Thompson Jeremy R
Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
Present address: Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand.
J Gen Virol. 2022 Oct;103(10). doi: 10.1099/jgv.0.001789.
In this study 163 complete whole-genome sequences of the emerging pathogen grapevine red blotch virus (GRBV; genus , family ) were used to reconstruct phylogenies using Bayesian analyses on time-tipped (heterochronous) data. Using different combinations of priors, Bayes factors identified heterochronous datasets (3×200 million chains) generated from strict clock and exponential tree priors as being the most robust. Substitution rates of 3.2×10 subsitutions per site per year (95% HPD 4.3-2.1×10) across the whole of the GRBV genome were estimated, suggesting ancestral GRBV diverged from ancestral wild Vitis latent virus 1 around 9 000 years ago, well before the first documented arrival of in North America. Whole-genome analysis of GRBV isolates in a single infected field-grown grapevine across 12 years identified 12 single nucleotide polymorphisms none of which were fixed substitutions: an observation not discordant with the estimate. The substitution rate estimated here is lower than those estimated for other geminiviruses and is the first for a woody-host-infecting geminivirus.
在本研究中，利用新兴病原体葡萄红环斑病毒（GRBV；属，科）的163个完整全基因组序列，通过对时间标定（异时）数据进行贝叶斯分析来重建系统发育树。使用不同的先验组合，贝叶斯因子确定了由严格分子钟和指数树先验生成的异时数据集（3×2亿条链）最为稳健。估计整个GRBV基因组的替换率为每年每个位点3.2×10个替换（95%最高后验密度区间为4.3 - 2.1×10），这表明祖先GRBV大约在9000年前从祖先野生葡萄潜伏病毒1分化而来，远早于首次有记录的[此处原文缺失相关内容]抵达北美之前。对一株感染的田间种植葡萄藤上的GRBV分离株进行了12年的全基因组分析，鉴定出12个单核苷酸多态性，其中没有一个是固定替换：这一观察结果与[此处原文缺失相关内容]估计结果并不矛盾。此处估计的替换率低于其他双生病毒的估计值，并且是首次针对感染木本宿主的双生病毒的估计。
