study provided baseline data for future comparison with P. vivax in Duffy negative individuals and help develop a panel of genetic markers that are informative at a micro-geographical scale.
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Affiliation(s)
- Anthony Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
| | - Daniel Kepple
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Ethiopia
| | - Jordan Connors
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Richard Pearson
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United States of America
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Colby Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Louis H. Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Julian C. Rayner
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 OXY, United Kingdom
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, United States of America
- * E-mail: (AF); (GY); (EL)
| | | | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
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14
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Hemming-Schroeder E, Zhong D, Kibret S, Chie A, Lee MC, Zhou G, Atieli H, Githeko A, Kazura JW, Yan G. Microgeographic Epidemiology of Malaria Parasites in an Irrigated Area of Western Kenya by Deep Amplicon Sequencing. J Infect Dis 2020; 223:1456-1465. [PMID: 32803223 DOI: 10.1093/infdis/jiaa520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
To improve food security, investments in irrigated agriculture are anticipated to increase throughout Africa. However, the extent to which environmental changes from water resource development will impact malaria epidemiology remains unclear. This study was designed to compare the sensitivity of molecular markers used in deep amplicon sequencing for evaluating malaria transmission intensities and to assess malaria transmission intensity at various proximities to an irrigation scheme. Compared to ama1, csp, and msp1 amplicons, cpmp required the smallest sample size to detect differences in infection complexity between transmission risk zones. Transmission intensity was highest within 5 km of the irrigation scheme by polymerase chain reaction positivity rate, infection complexity, and linkage disequilibrium. The irrigated area provided a source of parasite infections for the surrounding 2- to 10-km area. This study highlights the suitability of the cpmp amplicon as a measure for transmission intensities and the impact of irrigation on microgeographic epidemiology of malaria parasites.
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Affiliation(s)
- Elizabeth Hemming-Schroeder
- Program in Public Health, University of California, Irvine, Irvine, California, USA.,Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daibin Zhong
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Solomon Kibret
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Amanda Chie
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Ming-Chieh Lee
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Guofa Zhou
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Harrysone Atieli
- School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - Andrew Githeko
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, Irvine, California, USA
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15
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Brashear AM, Huckaby AC, Fan Q, Dillard LJ, Hu Y, Li Y, Zhao Y, Wang Z, Cao Y, Miao J, Guler JL, Cui L. New Plasmodium vivax Genomes From the China-Myanmar Border. Front Microbiol 2020; 11:1930. [PMID: 32849480 PMCID: PMC7432439 DOI: 10.3389/fmicb.2020.01930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS.
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Affiliation(s)
- Awtum M. Brashear
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Adam C. Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Qi Fan
- Dalian Institute of Science and Technology, Dalian, China
| | - Luke J. Dillard
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Zenglei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Jennifer L. Guler
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
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16
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Brashear AM, Fan Q, Hu Y, Li Y, Zhao Y, Wang Z, Cao Y, Miao J, Barry A, Cui L. Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. PLoS Negl Trop Dis 2020; 14:e0008506. [PMID: 32745103 PMCID: PMC7425983 DOI: 10.1371/journal.pntd.0008506] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/13/2020] [Accepted: 06/22/2020] [Indexed: 01/31/2023] Open
Abstract
Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from the China-Myanmar border (CMB) and used 21 high-coverage samples to compare to over 200 samples from the rest of the GMS. Using genome-wide single nucleotide polymorphisms (SNPs), we analyzed population differentiation, genetic structure, migration and potential selection using an array of methods. The CMB parasites displayed a higher proportion of monoclonal infections, and 52% shared over 90% of their genomes in identity-by-descent segments with at least one other sample from the CMB, suggesting preferential expansion of certain parasite strains in this region, likely resulting from the P. vivax outbreaks occurring during this study period. Principal component, admixture, fixation index and phylogenetic analyses all identified that parasites from the CMB were genetically distinct from parasites from eastern parts of the GMS (Cambodia, Laos, Vietnam, and Thailand), whereas the eastern GMS parasite populations were largely undifferentiated. Such a genetic differentiation pattern of the P. vivax populations from the GMS parasite was largely explainable through geographic distance. Using the genome-wide SNPs, we narrowed down to a set of 36 SNPs for differentiating parasites from different areas of the GMS. Genome-wide scans to determine selection in the genome with two statistical methods identified genes potentially under drug selection, including genes associated with antifolate resistance and genes linked to chloroquine resistance in Plasmodium falciparum.
