Integrated sequence and immunology filovirus database at Los Alamos

Database

Volumn 2016, Issue , 2016, Pages

  Yusim, Karina ^a   Yoon, Hyejin ^a   Foley, Brian ^a   Feng, Shihai ^a   Macke, Jennifer ^a   Dimitrijevic, Mira ^a   Abfalterer, Werner ^a   Szinger, James ^a   Fischer, Will ^a   Kuiken, Carla ^a   Korber, Bette ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER INTERFACE; FILOVIRIDAE; FILOVIRUS INFECTION; GENETIC DATABASE; GENETICS; HUMAN; IMMUNOLOGY; INTERNET; NEW MEXICO; VIROLOGY;

DATABASES, GENETIC; FILOVIRIDAE; FILOVIRIDAE INFECTIONS; HUMANS; INTERNET; NEW MEXICO; USER-COMPUTER INTERFACE;

EID: 84971009175     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/baw047     Document Type: Article

References (68)

1. Siegert, R., Shu, H.L., Slenczka, W. et al. (1967) On the etiology of an unknown human infection originating from monkeys. Dtsch. Med.Wochenschr., 92, 2341-2343.
2. Kuhn, J.H., Andersen, K.G., Bao, Y. et al. (2014) Filovirus RefSeq entries: Evaluation and selection of filovirus type variants, type sequences, and names. Viruses, 6, 3663-3682.
3. Carroll, M.W., Matthews, D.A., Hiscox, J.A. et al. (2015) Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature, 524, 97-101.
4. Enserink, M. (2015) The Ebola epidemic. High hopes for Guinean vaccine trial. Science, 347, 219-220.
5. Kibuuka, H., Berkowitz, N.M., Millard, M., Enama, M.E., Tindikahwa, A., Sekiziyivu, A.B., Costner, P., Sitar, S., Glover, D., Hu, Z. et al. (2015) Safety and immunogenicity of Ebola virus and Marburg virus glycoprotein DNA vaccines assessed separately and concomitantly in healthy Ugandan adults: A phase 1b, randomised, double-blind, placebo-controlled clinical trial. Lancet, 385, 1545-1554.
6. Gulland, A. (2015) Trials of Ebola vaccine set to begin in west Africa. BMJ, 350, h165.
7. Stanley, D.A., Honko, A.N., Asiedu, C. et al. (2014) Chimpanzee adenovirus vaccine generates acute and durable protective immunity against ebolavirus challenge. Nat. Med., 20, 1126-1129.
8. Geisbert, T.W., Geisbert, J.B., Leung, A. et al. (2009) Single-injection vaccine protects nonhuman primates against infection with Marburg virus and three species of Ebola virus. J. Virol., 83, 7296-7304.
9. McCarthy, M. (2014) US signs contract with ZMapp maker to accelerate development of the Ebola drug. BMJ, 349, g5488.
10. Qiu, X., Wong, G., Audet, J. et al. (2014) Reversion of advanced Ebola virus disease in nonhuman primates with ZMapp. Nature, 514, 47-53.
11. Wojda, T.R., Valenza, P.L., Cornejo, K. et al. (2015) The Ebola outbreak of 2014-2015: From coordinated multilateral action to effective disease containment, vaccine development, and beyond. J. Glob. Infect. Dis., 7, 127-138.
12. Li, H., Ying, T., Yu, F. et al. (2015) Development of therapeutics for treatment of Ebola virus infection. Microbes Infect., 17, 109-117.
13. CDC. (2014) Marburg hemorrhagic fever (Marburg HF). http://www.cdc.gov/vhf/marburg/resources/(December 2015, date last accessed). Center for Disease Control and Prevention.
14. CDC. (2015) Ebola (Ebola Virus Disease). http://www.cdc.gov/vhf/ebola/(December 2015, date last accessed). Center for Disease Control and Prevention.
15. WHO. (2014) Ebola virus disease. http://www.who.int/csr/disease/ebola/en/(December 2015, date last accessed). World Health Organization.
16. Vita, R., Zarebski, L., Greenbaum, J.A. et al. (2010) The immune epitope database 2.0. Nucleic Acids Res, 38, D854-D862.
17. Rosenbloom, K.R., Armstrong, J., Barber, G.P. et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
18. NCBI. Virus Variations Ebolavirus Resource. http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ebola/(December 2015, date last accessed).
