BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission
BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission
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DOI：
10.1016/j.scs.2020.102466
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发表时间：
2020-12-01
影响因子：
11.7
通讯作者：
Ge, Xing-Yi
中科院分区：
文献类型：
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作者：
Zhou, Zhi-Jian;Qiu, Ye;Ge, Xing-Yi
新型人类冠状病毒（SARS-CoV-2）导致2019年冠状病毒病（COVID-19）全球大流行。控制新冠疫情对公共卫生至关重要，是维护社会稳定的前提。然而，SARS-CoV-2的起源和传播途径尚不清楚，给病毒的控制带来了巨大的困难。监测病毒变异和筛选功能突变位点对于预防和控制传染病至关重要。在这项研究中，我们开发了一个用户友好的软件，名为BioAider，快速序列注释和突变分析的大规模基因组测序数据。在此，我们在3，240个SARS-CoV-2基因组序列中检测到14个替换热点，包括3组潜在连锁的替换。NSP 13-Y 541 C是影响病毒解旋酶解旋活性的关键位点。特别是，我们发现了一个不同于SARS-CoV-2的SR富集区，表明SARS-CoV-2的复制机制更复杂，N-M相互作用更独特。有趣的是，SARS-CoV-2中SSRX重复片段的数量提供了其动物来源的进一步证据。总体而言，我们开发了一种快速鉴定病毒基因组突变的有效工具，可以促进病毒基因组研究。利用该工具，我们发现了SARS冠状病毒传播途径的关键线索，为病原性冠状病毒的流行控制提供了理论支持。
The novel human coronavirus (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19) pandemic worldwide. Control of COVID-19 pandemic is vital for public health and is the prerequisite to maintain social stability. However, the origin and transmission route of SARS-CoV-2 is unclear, bringing huge difficult to virus control. Monitoring viral variation and screening functional mutation sites are crucial for prevention and control of infectious diseases. In this study, we developed a user-friendly software, named BioAider, for quick sequence annotation and mutation analysis on large-scale genome-sequencing data. Herein, we detected 14 substitution hotspots within 3,240 SARS-CoV-2 genome sequences, including 3 groups of potentially linked substitution. NSP13-Y541C was crucial substitution which might affect the unwinding activity of the viral helicase. In particular, we discovered a SR-rich region of SARS-CoV-2 distinct from SARS-CoV, indicating more complex replication mechanism and unique N-M interaction of SARS-CoV-2. Interestingly, the quantity of SSRX repeat fragments in SARS-CoV-2 provided further evidence of its animal origin. Overall, we developed an efficient tool for rapid identification of viral genome mutations which could facilitate viral genomic studies. Using this tool, we have found critical clues for the transmission route of SARS-CoV-2 which would provide theoretical support for the epidemic control of pathogenic coronaviruses.