The establishment of reference sequence for SARS-CoV-2 and variation analysis
The establishment of reference sequence for SARS-CoV-2 and variation analysis
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DOI：
10.1002/jmv.25762
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发表时间：
2020-03-20
影响因子：
12.7
通讯作者：
Zhang, Zhenhua
中科院分区：
文献类型：
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作者：
Wang, Changtai;Liu, Zhongping;Zhang, Zhenhua
2019年12月左右开始，世界卫生组织将其命名为COVID-19的肺炎疫情在中国武汉爆发，并正在全球蔓延。国际病毒分类委员会冠状病毒研究小组很快发现一种新型冠状病毒是造成这种情况的原因，该新型冠状病毒被命名为严重急性呼吸综合征冠状病毒2（SARS-CoV-2）。目前临床核酸检测的灵敏度有限，尚不清楚是否与遗传变异有关。在本研究中，我们从国家生物技术信息中心和GISAID数据库中检索了95个SARS-CoV-2毒株的全长基因组序列，通过多重序列比对和系统发育分析建立了参考序列，并分析了SARS-CoV-2基因组的序列变异。各毒株之间的同源性普遍较高，其中核苷酸水平同源性达99.99%（99.91%-100%），氨基酸水平同源性达99.99%（99.79%-100%）。尽管开放阅读框（ORF）区域的总体变异较低，但在1a、1b、S、3a、M、8和N区域中鉴定出13个变异位点，其中ORF 8中的nt28144和ORF 1a中的nt8782位置的突变率分别为30.53％（29/95）和29.47％（28/95）。这些发现提示SARS-COV-2可能存在选择性突变，设计引物和探针时需要避开某些区域。 SARS-CoV-2参考序列的建立不仅有利于对该病毒的生物学研究，而且有利于未来SARS-CoV-2感染的诊断、临床监测和干预。
Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full-length genomic sequences of SARAS-CoV-2 strains from the National Center for Biotechnology Information and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS-CoV-2 genome. The homology among all viral strains was generally high, among them, 99.99% (99.91%-100%) at the nucleotide level and 99.99% (99.79%-100%) at the amino acid level. Although overall variation in open-reading frame (ORF) regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95), respectively. These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS-CoV-2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future.