19. Pickett, B.E., Greer, D.S., Zhang, Y. et al. (2012) Virus pathogen database and analysis resource (ViPR): A comprehensive bioinformatics database and analysis resource for the coronavirus research community. Viruses, 4, 3209-3226.
20. Kuiken, C., Thurmond, J., Dimitrijevic, M. and Yoon, H. (2012) The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses. Nucleic Acids Res., 40, D587-D592.
21. Kuiken, C., Hraber, P., Thurmond, J. and Yusim, K. (2008) The hepatitis C sequence database in Los Alamos. Nucleic Acids Res., 36, D512-D516.
22. Yusim, K., Richardson, R., Tao, N. et al. (2005) Los alamos hepatitis C immunology database. Appl. Bioinform., 4, 217-225.
23. Sayers, E.W., Barrett, T., Benson, D.A. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
24. Skinner, M.E., Holmes, I.H. et al. (2010) Setting up the JBrowse genome browser. Curr. Protoc. Bioinform., Chapter 9, Unit 9 13.
25. Skinner, M.E., Uzilov, A.V., Stein, L.D. et al. (2009) JBrowse: A next-generation genome browser. Genome Res., 19, 1630-1638.
26. Kuhn, J.H., Bao, Y., Bavari, S. et al. (2014) Virus nomenclature below the species level: A standardized nomenclature for filovirus strains and variants rescued from cDNA. Arch Virol, 159, 1229-1237.
27. Kuhn, J.H., Andersen, K.G., Baize, S. et al. (2014) Nomenclatureand database-compatible names for the two Ebola virus variants that emerged in Guinea and the Democratic Republic of the Congo in 2014. Viruses, 6, 4760-4799.
28. Kuhn, J.H., Bao, Y., Bavari, S. et al. (2013) Virus nomenclature below the species level: A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae. Arch. Virol., 158, 1425-1432.
29. Kuhn, J.H., Bao, Y., Bavari, S. et al. (2013) Virus nomenclature below the species level: A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. Arch. Virol., 158, 301-311.
30. Kuhn, J.H., Becker, S., Ebihara, H. et al. (2010) Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch. Virol., 155, 2083-2103.
31. Katoh, K. and Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.
32. Sanchez, A., Trappier, S.G., Mahy, B.W. et al. (1996) The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing. Proc. Natl Acad. Sci. U. S. A., 93, 3602-3607.
33. Mehedi, M., Falzarano, D., Seebach, J. et al. (2011) A new Ebola virus nonstructural glycoprotein expressed through RNA editing. J. Virol., 85, 5406-5414.
34. Kugelman, J.R., Lee, M.S., Rossi, C.A. et al. (2012) Ebola virus genome plasticity as a marker of its passaging history: A comparison of in vitro passaging to non-human primate infection. PLoS One, 7, e50316.
35. Volchkova, V.A., Dolnik, O., Martinez, M.J. et al. (2011) Genomic RNA editing and its impact on Ebola virus adaptation during serial passages in cell culture and infection of guinea pigs. J. Infect. Dis., 204, S941-S946.
36. Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
37. Guindon, S., Dufayard, J.F., Lefort, V. et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
38. Bausch, D.G., Nichol, S.T., Muyembe-Tamfum, J.J. et al. (2006) Marburg hemorrhagic fever associated with multiple genetic lineages of virus. N. Engl. J. Med., 355, 909-919.
39. Towner, J.S., Amman, B.R., Sealy, T.K. et al. (2009) Isolation of genetically diverse Marburg viruses from Egyptian fruit bats. PLoS Pathog., 5, e1000536.
40. Amman, B.R., Carroll, S.A., Reed, Z.D. et al. (2012) Seasonal pulses of Marburg virus circulation in juvenile Rousettus aegyptiacus bats coincide with periods of increased risk of human infection. PLoS Pathog., 8, e1002877.
