Data from: Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area

Plasmodium falciparum malaria is a major global health problem that is being targeted for progressive elimination. Knowledge of local disease transmission patterns in endemic countries is critical to these elimination efforts. To investigate fine-scale patterns of malaria transmission, we have compared repertoires of rapidly evolving var genes in a highly endemic area. A total of 3680 high quality DBLα sequences were obtained from 68 P. falciparum isolates from ten villages spread over two distinct catchment areas on the north coast of Papua New Guinea (PNG). Modeling of the extent of var gene diversity in the two parasite populations predicts more than twice as many var gene alleles circulating within each catchment (Mugil=906; Wosera=1094) than previously recognized in PNG (Amele=369). In addition, there were limited levels of var gene sharing between populations, consistent with local parasite population structure. Phylogeographic analyses demonstrate that while neutrally evolving microsatellite markers identified population structure only at the catchment level, var gene repertoires reveal further fine-scale geospatial clustering of parasite isolates. The clustering of parasite isolates by village in Mugil, but not in Wosera was consistent with the physical and cultural isolation of the human populations in the two catchments. The study highlights the micro-heterogeneity of P. falciparum transmission in highly endemic areas and demonstrates the potential of var genes as markers of local patterns of parasite population structure.

恶性疟原虫疟疾是全球主要公共卫生问题之一，目前正被纳入逐步消除的防控目标。了解流行地区的本地疾病传播模式，对于此类消除行动至关重要。为探究疟疾传播的精细尺度模式，本研究对高流行区域内快速演化的var基因（var gene）库进行了比较分析。我们从巴布亚新几内亚（PNG）北海岸两个独立集水区的10个村落的68株恶性疟原虫分离株中，共获得3680条高质量DBLα序列。通过对两个寄生虫种群的var基因多样性程度进行建模分析，预测每个集水区内传播的var基因等位基因数量是此前在巴布亚新几内亚记录的两倍以上：Mugil集水区为906个，Wosera集水区为1094个，而此前记录的Amele集水区仅为369个。此外，种群间的var基因共享水平有限，这与本地寄生虫种群结构特征相符。系统地理学分析显示，尽管仅能通过中性演化的微卫星标记（microsatellite marker）在集水区尺度上分辨种群结构，但var基因库却能揭示寄生虫分离株更精细的地理空间聚类特征。Mugil集水区内寄生虫分离株呈现按村落聚类的特征，而Wosera集水区则无此现象，这与两个集水区内人群的地理与文化隔离状况相符。本研究凸显了高流行区域内恶性疟原虫传播的微观异质性，并证实var基因可作为解析本地寄生虫种群结构模式的分子标记。