title: Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone.
abstract: A novel Ebola virus (EBOV) first identified in March 2014 has infected more than 25,000 people in West Africa, resulting in more than 10,000 deaths. Preliminary analyses of genome sequences of 81 EBOV collected from March to June 2014 from Guinea and Sierra Leone suggest that the 2014 EBOV originated from an independent transmission event from its natural reservoir followed by sustained human-to-human infections. It has been reported that the EBOV genome variation might have an effect on the efficacy of sequence-based virus detection and candidate therapeutics. However, only limited viral information has been available since July 2014, when the outbreak entered a rapid growth phase. Here we describe 175 full-length EBOV genome sequences from five severely stricken districts in Sierra Leone from 28 September to 11 November 2014. We found that the 2014 EBOV has become more phylogenetically and genetically diverse from July to November 2014, characterized by the emergence of multiple novel lineages. The substitution rate for the 2014 EBOV was estimated to be 1.23 × 10(-3) substitutions per site per year (95% highest posterior density interval, 1.04 × 10(-3) to 1.41 × 10(-3) substitutions per site per year), approximating to that observed between previous EBOV outbreaks. The sharp increase in genetic diversity of the 2014 EBOV warrants extensive EBOV surveillance in Sierra Leone, Guinea and Liberia to better understand the viral evolution and transmission dynamics of the ongoing outbreak. These data will facilitate the international efforts to develop vaccines and therapeutics.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yi-Gang
authors.initials: YG
authors.lastname: Tong
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Taian 271000, China.
authors.forename: Wei-Feng
authors.initials: WF
authors.lastname: Shi
authors.affiliation: Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Di
authors.initials: D
authors.lastname: Liu
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Qian
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Long
authors.initials: L
authors.lastname: Liang
authors.affiliation: Beijing Key Laboratory of New Molecular Diagnostics Technology, Beijing 100850, China.
authors.forename: Xiao-Chen
authors.initials: XC
authors.lastname: Bo
authors.affiliation: Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Hong-Guang
authors.initials: HG
authors.lastname: Ren
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Fan
authors.affiliation: Beijing Key Laboratory of New Molecular Diagnostics Technology, Beijing 100850, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Ni
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Jin
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Teng
authors.affiliation: Beijing Key Laboratory of New Molecular Diagnostics Technology, Beijing 100850, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
authors.affiliation: Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone.
authors.forename: David
authors.initials: D
authors.lastname: Kargbo
authors.affiliation: Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone.
authors.forename: Foday
authors.initials: F
authors.lastname: Dafae
authors.affiliation: Sierra Leone-China Friendship Hospital, Freetown, Sierra Leone.
authors.forename: Alex
authors.initials: A
authors.lastname: Kanu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Cheng-Chao
authors.initials: CC
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhi-Heng
authors.initials: ZH
authors.lastname: Lan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors.forename: Yang
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Hui-Jun
authors.initials: HJ
authors.lastname: Lu
authors.affiliation: Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Xiao-Guang
authors.initials: XG
authors.lastname: Zhang
authors.affiliation: Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100730, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Yu-Xi
authors.initials: YX
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yong-Qiang
authors.initials: YQ
authors.lastname: Deng
authors.affiliation: Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100730, China.
authors.forename: Hao-Xiang
authors.initials: HX
authors.lastname: Su
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Wen-Sen
authors.initials: WS
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Zhuang
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Cheng-Yu
authors.initials: CY
authors.lastname: Wang
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Zhao-Yang
authors.initials: ZY
authors.lastname: Bu
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Zhen-Dong
authors.initials: ZD
authors.lastname: Guo
authors.affiliation: Institute of Environmental Health and Related Product Safety, Chinese Center for Disease Control and Prevention, Beijing 100021, China.
authors.forename: Liu-Bo
authors.initials: LB
authors.lastname: Zhang
authors.affiliation: The No. 302 Hospital, Beijing 100039, China.
authors.forename: Wei-Min
authors.initials: WM
authors.lastname: Nie
authors.affiliation: The No. 307 Hospital, Beijing 100071, China.
authors.forename: Chang-Qing
authors.initials: CQ
authors.lastname: Bai
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Xiao-Ping
authors.initials: XP
authors.lastname: An
authors.affiliation: Beijing Key Laboratory of New Molecular Diagnostics Technology, Beijing 100850, China.
authors.forename: Pei-Song
authors.initials: PS
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Xiang-Li-Lan
authors.initials: XL
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Mi
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Hong-Wu
authors.initials: HW
authors.lastname: Yao
authors.affiliation: Department of international cooperation, National Health and Family Planning Commission, Beijing 100044, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Zhi-Ping
authors.initials: ZP
authors.lastname: Xia
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Xue-Xing
authors.initials: XX
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China.
authors.forename: Song-Tao
authors.initials: ST
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Jia-Fu
authors.initials: JF
authors.lastname: Jiang
authors.affiliation: Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone.
authors.forename: Brima
authors.initials: B
authors.lastname: Kargbo
authors.affiliation: State Key Laboratory of Proteomics, Beijing 102206, China.
authors.forename: Fu-Chu
authors.initials: FC
authors.lastname: He
authors.affiliation: 1] Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China [2] Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China [3] Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: George F
authors.initials: GF
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
authors.forename: Wu-Chun
authors.initials: WC
authors.lastname: Cao
mesh_terms: D001483:Base Sequence; D004196:Disease Outbreaks / Q000706:statistics & numerical data; D029043:Ebolavirus / Q000235:genetics* / Q000302:isolation & purification; D062665:Epidemiological Monitoring; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D006801:Humans; D017720:Molecular Epidemiology; D059645:Mutation Rate; D010802:Phylogeny; D058974:Phylogeography; D012807:Sierra Leone / Q000453:epidemiology