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Miao M, Wang Z, Yang Z, Yuan L, Parker DM, Putaporntip C, Jongwutiwes S, Xangsayarath P, Pongvongsa T, Moji H, Dinh Tuong T, Abe T, Nakazawa S, Kyaw MP, Yan G, Sirichaisinthop J, Sattabongkot J, Mu J, Su XZ, Kaneko O, Cui L. Genetic diversity and lack of artemisinin selection signature on the Plasmodium falciparum ATP6 in the Greater Mekong Subregion. PLoS One 2013; 8:e59192. [PMID: 23555629 PMCID: PMC3608609 DOI: 10.1371/journal.pone.0059192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/12/2013] [Indexed: 11/30/2022] Open
Abstract
The recent detection of clinical Artemisinin (ART) resistance manifested as delayed parasite clearance in the Cambodia-Thailand border area raises a serious concern. The mechanism of ART resistance is not clear; but the P. falciparum sarco/endoplasmic reticulum Ca2+-ATPase (PfSERCA or PfATP6) has been speculated to be the target of ARTs and thus a potential marker for ART resistance. Here we amplified and sequenced pfatp6 gene (∼3.6 Kb) in 213 samples collected after 2005 from the Greater Mekong Subregion, where ART drugs have been used extensively in the past. A total of 24 single nucleotide polymorphisms (SNPs), including 8 newly found in this study and 13 nonsynonymous, were identified. However, these mutations were either uncommon or also present in other geographical regions with limited ART use. None of the mutations were suggestive of directional selection by ARTs. We further analyzed pfatp6 from a worldwide collection of 862 P. falciparum isolates in 19 populations from Asia, Africa, South America and Oceania, which include samples from regions prior to and after deployments ART drugs. A total of 71 SNPs were identified, resulting in 106 nucleotide haplotypes. Similarly, many of the mutations were continent-specific and present at frequencies below 5%. The most predominant and perhaps the ancestral haplotype occurred in 441 samples and was present in 16 populations from Asia, Africa, and Oceania. The 3D7 haplotype found in 54 samples was the second most common haplotype and present in nine populations from all four continents. Assessment of the selection strength on pfatp6 in the 19 parasite populations found that pfatp6 in most of these populations was under purifying selection with an average dN/dS ratio of 0.333. Molecular evolution analyses did not detect significant departures from neutrality in pfatp6 for most populations, challenging the suitability of this gene as a marker for monitoring ART resistance.
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Affiliation(s)
- Miao Miao
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zenglei Wang
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zhaoqing Yang
- Parasitology Department, Kunming Medical College, Kunming, Yunnan, China
| | - Lili Yuan
- Parasitology Department, Kunming Medical College, Kunming, Yunnan, China
| | - Daniel M. Parker
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Chulalongkorn University, Bangkok, Thailand
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Chulalongkorn University, Bangkok, Thailand
| | - Phonepadith Xangsayarath
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN) and the Global Center of Excellence program, Nagasaki University, Japan
| | - Tiengkham Pongvongsa
- Station of Malariology, Parasitology and Entomology, North Phonesavang Village, Kaysone District, Savannakhet Province, Laos
| | - Hazuhiko Moji
- Research Institute for Humanity and Nature, Kyoto, Japan
| | - Trinh Dinh Tuong
- Department of Epidemiology, National Institute of Malariology, Parasitology, and Entomology, Hanoi, Vietnam
| | - Tomoko Abe
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN) and the Global Center of Excellence program, Nagasaki University, Japan
| | - Shusuke Nakazawa
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN) and the Global Center of Excellence program, Nagasaki University, Japan
| | - Myat Phone Kyaw
- Parasitology Research Division, Department of Medical Research-Lower Myanmar, Yangon, Myanmar
| | - Guiyun Yan
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
| | | | | | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN) and the Global Center of Excellence program, Nagasaki University, Japan
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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