Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
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DOI：
10.1093/bioinformatics/btaa145
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发表时间：
2020-06-01
期刊：
影响因子：
5.8
通讯作者：
de Oliveira, Tulio
中科院分区：
文献类型：
--
作者：
Cleemput, Sara;Dumon, Wim;de Oliveira, Tulio
基因组侦探是一款基于网络、用户友好的软件应用程序，可从下一代测序数据集中快速准确地组装所有已知病毒基因组。该应用程序允许从 FASTA 格式的组装基因组中识别系统发育簇和基因型。自2019年发布以来，我们已经制作了许多针对引起大规模爆发的新兴病毒的打字工具，例如巴西的寨卡病毒和黄热病病毒。在这里，我们推出了基因组检测冠状病毒分型工具，该工具可以准确识别在中国和世界各地分离的新型严重急性呼吸综合征（SARS）相关冠状病毒（SARS-CoV-2）序列。该工具每次提交最多可接受 2000 个序列，新的全基因组序列的分析大约需要 1 分钟。该工具已经使用来自 10 个冠状病毒物种的数百个全基因组进行了测试和验证，并正确分类了所有 SARS 相关冠状病毒 (SARSr-CoV) 以及 SARS-CoV-2 的所有可用公共数据。随着疫情在全球范围内蔓延，该工具还可以跟踪新的病毒突变，这可能有助于加速新型诊断方法、药物和疫苗的开发，以阻止 COVID-19 疾病。
Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.