Ebolavirus comparative genomics
Abstract
The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Computational Sciences
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). UT-ORNL Graduate School of Genome Science and Technology
- Technical Univ. of Denmark, Lyngby (Denmark). Center for Biological Sequence Analysis; Univ. Nacional de San Martin, Buenos Aires (Argentina)
- Technical Univ. of Denmark, Lyngby (Denmark). Center for Biological Sequence Analysis
- Booze Allen Hamilton, McLean, VA (United States)
- Technical Univ. of Denmark, Lyngby (Denmark). Center for Biological Sequence Analysis; Chr. Hansen A/S, Horsholm (Denmark). Assays, Cultures and Enzymes Division
- Microbiology and Genomics Consultants, Zotzenheim (Germany)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1265422
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- FEMS Microbiology Reviews
- Additional Journal Information:
- Journal Volume: 39; Journal Issue: 5; Journal ID: ISSN 1574-6976
- Publisher:
- Federation of European Microbiological Societies
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Ebola Virus; comparative genomics; viral genomes; epitope prediction; Ebola virus disease (EVD); Filovirus
Citation Formats
Jun, Se-Ran, Leuze, Michael R., Nookaew, Intawat, Uberbacher, Edward C., Land, Miriam, Zhang, Qian, Wanchai, Visanu, Chai, Juanjuan, Nielsen, Morten, Trolle, Thomas, Lund, Ole, Buzard, Gregory S., Pedersen, Thomas D., Wassenaar, Trudy M., and Ussery, David W. Ebolavirus comparative genomics. United States: N. p., 2015.
Web. doi:10.1093/femsre/fuv031.
Jun, Se-Ran, Leuze, Michael R., Nookaew, Intawat, Uberbacher, Edward C., Land, Miriam, Zhang, Qian, Wanchai, Visanu, Chai, Juanjuan, Nielsen, Morten, Trolle, Thomas, Lund, Ole, Buzard, Gregory S., Pedersen, Thomas D., Wassenaar, Trudy M., & Ussery, David W. Ebolavirus comparative genomics. United States. https://doi.org/10.1093/femsre/fuv031
Jun, Se-Ran, Leuze, Michael R., Nookaew, Intawat, Uberbacher, Edward C., Land, Miriam, Zhang, Qian, Wanchai, Visanu, Chai, Juanjuan, Nielsen, Morten, Trolle, Thomas, Lund, Ole, Buzard, Gregory S., Pedersen, Thomas D., Wassenaar, Trudy M., and Ussery, David W. Tue .
"Ebolavirus comparative genomics". United States. https://doi.org/10.1093/femsre/fuv031. https://www.osti.gov/servlets/purl/1265422.
@article{osti_1265422,
title = {Ebolavirus comparative genomics},
author = {Jun, Se-Ran and Leuze, Michael R. and Nookaew, Intawat and Uberbacher, Edward C. and Land, Miriam and Zhang, Qian and Wanchai, Visanu and Chai, Juanjuan and Nielsen, Morten and Trolle, Thomas and Lund, Ole and Buzard, Gregory S. and Pedersen, Thomas D. and Wassenaar, Trudy M. and Ussery, David W.},
abstractNote = {The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.},
doi = {10.1093/femsre/fuv031},
journal = {FEMS Microbiology Reviews},
number = 5,
volume = 39,
place = {United States},
year = {Tue Jul 14 00:00:00 EDT 2015},
month = {Tue Jul 14 00:00:00 EDT 2015}
}
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Bats and Viruses: Friend or Foe?
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A Loop Region in the N-Terminal Domain of Ebola Virus VP40 Is Important in Viral Assembly, Budding, and Egress
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