Abstract Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus–host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next-generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence-free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC), six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.

中文翻译：

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遗传变异定量分析揭示苹果粒病毒分离物的种群结构


摘要 病毒的遗传多样性是由基因组突变和宿主选择驱动的，导致毒力和宿主反应的差异。对于杆状病毒来说，它是自然存在的昆虫病原体，经常被喷洒在数十万至数百万公顷的土地上，作为害虫的生物防治剂，病毒与宿主的共同进化现象具有特别的科学意义和经济重要性，因为杆状病毒的高毒力杆状病毒产品至关重要，需要尽可能避免宿主耐药性的出现。本研究以二代测序数据为基础，通过分析单个菌株的分布，对20个苹果蠹颗粒病毒（CpGV）分离株的种群结构进行了研究，其中包括来自不同地理来源的12个分离株和8个商业制剂。核苷酸多态性（SNP）。应用完全一致的无序列定量 SNP 分析来鉴定 753 个变异 SNP 位点，这些位点对单个以及 CpGV 分离株组具有特异性。基于定量 SNP 分析，鉴定了同源、异源以及混合分离株，并破译了它们的基因型比例，揭示了世界各地 CpGV 分离株的高度遗传多样性。基于主成分 (HCPC) 的层次聚类，确定了六个不同的分离株/类群簇，代表了所提出的 CpGV 主要系统发育谱系，但包含来自病毒混合物的完整基因组信息。 HCPC 中不同分离株的相对位置反映了不同基因型的可变组成的比例。 所建立的方法提供了新颖的分析工具来破译杆状病毒分离株中基因型混合物的分子复杂性，从而以比基于共识的分析更充分的形式描述杆状病毒分离株的群体结构。