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.

新型人类冠状病毒 (SARS-CoV-2) 导致 2019 年冠状病毒病 (COVID-19) 在全球范围内大流行。控制COVID-19大流行对于公共卫生至关重要，也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，给病毒控制带来巨大困难。监测病毒变异和筛选功能突变位点对于传染病的预防和控制至关重要。在本研究中，我们开发了一款用户友好的软件，名为 BioAider，用于对大规模基因组测序数据进行快速序列注释和突变分析。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 组潜在相关的替换。 NSP13-Y541C 是至关重要的取代，可能会影响病毒解旋酶的解旋活性。特别是，我们发现了 SARS-CoV-2 与 SARS-CoV 不同的 SR 丰富区域，表明 SARS-CoV-2 具有更复杂的复制机制和独特的 NM 相互作用。有趣的是，SARS-CoV-2 中 SSRX 重复片段的数量为其动物起源提供了进一步的证据。总的来说，我们开发了一种有效的工具来快速识别病毒基因组突变，这可以促进病毒基因组研究。利用这个工具，我们找到了SARS-CoV-2传播途径的关键线索，这将为病原冠状病毒的流行控制提供理论支持。