Fan Jiangbin, Jehle Johannes A, Wennmann Jörg T
Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany.
Virus Evol. 2020 Sep 29;7(1):veaa073. doi: 10.1093/ve/veaa073. eCollection 2021 Jan.
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.
病毒的遗传多样性是由基因组突变及其宿主选择驱动的，这导致了毒力以及宿主反应的差异。杆状病毒是昆虫的天然病原体，常作为害虫生物防治剂喷洒在数十万至数百万公顷的土地上，病毒 - 宿主共同进化现象具有特殊的科学意义和经济重要性，因为杆状病毒产品的高毒力至关重要，且需要尽可能避免宿主抗性的出现。在本研究中，基于下一代测序数据并通过分析单核苷酸多态性（SNP）的分布，对二十种苹果蠹蛾颗粒体病毒（CpGV）分离株的群体结构进行了研究，其中包括来自不同地理来源的十二个分离株和八个商业制剂。应用一种完全无共有序列的定量SNP分析来鉴定753个变异SNP位点，这些位点是单个或CpGV分离株组所特有的。基于定量SNP分析，鉴定出了同质、异质以及混合分离株，并解读了它们的基因型比例，揭示了来自世界各地的CpGV分离株具有高度的遗传多样性。基于主成分层次聚类（HCPC），鉴定出六个不同的分离株/组簇，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全基因组信息。不同分离株在HCPC中的相对位置反映了不同基因型可变组成的比例。所建立的方法提供了新的分析工具来解读杆状病毒分离株中基因型混合物的分子复杂性，从而以比基于共有序列的分析更合适的形式描绘杆状病毒分离株的群体结构。
