Leigh Deborah M, Peranić Karla, Prospero Simone, Cornejo Carolina, Ćurković-Perica Mirna, Kupper Quirin, Nuskern Lucija, Rigling Daniel, Ježić Marin
Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland.
Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia.
Virus Evol. 2021 Dec 1;7(2):veab101. doi: 10.1093/ve/veab101. eCollection 2021 Sep.
Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
宿主内动态是病毒进化的核心组成部分，但大多数宿主内数据来自范围狭窄的宿主或实验性感染。获取关于自然发生的病毒感染的宿主内多样性和动态的更广泛信息对于我们理解整个病毒圈的进化至关重要。在这里，我们使用PacBio长读长HiFi测序来表征RNA真菌病毒（CHV1）自然感染的宿主内群体。CHV1是栗疫病菌的一种生物防治剂，它与该真菌一起共同入侵了欧洲。我们对分布在克罗地亚和瑞士四个地点的38例自然CHV1感染的宿主内病毒多样性的突变和单倍型进行了表征。宿主内CHV1多样性值受到纯化选择、随时间积累的突变以及宿主基因组中防御位点的上位性相互作用的影响。地理景观特征通过限制传播和导致奠基者效应影响CHV1宿主间关系。有趣的是，少数宿主内病毒单倍型在大地理距离上显示出高序列相似性，不太可能通过传播联系起来。
