Interpreting imported malaria genomes: population-genomic sensitivity analyses of West Africa-associated Plasmodium falciparum isolates detected in China
- 1Department of Parasitology, School of Medicine, and Department of Blood Transfusion, Xi’an International Medical Center Hospital, Northwest University, Xi’an, Shaanxi, China
- 2College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
Abstract
Background: Genomes obtained through imported-malaria surveillance can support source attribution and monitoring of parasite movement. However, these genomes are sampled after travel, diagnosis, reporting, and specimen availability, and may not be directly interchangeable with parasites sampled in endemic settings. Comparisons with public reference data may also be affected by geographic composition, sequencing quality, genotype filtering, and within-host infection complexity.
Methods: We compared West Africa-associated P. falciparum isolates detected through China’s post-elimination malaria surveillance system with West African Pf3K and locally collected comparison isolates. We implemented country-balanced reference subsampling, a geographically restricted and quality-controlled population-structure analysis, and sensitivity analyses restricted to imported isolates with FWS>0.90 or 0.95. Population structure, within-host complexity, identity-by-descent, nucleotide diversity, gene-level FST, and Tajima’s D were evaluated using analysis-specific variant sets.
Results: In the quality-controlled D1 analysis, 31 China-imported isolates showed a population-structure distribution that did not fully overlap with the selected West African Pf3K reference panel. This broad placement was qualitatively compatible with the high-FWS D2a subset of four imported isolates. Country-balanced reference subsampling produced similar broad PCA placement. In the D2b analysis of nine imported isolates with FWS>0.90, central gene-level FST summaries were like those in the original analysis, whereas individual-gene estimates and Tajima’s D contrasts were sensitive to the revised filtering and sample restriction.
Conclusions: Imported malaria genomes provide a surveillance-defined view of parasite diversity and remain useful for regional population placement and surveillance applications. However, their comparison with endemic reference panels is sensitive to dataset composition, variant filtering, and infection complexity. Imported surveillance genomes should therefore not be interpreted as unbiased or directly interchangeable proxies for parasite populations in presumed source settings. The observed differences cannot be attributed solely to surveillance pathway.
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BibTeX
@article{du2026interpreting,
title = {{Interpreting imported malaria genomes: population-genomic sensitivity analyses of West Africa-associated Plasmodium falciparum isolates detected in China}},
author = {Xuli Du and Ye Hu and Haimo Shen and Mengyu Li and Yuxin Wang and Yanli Bai and Shenbo Chen and Yanting Fan},
journal = {Frontiers in Cellular and Infection Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fcimb.2026.1950822},
url = {https://doi.org/10.3389/fcimb.2026.1950822},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Interpreting imported malaria genomes: population-genomic sensitivity analyses of West Africa-associated Plasmodium falciparum isolates detected in China
AU - Xuli Du
AU - Ye Hu
AU - Haimo Shen
AU - Mengyu Li
AU - Yuxin Wang
AU - Yanli Bai
AU - Shenbo Chen
AU - Yanting Fan
PY - 2026
DA - 2026/10/12
JO - Frontiers in Cellular and Infection Microbiology
DO - 10.3389/fcimb.2026.1950822
UR - https://doi.org/10.3389/fcimb.2026.1950822
AB - Background: Genomes obtained through imported-malaria surveillance can support source attribution and monitoring of parasite movement. However, these genomes are sampled after travel, diagnosis, reporting, and specimen availability, and may not be directly interchangeable with parasites sampled in endemic settings. Comparisons with public reference data may also be affected by geographic composition, sequencing quality, genotype filtering, and within-host infection complexity. Methods: We compared West Africa-associated P. falciparum isolates detected through China’s post-elimination malaria surveillance system with West African Pf3K and locally collected comparison isolates. We implemented country-balanced reference subsampling, a geographically restricted and quality-controlled population-structure analysis, and sensitivity analyses restricted to imported isolates with FWS>0.90 or 0.95. Population structure, within-host complexity, identity-by-descent, nucleotide diversity, gene-level FST, and Tajima’s D were evaluated using analysis-specific variant sets. Results: In the quality-controlled D1 analysis, 31 China-imported isolates showed a population-structure distribution that did not fully overlap with the selected West African Pf3K reference panel. This broad placement was qualitatively compatible with the high-FWS D2a subset of four imported isolates. Country-balanced reference subsampling produced similar broad PCA placement. In the D2b analysis of nine imported isolates with FWS>0.90, central gene-level FST summaries were like those in the original analysis, whereas individual-gene estimates and Tajima’s D contrasts were sensitive to the revised filtering and sample restriction. Conclusions: Imported malaria genomes provide a surveillance-defined view of parasite diversity and remain useful for regional population placement and surveillance applications. However, their comparison with endemic reference panels is sensitive to dataset composition, variant filtering, and infection complexity. Imported surveillance genomes should therefore not be interpreted as unbiased or directly interchangeable proxies for parasite populations in presumed source settings. The observed differences cannot be attributed solely to surveillance pathway.
SN - 2235-2988
ER -