National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China.
National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China; School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou 310013, PR China.
Mol Biochem Parasitol. 2023 Jun;254:111558. doi: 10.1016/j.molbiopara.2023.111558. Epub 2023 Mar 12.
To reveal the genetic characteristics of one member of the Plasmodium falciparum repetitive interspersed family (rif), we sequenced the rif gene (PF3D7_1254800) in 53 field isolates collected from Ghana-imported cases into China and compared them with 350 publicly available P. falciparum rif sequences from global populations. In the Ghana-imported population, the nucleotide diversities were 0.05714 and 0.06616 for the full length and variable region of rif gene, respectively. Meanwhile, 22 and 20 haplotypes were identified for the full length and variable region of rif gene (Hd = 0.843 and 0.838, respectively). Diversity of rif gene in Ghana-imported population was higher than that observed in Cambodia, Thailand, Vietnam, Myanmar, Mali, Ghana, and Senegal populations. In this analysis, we found high genetic diversity of rif gene in global P. falciparum populations and identified 158 haplotypes. Tajima's D-test shows that there are large differences in the direction of selection between the conserved and variable region of rif gene. Tajima's D value for the variable region was 0.20074, indicating that balancing selection existed in this region. We found that the variable region was the main target of selection for positive diversification, and most mutation sites were located in this region. The population structure suggested optimized cluster values of K = 6. The five groups in Ghana-imported population included a unique subpopulation. Our results reveal the dynamics of the rif gene (PF3D7_1254800) in P. falciparum populations, which can aid in the rational design of P. falciparum rif-based vaccines.
为了揭示恶性疟原虫重复间隔家族（rif）成员的遗传特征，我们对来自中国输入性疟疾病例的 53 个分离株中的 rif 基因（PF3D7_1254800）进行了测序，并与来自全球人群的 350 个公开 rif 序列进行了比较。在输入性加纳人群中，rif 基因全长和可变区的核苷酸多样性分别为 0.05714 和 0.06616。同时，全长和可变区分别鉴定出 22 个和 20 个单倍型（Hd 分别为 0.843 和 0.838）。rif 基因在输入性加纳人群中的多样性高于柬埔寨、泰国、越南、缅甸、马里、加纳和塞内加尔人群。在这项分析中，我们发现全球恶性疟原虫种群 rif 基因具有高度遗传多样性，并鉴定出 158 个单倍型。Tajima 的 D 检验表明，rif 基因保守区和可变区的选择方向存在很大差异。可变区 Tajima 的 D 值为 0.20074，表明该区域存在平衡选择。我们发现可变区是正向多样化选择的主要靶区，大多数突变位点位于该区域。群体结构提示优化聚类值 K=6。加纳输入性人群中的 5 个群体包括一个独特的亚群。我们的研究结果揭示了 rif 基因（PF3D7_1254800）在恶性疟原虫种群中的动态变化，这有助于合理设计基于 rif 的恶性疟原虫疫苗。