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Affiliation(s)
- Awtum M. Brashear
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
- Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Qi Fan
- Dalian Institute of Technology, Dalian, Liaoning Province, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Zenglei Wang
- MHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Alyssa Barry
- Infection Systems Epidemiology, School of Medicine, Faculty of Health, Deakin University, Geelong, VIC, Australia
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
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17
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Li Y, Hu Y, Zhao Y, Wang Q, Ngassa Mbenda HG, Kittichai V, Lawpoolsri S, Sattabongkot J, Menezes L, Liu X, Cui L, Cao Y. Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination. Malar J 2020; 19:145. [PMID: 32268906 PMCID: PMC7140319 DOI: 10.1186/s12936-020-03221-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Countries within the Greater Mekong Sub-region (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although the malaria situation has greatly improved, malaria transmission remains at international border regions. In some areas, Plasmodium vivax has become the predominant parasite. To gain a better understanding of transmission dynamics, knowledge on the changes of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. Methods This study investigated genetic diversity and population structures in 206 P. vivax clinical samples collected at two time points in two international border areas: the China-Myanmar border (CMB) (n = 50 in 2004 and n = 52 in 2016) and Thailand-Myanmar border (TMB) (n = 50 in 2012 and n = 54 in 2015). Parasites were genotyped using 10 microsatellite markers. Results Despite intensified control efforts, genetic diversity remained high (HE = 0.66–0.86) and was not significantly different among the four populations (P > 0.05). Specifically, HE slightly decreased from 0.76 in 2004 to 0.66 in 2016 at the CMB and increased from 0.80 in 2012 to 0.86 in 2015 at the TMB. The proportions of polyclonal infections varied significantly among the four populations (P < 0.05), and showed substantial decreases from 48.0% in 2004 to 23.7 at the CMB and from 40.0% in 2012 to 30.7% in 2015 at the TMB, with corresponding decreases in the multiplicity of infection. Consistent with the continuous decline of malaria incidence in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and sub-division among the four tested populations. Temporal genetic differentiation was observed at each site (FST = 0.081 at the CMB and FST = 0.133 at the TMB). Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB and the 2016 CMB and 2012 TMB populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 TMB population was genetically distinctive, which may reflect a process of population replacement. Whereas the effective population size (Ne) at the CMB showed a decrease from 4979 in 2004 to 3052 in 2016 with the infinite allele model, the Ne at the TMB experienced an increase from 6289 to 10,259. Conclusions With enhanced control efforts on malaria, P. vivax at the TMB and CMB showed considerable spatial and temporal differentiation, but the presence of large P. vivax reservoirs still sustained genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in these border areas of the GMS. Coordinated and integrated control efforts on both sides of international borders are essential to reach the goal of regional malaria elimination.
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Affiliation(s)
- Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.,Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, Liaoning, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Huguette Gaelle Ngassa Mbenda
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Saranath Lawpoolsri
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Lynette Menezes
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA. .,Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
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18
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Abstract
The relative contribution of imported vs. locally acquired infections to urban malaria burden remains largely unexplored in Latin America, the most urbanised region in the developing world. Here we use a simple molecular epidemiology framework to examine the transmission dynamics of Plasmodium vivax in Mâncio Lima, the Amazonian municipality with the highest malaria incidence rate in Brazil. We prospectively genotyped 177 P. vivax infections diagnosed in urban residents between June 2014 and July 2015 and showed that local parasites are structured into several lineages of closely related microsatellite haplotypes, with the largest genetic cluster comprising 32% of all infections. These findings are very unlikely under the hypothesis of multiple independent imports of parasite strains from the rural surroundings. Instead, the presence of an endemic near-clonal parasite lineage circulating over 13 consecutive months is consistent with a local P. vivax transmission chain in the town, with major implications for malaria elimination efforts in this and similar urban environments across the Amazon.
