Haffener Paige E, Hopson Helena D, Herbert-Mainero Alejandra, Ramirez Anayansi, Leffler Ellen M
Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
PLoS Pathog. 2025 Jun 18;21(6):e1013240. doi: 10.1371/journal.ppat.1013240. eCollection 2025 Jun.
Hepatocystis are apicomplexan parasites nested within the Plasmodium genus that infect primates and other vertebrates, yet few isolates have been genetically characterized. Using taxonomic classification and mapping characteristics, we searched for Hepatocystis infections within publicly available, blood-derived whole genome sequence (WGS) data from 326 wild non-human primates (NHPs) in 17 genera. We identified 37 Hepatocystis infections in Papio cynocephalus (yellow baboons) and four species of Chlorocebus monkeys (grivets, green monkeys, vervet monkeys, and malbroucks) sampled from locations in west, east, and south Africa. Hepatocystis cytb sequences from Papio and Chlorocebus hosts each clustered within host species among previously reported isolates from other NHP taxa. Utilizing the low-coverage sequence data (0.11-0.76X per sample) recovered across the nuclear Hepatocystis genome, we identified 349,893 polymorphic sites. Principle components analysis based on genotype likelihoods across all samples showed evidence for population structure by primate host species. Across the genome, windows of high SNP density revealed candidate hypervariable loci including Hepatocystis-specific gene families possibly involved in immune evasion and genes that may be involved in adaptation to their insect vector and hepatocyte invasion. Overall, this work demonstrates how WGS data from wild NHPs can be leveraged to study the evolution of apicomplexan parasites and potentially test for association between host genetic variation and parasite infection.
肝囊原虫是疟原虫属内的顶复门寄生虫，可感染灵长类动物和其他脊椎动物，但仅有少数分离株进行过基因特征分析。利用分类学分类和图谱特征，我们在来自17个属的326只野生非人灵长类动物（NHP）的公开血液全基因组序列（WGS）数据中搜索肝囊原虫感染情况。我们在采自西非、东非和南非的豚尾狒狒（黄狒狒）以及四种绿猴属猴子（灰绿猴、绿猴、草原猴和赤猴）中鉴定出37例肝囊原虫感染。来自豚尾狒狒和绿猴属宿主的肝囊原虫细胞色素b序列在之前报道的其他NHP分类群的分离株中，各自聚类在宿主物种内。利用在整个肝囊原虫核基因组中回收的低覆盖度序列数据（每个样本0.11 - 0.76X），我们鉴定出349,893个多态性位点。基于所有样本的基因型似然性进行的主成分分析显示，存在按灵长类宿主物种划分的种群结构证据。在整个基因组中，高SNP密度窗口揭示了候选高变位点，包括可能参与免疫逃避的肝囊原虫特异性基因家族以及可能参与适应其昆虫媒介和肝细胞入侵的基因。总体而言，这项工作展示了如何利用野生NHP的WGS数据来研究顶复门寄生虫的进化，并有可能测试宿主遗传变异与寄生虫感染之间的关联。
