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Intra-host dynamics of Ebola virus during 2014

Nature Microbiology volume 1, Article number: 16151 (2016) Cite this article

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Abstract

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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Figure 1: EBOV iSNVs among patients.
Figure 2: EBOV iSNV distributions along the viral genome.
Figure 3: Allele frequencies of EBOV iSNVs.
Figure 4: Co-occurring iSNVs among Ebola patients.
Figure 5: Ebola mini-genome reporting system to examine T-to-C substitutions at positions 3008 and 3011.
Figure 6: EBOV iSNVs along the GP protein.

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References

  1. Ebola Situation Reports WHO (2015); http://apps.who.int/ebola/current-situation/

  2. Lyon, G. M. et al. Clinical care of two patients with Ebola virus disease in the United States. New Engl. J. Med. 371, 2402–2409 (2014).

    Article  CAS  PubMed  Google Scholar 

  3. Parra, J. M., Salmeron, O. J. & Velasco, M. The first case of Ebola virus disease acquired outside Africa. New Engl. J. Med. 371, 2439–2440 (2014).

    Article  PubMed  Google Scholar 

  4. Varkey, J. B. et al. Persistence of Ebola virus in ocular fluid during convalescence. New Engl. J. Med. 372, 2423–2427 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Deen, G. F. et al. Ebola RNA persistence in semen of Ebola virus disease survivors—preliminary report. New Engl. J. Med. http://dx.doi.org/10.1056/NEJMoa1511410 (2015).

  6. Mate, S. E. et al. Molecular evidence of sexual transmission of Ebola virus. New Engl. J. Med. 373, 2448–2454 (2015).

    Article  CAS  PubMed  Google Scholar 

  7. Gire, S. K. et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369–1372 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Tong, Y. G. et al. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature 524, 93–96 (2015).

    Article  CAS  PubMed  Google Scholar 

  9. Carroll, M. W. et al. Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa. Nature 524, 97–101 (2015).

    Article  CAS  PubMed  Google Scholar 

  10. Simon-Loriere, E. et al. Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic. Nature 524, 102–104 (2015).

    Article  CAS  PubMed  Google Scholar 

  11. Park, D. J. et al. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell 161, 1516–1526 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Domingo, E., Sheldon, J. & Perales, C. Viral quasispecies evolution. Microbiol. Mol. Biol. Rev. 76, 159–216 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Acevedo, A., Brodsky, L. & Andino, R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505, 686–690 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. Li, Y. et al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat. Genet. 42, 969–972 (2010).

    Article  CAS  PubMed  Google Scholar 

  15. Boyko, A. R. et al. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4, e1000083 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Emmett, K. J., Lee, A., Khiabanian, H. & Rabadan, R. High-resolution genomic surveillance of 2014 Ebolavirus using shared subclonal variants. PLoS Curr. Outbreak http://dx.doi.org/10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90 (2015).

  17. Liang, B. et al. Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy. Cell 162, 314–327 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Pickett, B. E. et al. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40, D593–D598 (2012).

    Article  CAS  PubMed  Google Scholar 

  19. Andino, R. & Domingo, E. Viral quasispecies. Virology 479–480, 46–51 (2015).

    Article  PubMed  Google Scholar 

  20. Josefsson, L. et al. The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proc. Natl Acad. Sci. USA 110, E4987–E4996 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Sobesky, R. et al. Distinct hepatitis C virus core and F protein quasispecies in tumoral and nontumoral hepatocytes isolated via microdissection. Hepatology 46, 1704–1712 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Del Portillo, A. et al. Multiploid inheritance of HIV-1 during cell-to-cell infection. J. Virol. 85, 7169–7176 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jung, A. et al. Recombination: multiply infected spleen cells in HIV patients. Nature 418, 144 (2002).

    Article  CAS  PubMed  Google Scholar 

  24. McWilliam Leitch, E. C. & McLauchlan, J. Determining the cellular diversity of hepatitis C virus quasispecies by single-cell viral sequencing. J. Virol. 87, 12648–12655 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Bornholdt, Z. A. et al. Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle. Cell 154, 763–774 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Adu-Gyamfi, E. et al. Host cell plasma membrane phosphatidylserine regulates the assembly and budding of Ebola virus. J. Virol. 89, 9440–9453 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kouznetsova, J. et al. Identification of 53 compounds that block Ebola virus-like particle entry via a repurposing screen of approved drugs. Emerg. Microbe. Infect. 3, e84 (2014).

    CAS  Google Scholar 

  28. Stahelin, R. V. Could the Ebola virus matrix protein VP40 be a drug target? Exp. Opin. Therapeut. Targets 18, 115–120 (2014).

    Article  CAS  Google Scholar 

  29. Gelinas, J. F., Clerzius, G., Shaw, E. & Gatignol, A. Enhancement of replication of RNA viruses by ADAR1 via RNA editing and inhibition of RNA-activated protein kinase. J. Virol. 85, 8460–8466 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Schirmer, M. et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 43, e37 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sickle: A Sliding-Window, Adaptive, Quality-Based Trimming Tool for FastQ Files v.1.33 (Joshi, N. A. & Fass, J. N., 2011); https://github.com/najoshi/sickle

  32. Nikolenko, S. I., Korobeynikov, A. I. & Alekseyev, M. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 14(Suppl. 1), S7 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755 (2001).

    Article  CAS  PubMed  Google Scholar 

  37. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).

    Article  CAS  PubMed  Google Scholar 

  38. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cline, M. S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366–2382 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

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).

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Author notes

  1. Ming Ni, Chen Chen and Jun Qian: These authors contributed equally to this work.

Authors and Affiliations

  1. Beijing Institute of Radiation Medicine, 100850, Beijing, 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, 100102, Beijing, China

    Chen Chen, Hai-Yin Wang & Hui Zeng

  3. Beijing Key Laboratory of Emerging Infectious Diseases, 100102, Beijing, China

    Chen Chen & Hui Zeng

  4. Key Laboratory of Jilin Province for Zoonosis Prevention and Control, 130122, Changchun, 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, 100101, Beijing, 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, 300308, Tianjin, China

    Hai-Xia Xiao

  7. Institute of Pathogen Biology, Taishan Medical College, 271016, Taian, China

    Wei-Feng Shi

  8. Wellcome Trust Sanger Institute, CB10 1SA, Cambridge, UK

    Yang Luo

  9. Zhiyuan Medical Inspection Institute, 310009, Zhejiang, China

    Pei-Song Xu

  10. Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, 518112, Shenzhen, China

    Yuhai Bi & George F. Gao

  11. Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China

    Wei Li, Juncai Ma & Di Liu

  12. State Key Laboratory of Pathogen and Biosecurity, 100071, Beijing, China

    Yi-Gang Tong

  13. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China

    George F. Gao

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  1. Ming Ni
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Contributions

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.

Corresponding authors

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

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The authors declare no competing financial interests.

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Ni, M., Chen, C., Qian, J. et al. Intra-host dynamics of Ebola virus during 2014. Nat Microbiol 1, 16151 (2016). https://doi.org/10.1038/nmicrobiol.2016.151

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