塞拉利昂恶性疟原虫的综合基因组研究：遗传变异与抗药模式

Comprehensive genomic study of Plasmodium falciparum in Sierra leone: genetic variation and resistance patterns.

作者信息

Zhan Xin-Jie, Chen Shen-Bo, Wang Tian-Yu, Duan Yi-Wen, Shen Hai-Mo, Chen Jun-Hu, Xie Jing-Jing

机构信息

Department of laboratory, People's Hospital of Ningxiang City, Changsha, Hunan Province, China.

The 23rd batch of China Medical Team in Sierra Leone, Jui, Freetown, Sierra Leone.

出版信息

BMC Genomics. 2025 Jul 1;26(1):584. doi: 10.1186/s12864-025-11771-y.

DOI:10.1186/s12864-025-11771-y

PMID:40597624

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12210811/

Abstract

BACKGROUND

Malaria remains a significant global health concern, with being the most dangerous of the malaria-causing parasites. Sierra Leone, with year-round transmission of malaria, continues to experience high infection rates, largely due to . Although genomic databases have provided valuable insights into malaria transmission patterns, drug resistance, and population structure, data from Sierra Leone has been limited. This study aims to build on our previous report by incorporating new samples and providing a more comprehensive genomic analysis of in Sierra Leone, with a particular focus on genetic diversity, population structure, and drug resistance.

METHODS

We collected samples from Freetown, Sierra Leone, between December 2022 and March 2023. A total of 35 samples underwent sequencing using the MGISEQ and Illumina platforms, resulting in high-coverage genomic data. Population structure was assessed using PCA, NJ trees, and STRUCTURE analysis, alongside comparisons with a global dataset from the project. Genetic diversity was evaluated using metrics such as [Formula: see text], [Formula: see text], Tajima’s D, and iHS. XPEHH was used to examine selection pressures across different regions.

RESULTS

Sequencing yielded over 376,450 high-quality SNPs across 35 Sierra Leone isolates, indicating substantial genetic variability. PCA, NJ trees, and STRUCTURE analysis revealed that the Sierra Leone isolates formed distinct clusters from both West African and Southeast Asian samples, with evidence of region-specific genetic adaptation. The low IBD we found suggested that infections were largely independent. Meanwhile the Tajima’s D and iHS analysis showed strong directional selection in genes associated with immune evasion and drug resistance genes, exhibiting ongoing evolutionary pressure due to therapeutic behavior.

CONCLUSION

This study provides us not only a genomic database but also a profile of in Sierra Leone, revealing high genetic diversity, strong selection pressure on drug resistance genes, and unique population structures. Our data emphasize the need for continued genomic surveillance to better manage malaria.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12864-025-11771-y.

摘要

背景

疟疾仍然是全球重大的健康问题，其中[疟原虫名称]是最危险的疟原虫。在疟疾全年传播的塞拉利昂，感染率持续居高不下，主要原因是[具体原因]。尽管基因组数据库为疟疾传播模式、耐药性和种群结构提供了有价值的见解，但来自塞拉利昂的数据一直有限。本研究旨在基于我们之前的报告，纳入新样本并对塞拉利昂的[疟原虫名称]进行更全面的基因组分析，特别关注遗传多样性、种群结构和耐药性。

方法

我们于2022年12月至2023年3月期间从塞拉利昂弗里敦采集了[样本数量]个样本。总共35个样本使用MGISEQ和Illumina平台进行测序，得到了高覆盖度的基因组数据。使用主成分分析（PCA）、邻接树（NJ树）和结构分析（STRUCTURE分析）评估种群结构，并与[项目名称]的全球数据集进行比较。使用诸如[公式：见原文]、[公式：见原文]、 Tajima's D和iHS等指标评估遗传多样性。使用交叉种群扩展单倍型纯合性检验（XPEHH）来检查不同区域的选择压力。

结果

测序在35个塞拉利昂分离株中产生了超过376,450个高质量单核苷酸多态性（SNP），表明存在大量遗传变异。PCA、NJ树和STRUCTURE分析表明，塞拉利昂分离株与西非和东南亚样本形成了不同的聚类，有区域特异性遗传适应的证据。我们发现的低遗传同质性（IBD）表明感染在很大程度上是独立的。同时，Tajima's D和iHS分析显示与免疫逃避和耐药基因相关的基因存在强烈的定向选择，由于治疗行为而表现出持续的进化压力。