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Liu Y, Zhang T, Chen SB, Cui YB, Wang SQ, Zhang HW, Shen HM, Chen JH. Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s. Front Microbiol 2023; 14:1071689. [PMID: 36846776 PMCID: PMC9948256 DOI: 10.3389/fmicb.2023.1071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction In malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China. Methods The samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection. Results China's inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades. Discussion Our data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.
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Affiliation(s)
- Ying Liu
- 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,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 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
| | - 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
| | - Shu-Qi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hong-Wei Zhang
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, 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,Hai-Mo Shen, ✉
| | - 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,*Correspondence: Jun-Hu Chen, ✉
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