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19
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Ngassa Mbenda HG, Wang M, Guo J, Siddiqui FA, Hu Y, Yang Z, Kittichai V, Sattabongkot J, Cao Y, Jiang L, Cui L. Evolution of the Plasmodium vivax multidrug resistance 1 gene in the Greater Mekong Subregion during malaria elimination. Parasit Vectors 2020; 13:67. [PMID: 32051017 PMCID: PMC7017538 DOI: 10.1186/s13071-020-3934-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/03/2020] [Indexed: 11/10/2022] Open
Abstract
Background The malaria elimination plan of the Greater Mekong Subregion (GMS) is jeopardized by the increasing number of Plasmodium vivax infections and emergence of parasite strains with reduced susceptibility to the frontline drug treatment chloroquine/primaquine. This study aimed to determine the evolution of the P. vivax multidrug resistance 1 (Pvmdr1) gene in P. vivax parasites isolated from the China–Myanmar border area during the major phase of elimination. Methods Clinical isolates were collected from 275 P. vivax patients in 2008, 2012–2013 and 2015 in the China–Myanmar border area and from 55 patients in central China. Comparison was made with parasites from three border regions of Thailand. Results Overall, genetic diversity of the Pvmdr1 was relatively high in all border regions, and over the seven years in the China–Myanmar border, though slight temporal fluctuation was observed. Single nucleotide polymorphisms previously implicated in reduced chloroquine sensitivity were detected. In particular, M908L approached fixation in the China–Myanmar border area. The Y976F mutation sharply decreased from 18.5% in 2008 to 1.5% in 2012–2013 and disappeared in 2015, whereas F1076L steadily increased from 33.3% in 2008 to 77.8% in 2015. While neutrality tests suggested the action of purifying selection on the pvmdr1 gene, several likelihood-based algorithms detected positive as well as purifying selections operating on specific amino acids including M908L, T958M and F1076L. Fixation and selection of the nonsynonymous mutations are differently distributed across the three border regions and central China. Comparison with the global P. vivax populations clearly indicated clustering of haplotypes according to geographic locations. It is noteworthy that the temperate-zone parasites from central China were completely separated from the parasites from other parts of the GMS. Conclusions This study showed that P. vivax populations in the China–Myanmar border has experienced major changes in the Pvmdr1 residues proposed to be associated with chloroquine resistance, suggesting that drug selection may play an important role in the evolution of this gene in the parasite populations.![]()
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Affiliation(s)
- Huguette Gaelle Ngassa Mbenda
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Meilian Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji School of Medicine, Shanghai, China
| | - Faiza Amber Siddiqui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Yue Hu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, China
| | - Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Lubin Jiang
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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Hedtke SM, Kuesel AC, Crawford KE, Graves PM, Boussinesq M, Lau CL, Boakye DA, Grant WN. Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions. Front Genet 2020; 10:1282. [PMID: 31998356 PMCID: PMC6964045 DOI: 10.3389/fgene.2019.01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Annette C. Kuesel
- Unicef/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Katie E. Crawford
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Patricia M. Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Michel Boussinesq
- Unité Mixte Internationale 233 "TransVIHMI", Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Colleen L. Lau
- Department of Global Health, Research School of Population Health, Australian National University, Acton, ACT, Australia
| | - Daniel A. Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Warwick N. Grant
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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21
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Pringle JC, Wesolowski A, Berube S, Kobayashi T, Gebhardt ME, Mulenga M, Chaponda M, Bobanga T, Juliano JJ, Meshnick S, Moss WJ, Carpi G, Norris DE. High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo. Malar J 2019; 18:400. [PMID: 31801548 PMCID: PMC6894251 DOI: 10.1186/s12936-019-3023-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/21/2019] [Indexed: 01/25/2023] Open
Abstract
Background While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning. Methods Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June–July 2016 and January–March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC). Results High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes. Conclusions Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.
