Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe
Abstract Background Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies. Methods This study collected surveillance data and generated amplicon sequ...
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Nature Portfolio
2025-05-01
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| Series: | Communications Medicine |
| Online Access: | https://doi.org/10.1038/s43856-025-00905-8 |
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| author | Ying‑An Chen Peng-Yin Ng Daniel Garcia-Ruiz Aaron Elliot Brian Palmer Ronalg Mendes Costa d’ Assunção Carvalho Lien-Fen Tseng Cheng-Sheng Lee Kun-Hsien Tsai Bryan Greenhouse Hsiao-Han Chang |
| author_facet | Ying‑An Chen Peng-Yin Ng Daniel Garcia-Ruiz Aaron Elliot Brian Palmer Ronalg Mendes Costa d’ Assunção Carvalho Lien-Fen Tseng Cheng-Sheng Lee Kun-Hsien Tsai Bryan Greenhouse Hsiao-Han Chang |
| author_sort | Ying‑An Chen |
| collection | DOAJ |
| description | Abstract Background Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies. Methods This study collected surveillance data and generated amplicon sequencing data from 980 samples between 2010 and 2016 to examine the genetic structure of the parasite population. Results Here we show that the mean multiplicity of infection (MOI) is 1.3, with 11% polyclonal infections, indicating low transmission intensity. Temporal trends of these genetic metrics do not align with incidence rates, suggesting that changes in genetic metrics may not straightforwardly reflect changes in transmission intensity, particularly in low transmission settings where genetic drift and importation have a substantial impact. While 88% of samples are genetically linked, continuous turnover in genetic clusters and changes in drug-resistance haplotypes are observed. Principal component analysis reveals some STP samples are genetically similar to those from Central and West Africa, indicating possible importation. Conclusions These findings highlight the need to prioritize several interventions, such as targeted interventions against transmission hotspots, reactive case detection, and strategies to reduce the introduction of new parasites into this island nation as it approaches elimination. This study also serves as a case study for implementing genetic surveillance in a low transmission setting. |
| format | Article |
| id | doaj-art-64689060cd8a40eeb4d75081ebd58381 |
| institution | OA Journals |
| issn | 2730-664X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Medicine |
| spelling | doaj-art-64689060cd8a40eeb4d75081ebd583812025-08-20T02:03:32ZengNature PortfolioCommunications Medicine2730-664X2025-05-015111210.1038/s43856-025-00905-8Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and PrincipeYing‑An Chen0Peng-Yin Ng1Daniel Garcia-Ruiz2Aaron Elliot3Brian Palmer4Ronalg Mendes Costa d’ Assunção Carvalho5Lien-Fen Tseng6Cheng-Sheng Lee7Kun-Hsien Tsai8Bryan Greenhouse9Hsiao-Han Chang10EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of CaliforniaInstitute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua UniversityInstitute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua UniversityEPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of CaliforniaEPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of CaliforniaTaiwanese Medical MissionTaiwan Anti-Malarial Advisory MissionInstitute of Molecular and Cellular Biology, College of Life Sciences and Medicine, National Tsing Hua UniversityTaiwan Anti-Malarial Advisory MissionEPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of CaliforniaInstitute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua UniversityAbstract Background Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies. Methods This study collected surveillance data and generated amplicon sequencing data from 980 samples between 2010 and 2016 to examine the genetic structure of the parasite population. Results Here we show that the mean multiplicity of infection (MOI) is 1.3, with 11% polyclonal infections, indicating low transmission intensity. Temporal trends of these genetic metrics do not align with incidence rates, suggesting that changes in genetic metrics may not straightforwardly reflect changes in transmission intensity, particularly in low transmission settings where genetic drift and importation have a substantial impact. While 88% of samples are genetically linked, continuous turnover in genetic clusters and changes in drug-resistance haplotypes are observed. Principal component analysis reveals some STP samples are genetically similar to those from Central and West Africa, indicating possible importation. Conclusions These findings highlight the need to prioritize several interventions, such as targeted interventions against transmission hotspots, reactive case detection, and strategies to reduce the introduction of new parasites into this island nation as it approaches elimination. This study also serves as a case study for implementing genetic surveillance in a low transmission setting.https://doi.org/10.1038/s43856-025-00905-8 |
| spellingShingle | Ying‑An Chen Peng-Yin Ng Daniel Garcia-Ruiz Aaron Elliot Brian Palmer Ronalg Mendes Costa d’ Assunção Carvalho Lien-Fen Tseng Cheng-Sheng Lee Kun-Hsien Tsai Bryan Greenhouse Hsiao-Han Chang Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe Communications Medicine |
| title | Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe |
| title_full | Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe |
| title_fullStr | Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe |
| title_full_unstemmed | Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe |
| title_short | Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe |
| title_sort | genetic surveillance reveals low but sustained malaria transmission with clonal replacement in sao tome and principe |
| url | https://doi.org/10.1038/s43856-025-00905-8 |
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