Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.
复制标题
SARS-CoV-2 基因组的单核苷酸保守状态注释。
DOI：
10.1101/2020.07.13.201277
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
Ernst,Jason
中科院分区：
文献类型：
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作者：
Kwon,SooBin;Ernst,Jason
鉴于COVID-19的全球影响和严重性，迫切需要更好地了解SARS-CoV-2基因组和突变。冠状病毒多株序列比对为解释冠状病毒基因组及其变异提供了重要信息。我们应用比较基因组学方法，ConsHMM，冠状病毒的多菌株比对，注释每个碱基的SARS-CoV-2基因组的保守状态的基础上，冠状病毒之间的序列比对模式。所学习的保守状态显示出基因、蛋白质结构域和其他感兴趣区域的不同富集模式。某些州的SARS-CoV-2突变强烈富集或耗尽，可用于预测潜在的后续突变。我们希望保守状态是解释SARS-CoV-2基因组和突变的资源。
Given the global impact and severity of COVID-19, there is a pressing need for a better understanding of the SARS-CoV-2 genome and mutations. Multi-strain sequence alignments of coronaviruses (CoV) provide important information for interpreting the genome and its variation. We apply a comparative genomics method, ConsHMM, to the multi-strain alignments of CoV to annotate every base of the SARS-CoV-2 genome with conservation states based on sequence alignment patterns among CoV. The learned conservation states show distinct enrichment patterns for genes, protein domains, and other regions of interest. Certain states are strongly enriched or depleted of SARS-CoV-2 mutations, which can be used to predict potentially consequential mutations. We expect the conservation states to be a resource for interpreting the SARS-CoV-2 genome and mutations.