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Affiliation(s)
- Julia C Pringle
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Sophie Berube
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Mary E Gebhardt
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | | | - Thierry Bobanga
- Université Protestante au Congo and University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Steven Meshnick
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - William J Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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22
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Geng J, Malla P, Zhang J, Xu S, Li C, Zhao Y, Wang Q, Kyaw MP, Cao Y, Yang Z, Cui L. Increasing trends of malaria in a border area of the Greater Mekong Subregion. Malar J 2019; 18:309. [PMID: 31514740 PMCID: PMC6739967 DOI: 10.1186/s12936-019-2924-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/17/2019] [Indexed: 11/27/2022] Open
Abstract
Background Intensive malaria transmission along international borders is a significant impediment to malaria elimination in the Greater Mekong Subregion (GMS) of Southeast Asia. Passive case detection (PCD) was used to study the dynamics and trends of malaria transmission at the China–Myanmar border to provide epidemiologic information for improved malaria control. Methods PCD was conducted in one hospital and 12 clinics near the Laiza town in northeast Myanmar from 2011 to 2016. Clinical malaria was diagnosed by microscopy and demographic information was captured using a structured questionnaire at the time of the patient’s presentation for care. Results Over the study period, 6175 (19.7%) malaria cases were confirmed by microscopy from 31,326 suspected cases. The four human malaria parasite species were all identified, with Plasmodium vivax and Plasmodium falciparum accounting for 5607 (90.8%) and 481 (7.8%) of the confirmed cases, respectively. In contrast to the steady decline of malaria in the general GMS, the study site had an upward trend of malaria incidence with vivax malaria outbreaks in 2013 and 2016. Adult males, children under the age of 15, and those with occupations such as farming, being a soldier or student, had significantly higher risks of clinical malaria compared to having fevers from other aetiologies. A self-reported history of clinical malaria was also associated with a higher risk of confirmed malaria. Conclusions The China–Myanmar border area has experienced an overall upward trend of malaria incidence in recent years with P. vivax becoming the predominant species. Evidence-based control strategies need to focus on high-risk populations.
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Affiliation(s)
- Jinting Geng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Pallavi Malla
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA
| | - Jiaqi Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Shiling Xu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Cuiying Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | | | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA.
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23
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Pacheco MA, Schneider KA, Céspedes N, Herrera S, Arévalo-Herrera M, Escalante AA. Limited differentiation among Plasmodium vivax populations from the northwest and to the south Pacific Coast of Colombia: A malaria corridor? PLoS Negl Trop Dis 2019; 13:e0007310. [PMID: 30921317 PMCID: PMC6456216 DOI: 10.1371/journal.pntd.0007310] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 04/09/2019] [Accepted: 03/16/2019] [Indexed: 01/06/2023] Open
Abstract
Background Malaria remains endemic in several countries of South America with low to moderate transmission intensity. Regional human migration through underserved endemic areas may be responsible for significant parasite dispersion making the disease resilient to interventions. Thus, the genetic characterization of malarial parasites is an important tool to assess how endemic areas may connect via the movement of infected individuals. Here, four sites in geographically separated areas reporting 80% of the malaria morbidity in Colombia were studied. The sites are located on an imaginary transect line of 1,500 km from the northwest to the south Pacific Coast of Colombia with a minimal distance of 500 km between populations that display noticeable ethnic, economic, epidemiological, and ecological differences. Methodology/Principal findings A total of 624 Plasmodium vivax samples from the four populations were genotyped by using eight microsatellite loci. Although a strong geographic structure was expected between these populations, only moderate evidence of genetic differentiation was observed using a suite of population genetic analyses. High genetic diversity, shared alleles, and low linkage disequilibrium were also found in these P. vivax populations providing no evidence for a bottleneck or clonal expansions as expected from recent reductions in the transmission that could have been the result of scaling up interventions or environmental changes. These patterns are consistent with a disease that is not only endemic in each site but also imply that there is gene flow among these populations across 1,500 km. Conclusion /Significance The observed patterns in P. vivax are consistent with a “corridor” where connected endemic areas can sustain a high level of genetic diversity locally and can restore parasite-subdivided populations via migration of infected individuals even after local interventions achieved a substantial reduction of clinical cases. The consequences of these findings in terms of control and elimination are discussed. The regional movements of infected individuals that connect suitable transmission areas make malaria resilient to control efforts. Those movements are expected to leave genetic signatures in the parasite populations that can be detected using analytical tools. In this study, the genetic makeups of Plasmodium vivax populations were characterized to assess whether the most endemic areas in Colombia were connected. Samples were collected from passive surveillance studies in four locations across an imaginary transect line of 1,500 km from the northwest to the south Pacific Coast of Colombia (South America). Considering the distance, and contrary to expectations, we found weak levels of genetic differentiation between these parasite populations with no evidence indicating that their genetic diversity has been eroded as expected whenever the prevalence of the disease is successfully reduced, e.g., through control programs or environmental changes. Although the sampling lacks the geographic and temporal detail to describe how the dispersion of parasite lineages occurred, the observed patterns are consistent with a series of infected populations that are connected in space by human movements allowing the parasite to diffuse across this 1,500 km transect. This malaria corridor needs to be characterized to achieve elimination.
