Evolutionary analysis and lineage designation of SARS-CoV-2 genomes

	Evolutionary analysis and lineage designation of SARS-CoV-2 genomes
	Tang, XL; Ying, RC; Yao, XM; Li, GH; Wu, CC; Tang, YYL; Li, ZD; Kuang, BS; Wu, F; Chi, CS; Du, XM; Qin, Y; Gao, SH; Hu, SNA; Ma, JC; Liu, TG; Pang, XH; Wang, JW; Zhao, GP; Tan, WJ; Zhang, YP; Lu, XM; Lu, J
	2021
发表期刊	SCIENCE BULLETIN
ISSN	2095-9273
卷号	66 期号:22 页码:2297-2311
摘要	The pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has caused immense global disruption. With the rapid accumulation of SARS-CoV-2 genome sequences, however, thousands of genomic variants of SARSCoV-2 are now publicly available. To improve the tracing of the viral genomes' evolution during the development of the pandemic, we analyzed single nucleotide variants (SNVs) in 121,618 high-quality SARS-CoV-2 genomes. We divided these viral genomes into two major lineages (L and S) based on variants at sites 8782 and 28144, and further divided the L lineage into two major sublineages (L1 and L2) using SNVs at sites 3037, 14408, and 23403. Subsequently, we categorized them into 130 sublineages (37 in S, 35 in L1, and 58 in L2) based on marker SNVs at 201 additional genomic sites. This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages. We also provide a companion website (www.covid19evolution.net) that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification. Finally, we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2's evolution. These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2's genome evolution. (c) 2021 Science China Press. Published by Elsevier B.V. and Science China Press. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13149
专题	科研部门_适应性进化与进化医学（吕雪梅）昆明动物研究所
推荐引用方式 GB/T 7714	Tang, XL,Ying, RC,Yao, XM,et al. Evolutionary analysis and lineage designation of SARS-CoV-2 genomes[J]. SCIENCE BULLETIN,2021,66(22):2297-2311.
APA	Tang, XL.,Ying, RC.,Yao, XM.,Li, GH.,Wu, CC.,...&Lu, J.(2021).Evolutionary analysis and lineage designation of SARS-CoV-2 genomes.SCIENCE BULLETIN,66(22),2297-2311.
MLA	Tang, XL,et al."Evolutionary analysis and lineage designation of SARS-CoV-2 genomes".SCIENCE BULLETIN 66.22(2021):2297-2311.

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2023022117.pdf（3085KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文