通过基于树的学习预测病毒宿主密码体适应性和路径转移,以密码体使用偏差和基因组特征为基础
Shuquan Su1,2,3, Zhongran Ni4,5, Tian Lan2
1Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, China.
Scientific reports
|April 10, 2025
概括
本研究引入了一种定量方法来测量病毒密码体适应性 (VCF) 和其转移,这对于了解病原体传播至关重要. 机器学习模型使用病毒基因组属性预测VCF,揭示了摇摆位置.
科学领域:
- 病毒学 病毒学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 病毒密码体适应性 (VCF) 和它的转变对于病原体流行病学至关重要,但缺乏定量研究.
- 在基因组层面了解宿主病毒相互作用对于预测病毒行为至关重要.
研究的目的:
- 开发和应用病毒密码体适应性 (VCF) 和其转移的定量测量.
- 调查病毒基因组属性的预测能力,包括对宿主基因组适应性的相对同义代码使用 (RSCU).
- 建立一个人类病毒密码体适应性 (HVCF) 评分来评估感染人类的病毒.
主要方法:
- 利用基于树的机器学习模型来预测基于病毒基因组属性和RSCU的病毒宿主密码体能.
- 对RSCU数据进行统计分析,重点关注病毒编码子的摇摆位置.
- 开发了一个生物信息学工具来模拟基于编码子的病毒健康转移.
- 评估了包括SARS-CoV-2在内的人类和非人类病毒的HVCF得分,并比较了相关的蝙蝠冠状病毒.
主要成果:
- 相对同义代码组使用 (RSCU) 和其他基因组特征准确预测病毒宿主代码组适应性.
- 病毒密码体的摇摆位置对于区分宿主密码体适应性至关重要.
- 在SARS-CoV-2中没有观察到人类非传染性密码体适应性的显著转变.
- 蝙蝠冠状病毒Tylonycteris HKU4亲属在人类密码体适应性方面显示出与SARS-CoV-2的潜在相似之处.
- 同名突变在预测的密码体适应性转移途径中是丰富的.
结论:
- 开发的模型可靠地描述宿主密码体适应性,并可转化为人类病毒密码体适应性 (HVCF) 评分.
- HVCF分析提供了对病毒与宿主相互作用和进化轨迹的见解.
- 研究结果表明,蝙蝠冠状病毒和SARS-CoV-2之间的潜在进化联系涉及人类密码体适应性.
- 同名突变为病毒进化研究和环境监测提供了新的视角.
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