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Affiliation(s)
- M. Andreína Pacheco
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Nora Céspedes
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Sócrates Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Ananias A. Escalante
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Ahmed MA, Chu KB, Quan FS. The Plasmodium knowlesi Pk41 surface protein diversity, natural selection, sub population and geographical clustering: a 6-cysteine protein family member. PeerJ 2018; 6:e6141. [PMID: 30581686 PMCID: PMC6296336 DOI: 10.7717/peerj.6141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 12/05/2022] Open
Abstract
Introduction The zoonotic malaria parasite Plasmodium knowlesi has currently become the most dominant form of infection in humans in Malaysia and is an emerging infectious disease in most Southeast Asian countries. The P41 is a merozoite surface protein belonging to the 6-cysteine family and is a well-characterized vaccine candidate in P. vivax and P. falciparum; however, no study has been done in the orthologous gene of P. knowlesi. This study investigates the level of polymorphism, haplotypes and natural selection of pk41 genes in clinical isolates from Malaysia. Method Thirty-five full-length pk41 sequences from clinical isolates of Malaysia along with four laboratory lines (along with H-strain) were downloaded from public databases. For comparative analysis between species, orthologous P41 genes from P. falciparum, P. vivax, P. coatneyi and P. cynomolgi were also downloaded. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. Phylogenetic relationships between Pk41 genes were determined using MEGA 5.0 software. Results Analysis of 39 full-length pk41 sequences along with the H-strain identified 36 SNPs (20 non-synonymous and 16 synonymous substitutions) resulting in 31 haplotypes. Nucleotide diversity across the full-length gene was low and was similar to its ortholog in P. vivax; pv41. Domain-wise amino acid analysis of the two s48/45 domains indicated low level of polymorphisms for both the domains, and the glutamic acid rich region had extensive size variations. In the central domain, upstream to the glutamate rich region, a unique two to six (K-E)n repeat region was identified within the clinical isolates. Overall, the pk41 genes were indicative of negative/purifying selection due to functional constraints. Domain-wise analysis of the s48/45 domains also indicated purifying selection. However, analysis of Tajima’s D across the genes identified non-synonymous SNPs in the s48/45 domain II with high positive values indicating possible epitope binding regions. All the 6-cysteine residues within the s48/45 domains were conserved within the clinical isolates indicating functional conservation of these regions. Phylogenetic analysis of full-length pk41 genes indicated geographical clustering and identified three subpopulations of P. knowlesi; one originating in the laboratory lines and two originating from Sarawak, Malaysian Borneo. Conclusion This is the first study to report on the polymorphism and natural selection of pk41 genes from clinical isolates of Malaysia. The results reveal that there is low level of polymorphism in both s48/45 domains, indicating that this antigen could be a potential vaccine target. However, genetic and molecular immunology studies involving higher number of samples from various parts of Malaysia would be necessary to validate this antigen’s candidacy as a vaccine target for P. knowlesi.
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Affiliation(s)
- Md Atique Ahmed
- Department of Medical Zoology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ki-Back Chu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Fu-Shi Quan
- Department of Medical Zoology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea.,Biomedical Science Institute, Kyung Hee University, Seoul, Republic of Korea
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25
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Hemming-Schroeder E, Lo E, Salazar C, Puente S, Yan G. Landscape Genetics: A Toolbox for Studying Vector-Borne Diseases. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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26
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Mbenda HGN, Zeng W, Bai Y, Siddiqui FA, Yang Z, Cui L. Genetic diversity of the Plasmodium vivax phosphatidylinositol 3-kinase gene in two regions of the China-Myanmar border. INFECTION GENETICS AND EVOLUTION 2018; 61:45-52. [PMID: 29462718 DOI: 10.1016/j.meegid.2018.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 12/25/2022]
Abstract
Artemisinin resistance in Plasmodium falciparum was associated with mutations in the propeller domain of the PfK13 gene and increased phosphatidylinositol-3'-kinase (PfPI3K) activity. Assessment of the genetic diversity of the PfK13 ortholog PvK12 in Plasmodium vivax field samples from the same hotspots of P. falciparum artemisinin resistance revealed a limited genetic diversity of PvK12. Following the same logic, we analyzed genetic variations of the PvPI3K gene in 188 P. vivax field isolates from two geographic locations along the China-Myanmar border. Overall, high genetic diversity of PvPI3K was observed; parasites from Yunnan's Tengchong County had higher genetic diversity than those from Laiza Township, Kachin State, Myanmar. Almost all the neutrality tests applied detected statistically significant deviation from zero. The negative Tajima's D values in both populations implicated that PvPI3K gene might have experienced either a directional selection or an expansion in population size. There was low linkage disequilibrium between the PvPI3K mutations in both populations, suggesting the existence of large, almost panmictic, parasite populations that enabled effective recombination. This later result was confirmed by the detection of a minimum of five recombination events in each population with two major breakpoints. Multiple tests for selection confirmed a signature of purifying selection on PvPI3K. All the amino acid mutations were predicted to be neutral for the PI3K protein's function. These findings provide insights on the genetic diversity of P. vivax populations along the China-Myanmar border.
