检查分子时钟假设对狂犬病病毒的当代进化
Rowan Durrant1, Christina A Cobbold1,2, Kirstyn Brunker1
1Boyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom.
PLoS pathogens
|November 25, 2024
概括
由于可变的潜伏期,分子钟模型可能无法完全捕捉狂犬病病毒的演变. 建模每代突变率为推断传播和预测血统出现提供了潜在的可能性.
科学领域:
- 进化生物学是进化的生物学.
- 病毒学 病毒学
- 基因组学就是基因组学.
背景情况:
- 分子钟假设假设不断的突变速率,在像狂犬病病毒 (RABV) 这样的病毒中经常受到侵犯.
- 可变的RABV潜伏期 (几天到一年以上) 表明复制减少,质疑基于时间的突变模型的适用性.
- 现有的速度变化的模型可能不能完全代表复杂的进化过程.
研究的目的:
- 通过每单位时间和每代突变模型,研究可变化期对根到尖的分歧的影响.
- 评估这些模型对时间标记RABV序列的根到尖分歧的代表性.
- 为了确定每代建模对于RABV进化的适当性.
主要方法:
- 在每单位时间和每代突变模型下对根到尖的分歧模式进行比较分析.
- 使用时间印的RABV序列数据评估模型性能.
- 计算坦桑尼亚RABV数据集的平均替换率.
主要成果:
- 每个时间单位和每代模型之间的差异模式在低置换率 (每代每基因组<1个置换) 无法区分.
- 在这个值以上,不同采样率的差异变得明显.
- 坦桑尼亚RABV数据集的平均替代率计算为每代每基因组0.17个替代.
结论:
- 在RABV的典型替代率下,每代模型不太可能与当代疫情的分子时钟模型有显著差异.
- 极端的潜伏期倾向于在进化时间的平均值,最大限度地减少分歧模式的差异.
- 建模每代替代率显示出对推断传播树和预测病毒中血统出现等应用的承诺.
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