Integrated sequence and immunology filovirus database at Los Alamos
Abstract
The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlightmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1263542
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Database
- Additional Journal Information:
- Journal Volume: 2016; Journal ID: ISSN 1758-0463
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES
Citation Formats
Yusim, Karina, Yoon, Hyejin, Foley, Brian, Feng, Shihai, Macke, Jennifer, Dimitrijevic, Mira, Abfalterer, Werner, Szinger, James, Fischer, Will, Kuiken, Carla, and Korber, Bette. Integrated sequence and immunology filovirus database at Los Alamos. United States: N. p., 2016.
Web. doi:10.1093/database/baw047.
Yusim, Karina, Yoon, Hyejin, Foley, Brian, Feng, Shihai, Macke, Jennifer, Dimitrijevic, Mira, Abfalterer, Werner, Szinger, James, Fischer, Will, Kuiken, Carla, & Korber, Bette. Integrated sequence and immunology filovirus database at Los Alamos. United States. https://doi.org/10.1093/database/baw047
Yusim, Karina, Yoon, Hyejin, Foley, Brian, Feng, Shihai, Macke, Jennifer, Dimitrijevic, Mira, Abfalterer, Werner, Szinger, James, Fischer, Will, Kuiken, Carla, and Korber, Bette. Fri .
"Integrated sequence and immunology filovirus database at Los Alamos". United States. https://doi.org/10.1093/database/baw047. https://www.osti.gov/servlets/purl/1263542.
@article{osti_1263542,
title = {Integrated sequence and immunology filovirus database at Los Alamos},
author = {Yusim, Karina and Yoon, Hyejin and Foley, Brian and Feng, Shihai and Macke, Jennifer and Dimitrijevic, Mira and Abfalterer, Werner and Szinger, James and Fischer, Will and Kuiken, Carla and Korber, Bette},
abstractNote = {The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.},
doi = {10.1093/database/baw047},
journal = {Database},
number = ,
volume = 2016,
place = {United States},
year = {Fri Jan 01 00:00:00 EST 2016},
month = {Fri Jan 01 00:00:00 EST 2016}
}
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The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing.
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Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
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Genomic RNA Editing and Its Impact on Ebola Virus Adaptation During Serial Passages in Cell Culture and Infection of Guinea Pigs
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The UCSC Genome Browser database: 2015 update
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Characterization of the L gene and 5' trailer region of Ebola virus.
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Trials of Ebola vaccine set to begin in west Africa
journal, January 2015
- Gulland, A.
- BMJ, Vol. 350, Issue jan09 14
Design and Pre-Clinical Evaluation of a Universal HIV-1 Vaccine
journal, October 2007
- Létourneau, Sven; Im, Eung-Jun; Mashishi, Tumelo
- PLoS ONE, Vol. 2, Issue 10, Article No. e984
Designing and Testing Broadly-Protective Filoviral Vaccines Optimized for Cytotoxic T-Lymphocyte Epitope Coverage
journal, October 2012
- Fenimore, Paul W.; Muhammad, Majidat A.; Fischer, William M.
- PLoS ONE, Vol. 7, Issue 10
Ebola Virus Genome Plasticity as a Marker of Its Passaging History: A Comparison of In Vitro Passaging to Non-Human Primate Infection
journal, November 2012
- Kugelman, Jeffrey R.; Lee, Michael S.; Rossi, Cynthia A.
- PLoS ONE, Vol. 7, Issue 11
Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats
journal, July 2009
- Towner, Jonathan S.; Amman, Brian R.; Sealy, Tara K.
- PLoS Pathogens, Vol. 5, Issue 7
Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes
journal, July 2010
- Belyi, Vladimir A.; Levine, Arnold J.; Skalka, Anna Marie
- PLoS Pathogens, Vol. 6, Issue 7
Discovery of an Ebolavirus-Like Filovirus in Europe
journal, October 2011
- Negredo, Ana; Palacios, Gustavo; Vázquez-Morón, Sonia
- PLoS Pathogens, Vol. 7, Issue 10
Ecologic and Geographic Distribution of Filovirus Disease
journal, January 2004
- Peterson, A. Townsend; Bauer, John T.; Mills, James N.
- Emerging Infectious Diseases, Vol. 10, Issue 01
Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community
journal, November 2012
- Pickett, Brett; Greer, Douglas; Zhang, Yun
- Viruses, Vol. 4, Issue 11
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names
journal, September 2014
- Kuhn, Jens; Andersen, Kristian; Bào, Yīmíng
- Viruses, Vol. 6, Issue 9
Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014
journal, November 2014
- Kuhn, Jens; Andersen, Kristian; Baize, Sylvain
- Viruses, Vol. 6, Issue 11
The Ebola outbreak of 2014-2015: From coordinated multilateral action to effective disease containment, vaccine development, and beyond
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Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene
journal, January 2014
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