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Affiliation(s)
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yao Bai
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Faiza Amber Siddiqui
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA.
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Htun MW, Mon NCN, Aye KM, Hlaing CM, Kyaw MP, Handayuni I, Trimarsanto H, Bustos D, Ringwald P, Price RN, Auburn S, Thriemer K. Chloroquine efficacy for Plasmodium vivax in Myanmar in populations with high genetic diversity and moderate parasite gene flow. Malar J 2017; 16:281. [PMID: 28693552 PMCID: PMC5504659 DOI: 10.1186/s12936-017-1912-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/26/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax malaria remains a major public health burden in Myanmar. Resistance to chloroquine (CQ), the first-line treatment for P. vivax, has been reported in the country and has potential to undermine local control efforts. METHODS Patients over 6 years of age with uncomplicated P. vivax mono-infection were enrolled into clinical efficacy studies in Myawaddy in 2014 and Kawthoung in 2012. Study participants received a standard dose of CQ (25 mg/kg over 3 days) followed by weekly review until day 28. Pvmdr1 copy number (CN) and microsatellite diversity were assessed on samples from the patients enrolled in the clinical study and additional cross-sectional surveys undertaken in Myawaddy and Shwegyin in 2012. RESULTS A total of 85 patients were enrolled in the CQ clinical studies, 25 in Myawaddy and 60 in Kawthoung. One patient in Myawaddy (1.2%) had an early treatment failure and two patients (2.3%) in Kawthoung presented with late treatment failures on day 28. The day 28 efficacy was 92.0% (95% CI 71.6-97.9) in Myawaddy and 98.3% (95% CI 88.7-99.8) in Kawthoung. By day 2, 92.2% (23/25) in Myawaddy and 85.0% (51/60) in Kawthoung were aparasitaemic. Genotyping and pvmdr1 CN assessment was undertaken on 43, 52 and 46 clinical isolates from Myawaddy, Kawthoung and Shwegyin respectively. Pvmdr1 amplification was observed in 3.2% (1/31) of isolates in Myawaddy, 0% (0/49) in Kawthoung and 2.5% (1/40) in Shwegyin. Diversity was high in all sites (H E 0.855-0.876), with low inter-population differentiation (F ST 0.016-0.026, P < 0.05). CONCLUSIONS Treatment failures after chloroquine were observed following chloroquine monotherapy, with pvmdr1 amplification present in both Myawaddy and Shwegyin. The results emphasize the importance of ongoing P. vivax drug resistance surveillance in Myanmar, particularly given the potential connectivity between parasite population at different sites.
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Affiliation(s)
- Myo Win Htun
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Nan Cho Nwe Mon
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Khin Myo Aye
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Chan Myae Hlaing
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Myat Phone Kyaw
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Irene Handayuni
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
| | - Hidayat Trimarsanto
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jl. Diponegoro 69, Central Jakarta, 10430 Indonesia ,grid.466915.9The Ministry of Research and Technology (RISTEK), Jakarta, Indonesia ,0000 0001 0746 0534grid.432292.cAgency for Assessment and Application of Technology, Jl. MH Thamrin 8, Jakarta, 10340 Indonesia
| | - Dorina Bustos
- 0000 0004 0576 2573grid.415836.dWorld Health Organization, Country Office for Thailand, Ministry of Public Health, Nonthaburi, Thailand
| | - Pascal Ringwald
- 0000000121633745grid.3575.4Global Malaria Programme, World Health Organization, 20 Avenue Appia, 1211 Geneva, 27, Switzerland
| | - Ric N. Price
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia ,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Sarah Auburn
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
| | - Kamala Thriemer
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
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