PHDtools:一种用于病原体检测和多维遗传签名解码的平台,以实现病原体基因组学数据分析在线分析.
Dongyan Xiong1, Xiaoxu Zhang2, Bohan Xu3
1CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
Gene
|February 26, 2024
概括
一个新的平台,PHDtools,帮助临床实验室分析新出现疾病的病原体基因组学. 它确定了共感染和Omicron变体的演变,指导了抗病毒和疫苗的开发.
科学领域:
- 基因组学和生物信息学
- 传染病监测 传染病监测 传染病
- 病毒进化是病毒的进化
背景情况:
- 新出现的传染病需要快速的病原体识别和基因组表征.
- 高通量测序产生复杂的数据,需要专门的生物信息学工具.
- 临床实验室往往缺乏生物信息学专业知识来分析大型基因组数据集.
研究的目的:
- 开发一个可访问,用户友好的在线平台 (PHDtools) 用于分析元基因组数据.
- 为了实现病原体识别和多维基因组特征分析,包括宿主内部/宿主间和血统变异.
- 支持临床实验室解码复杂的基因组大数据,用于新兴疾病管理.
主要方法:
- 开发一个交互式在线平台,PHDtools,具有15个不同的分析功能.
- 利用了元基因组下一代测序 (mNGS) 数据分析.
- 应用PHD工具来分析来自172个进口COVID-19病例的基因组数据.
主要成果:
- 在27名患者中确诊的同时感染:SARS-CoV-2与流感病毒 (n=9) 或人类皮科比纳病毒 (n=19).
- 确定了Omicron亚系,并观察到非结构性和M基因的突变增加.
- 在E和M基因的宿主内部变异中检测到阳性选择 (Ka/Ks>1),表明了适应性进化.
结论:
- 对于具有有限生物信息学背景的临床用户来说,PHDtools是准确,用户友好和方便的.
- 使用PHDtools进行的临床监测揭示了SARS-CoV-2的潜在进化特征.
- 抗病毒药物和疫苗的开发应该考虑S基因以外的基因变异.
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