Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom.
Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Elife. 2019 Jul 12;8:e40845. doi: 10.7554/eLife.40845.
Individual malaria infections can carry multiple strains of with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Furthermore, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.
个体疟疾感染可能携带多种具有不同亲缘关系的株系。然而，局部流行病学如何影响此类混合感染的特性尚不清楚。在这里，我们开发了一种从基因组测序数据中推断株系的增强方法，该方法估计了株系的数量、它们的比例、同源性（IBD）分布和个体单倍型。将其应用于 Pf3k 数据集，我们发现混合感染的发生率在不同国家从 29%到 63%不等，51%的混合感染涉及两种以上的株系。此外，我们估计，47%的有症状双重感染包含同胞株系，这些株系很可能是由一只蚊子同时传播的，并且有证据表明混合感染是在连续的感染循环中传播的。最后，利用来自疟疾地图集项目的数据，我们发现非洲内部而非亚洲内部，混合感染的发生率与 IBD 水平相关。
