Date of origin of the SARS coronavirus strains

	Date of origin of the SARS coronavirus strains
	Lu, HC ; Zhao, Y ; Zhang, JF ; Wang, YL ; Li, W ; Zhu, XP ; Sun, SW ; Xu, JY ; Ling, LJ ; Cai, L ; Bu, DB ; Chen, RS
	2004-02-06
发表期刊	BMC INFECTIOUS DISEASES
ISSN	1471-2334
卷号	4 页码:6
摘要	Background: A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS coronavirus as it spreads through the population. Moreover, finding a date for the last common ancestor of SARS coronavirus strains would be useful for understanding the circumstances surrounding the emergence of the SARS pandemic and the rate at which SARS coronavirus diverge. Methods: We propose a mathematical model to estimate the evolution rate of the SARS coronavirus genome and the time of the last common ancestor of the sequenced SARS strains. Under some common assumptions and justifiable simplifications, a few simple equations incorporating the evolution rate ( K) and time of the last common ancestor of the strains (T-0) can be deduced. We then implemented the least square method to estimate K and T-0 from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results. Results: Based on 6 strains with accurate dates of host death, we estimated the time of the last common ancestor to be about August or September 2002, and the evolution rate to be about 0.16 base/day, that is, the SARS coronavirus would on average change a base every seven days. We validated our method by dividing the strains into two groups, which coincided with the results from comparative genomics. Conclusion: The applied method is simple to implement and avoid the difficulty and subjectivity of choosing the root of phylogenetic tree. Based on 6 strains with accurate date of host death, we estimated a time of the last common ancestor, which is coincident with epidemic investigations, and an evolution rate in the same range as that reported for the HIV-1 virus.
收录类别	SCI
语种	英语
WOS研究方向	Infectious Diseases
WOS类目	Infectious Diseases
WOS记录号	WOS:000220209800001
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：19[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/13818
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chen, RS
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Bioinformat Res Grp, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Lu, HC,Zhao, Y,Zhang, JF,et al. Date of origin of the SARS coronavirus strains[J]. BMC INFECTIOUS DISEASES,2004,4:6.
APA	Lu, HC.,Zhao, Y.,Zhang, JF.,Wang, YL.,Li, W.,...&Chen, RS.(2004).Date of origin of the SARS coronavirus strains.BMC INFECTIOUS DISEASES,4,6.
MLA	Lu, HC,et al."Date of origin of the SARS coronavirus strains".BMC INFECTIOUS DISEASES 4(2004):6.