Since 2013, West Africa has encountered the largest Ebola virus (EBOV) disease outbreak on record, and Sierra Leone is the worst-affected country, with nearly half of the infections. By means of next-generation sequencing and phylogeographic analysis, the epidemiology and transmission of EBOV have been well elucidated. However, the intra-host dynamics that mainly reflect viral–host interactions still need to be studied. Here, we show a total of 710 intra-host single nucleotide variations (iSNVs) from deep-sequenced samples from EBOV-infected patients, through a well-tailored bioinformatics pipeline. We present a comprehensive distribution of iSNVs during this outbreak and along the EBOV genome. Analyses of iSNV and its allele frequency reveal that VP40 is the most conserved gene during this outbreak, and thus it would be an ideal therapeutic target. In the co-occurring iSNV network, varied iSNV sites present different selection features. Intriguingly, the T-to-C substitutions at the 3′-UTR of the nucleoprotein (NP; positions 3008 and 3011), observed in many patients, result in the upregulation of the transcription of NP through an Ebola mini-genome reporting system. Additionally, no iSNV enrichment within B-cell epitopes of GP has been observed.

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The authors thank Wu-Chun Cao, Hui Wang and Hong-Wu Yao for helpful discussions and C. Tomkins-Tinch for technical support. This work was supported by the China Ministry of Science and Technology (MOST) Project ‘973’ (grant numbers 2015CB910501 and 2015CB910503), the China National Grand S&T Special Project (grant numbers 2013ZX09304101 and 2015ZX09102024), the MOST Key Research and Development Program (2016YFC1200805), the Natural Science Foundation of China (grant numbers 31471253, 81590761 and U1435222), the National Hi-Tech R&D Program of China (‘863’ Program) (grant numbers 2014AA021501, 2014AA021505 and 2015AA020108), the Special Foundation of President for Ebola Virus Research from the Chinese Academy of Sciences (CAS) and the Yangfan Program from Beijing Municipal Administration of Hospitals (to H.Z.). W.S. was supported by the ‘Taishan Scholar’ project of Shandong Province. G.W. was supported by the President's International Fellowship Initiative from CAS. G.F.G. is a leading principal investigator of the NSFC Innovative Research Group (grant no. 81321063).

Author information

Author notes

    • Ming Ni
    • , Chen Chen
    •  & Jun Qian

    These authors contributed equally to this work.


  1. Beijing Institute of Radiation Medicine, Beijing 100850, China

    • Ming Ni
    • , Zhen Li
    • , Su-Hong Chen
    • , Sheng-Qi Wang
    •  & Xiao-Chen Bo
  2. Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China

    • Chen Chen
    • , Hai-Yin Wang
    •  & Hui Zeng
  3. Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China

    • Chen Chen
    •  & Hui Zeng
  4. Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China

    • Jun Qian
    • , Zhi-Ping Xia
    •  & Hui-jun Lu
  5. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

    • Hai-Xia Xiao
    • , Jun Wu
    • , Gary Wong
    • , Yuhai Bi
    • , George F. Gao
    •  & Di Liu
  6. Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China

    • Hai-Xia Xiao
  7. Institute of Pathogen Biology, Taishan Medical College, Taian 271016, China

    • Wei-Feng Shi
  8. Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK

    • Yang Luo
  9. Zhiyuan Medical Inspection Institute, Zhejiang 310009, China

    • Pei-Song Xu
  10. Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China

    • Yuhai Bi
    •  & George F. Gao
  11. Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

    • Wei Li
    • , Juncai Ma
    •  & Di Liu
  12. State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China

    • Yi-Gang Tong
  13. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China

    • George F. Gao


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This study was conceived and designed by D.L., M.N., C.C., X.C.B. and G.F.G. Samples were collected and prepared by J.Q., H.J.L. and Z.P.X. Experiments were performed by Z.L., P.S.X. and H.X.X. The methods were developed and implemented by M.N., D.L. and C.C. The data were analysed by M.N., D.L., C.C., W.F.S., H.Y.W., H.X.X., Y.G.T., T.Y.G., Y.L., W.L. and J.W. The manuscript was prepared by D.L., M.N., C.C., W.F.S., G.W., X.C.B., H.Z. and G.F.G. This study was supervised by D.L., X.C.B., G.F.G., H.Z., J.M. and S.Q.W.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sheng-Qi Wang or George F. Gao or Xiao-Chen Bo or Di Liu.

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