41. Peterson, A.T., Bauer, J.T. and Mills, J.N. (2004) Ecologic and geographic distribution of filovirus disease. Emerg. Infect. Dis., 10, 40-47.
42. Carroll, S.A., Towner, J.S., Sealy, T.K. et al. (2013) Molecular evolution of viruses of the family Filoviridae based on 97 wholegenome sequences. J. Virol., 87, 2608-2616.
43. Maganga, G.D., Kapetshi, J., Berthet, N. et al. (2014) Ebola virus disease in the Democratic Republic of Congo. N. Engl. J. Med., 371, 2083-2091.
44. Volchkov, V.E., Volchkova, V.A., Chepurnov, A.A. et al. (1999) Characterization of the L gene and 5' trailer region of Ebola virus. J. Gen. Virol., 80, 355-362.
45. Baize, S., Pannetier, D., Oestereich, L. et al. (2014) Emergence of Zaire Ebola virus disease in Guinea. N. Engl. J. Med., 371, 1418-1425.
46. Gire, S.K., Goba, A., Andersen, K.G. et al. (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science, 345, 1369-1372.
47. Ota, T. and Nei, M. (1994) Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol. Biol. Evol., 11, 613-619.
48. Delport, W., Poon, A.F., Frost, S.D. et al. (2010) Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26, 2455-2457.
49. Pond, S.L. and Frost, S.D. (2005) Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 21, 2531-2533.
50. Kosakovsky Pond, S.L. and Frost, S.D. (2005) Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol., 22, 1208-1222.
51. Olal, D., Kuehne, A.I., Bale, S. et al. (2012) Structure of an antibody in complex with its mucin domain linear epitope that is protective against Ebola virus. J. Virol., 86, 2809-2816.
52. Fenimore, P.W., Muhammad, M.A., Fischer, W.M. et al. (2012) Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage. PLoS One, 7, e44769.
53. Hashiguchi, T., Fusco, M.L., Bornholdt, Z.A. et al. (2015) Structural basis for Marburg virus neutralization by a cross-reactive human antibody. Cell, 160, 904-912.
54. Flyak, A.I., Ilinykh, P.A., Murin, C.D. et al. (2015) Mechanism of human antibody-mediated neutralization of Marburg virus. Cell, 160, 893-903.
55. Belyi, V.A., Levine, A.J. and Skalka, A.M. (2010) Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS Pathog., 6, e1001030.
56. Taylor, D.J., Leach, R.W. and Bruenn, J. (2010) Filoviruses are ancient and integrated into mammalian genomes. BMC Evol. Biol., 10, 193.
57. Negredo, A., Palacios, G., Vazquez-Moron, S. et al. (2011) Discovery of an ebolavirus-like filovirus in Europe. PLoS Pathog., 7, e1002304.
58. Taylor, D.J., Ballinger, M.J., Zhan, J.J. et al. (2014) Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene. PeerJ, 2, e556.
59. Wertheim, J.O. and Kosakovsky Pond, S.L. (2011) Purifying selection can obscure the ancient age of viral lineages. Mol. Biol. Evol., 28, 3355-3365.
60. Shedlock, D.J., Aviles, J., Talbott, K.T. et al. (2013) Induction of broad cytotoxic T cells by protective DNA vaccination against Marburg and Ebola. Mol. Ther., 21, 1432-1444.
61. Sullivan, N.J., Hensley, L., Asiedu, C. et al. (2011) CD8 cellular immunity mediates rAd5 vaccine protection against Ebola virus infection of nonhuman primates. Nat. Med., 17, 1128-1131.
62. Yang, O.O., Ali, A., Kasahara, N. et al. (2015) Short conserved sequences of HIV-1 are highly immunogenic and shift immunodominance. J. Virol., 89, 1195-1204.
63. Borthwick, N., Ahmed, T., Ondondo, B. et al. (2014) Vaccine-elicited human T cells recognizing conserved protein regions inhibit HIV-1. Mol. Ther., 22, 464-475.
64. Stephenson, K.E., SanMiguel, A., Simmons, N.L. et al. (2012) Full-length HIV-1 immunogens induce greater magnitude and comparable breadth of T lymphocyte responses to conserved HIV-1 regions compared with conserved-region-only HIV-1 immunogens in rhesus monkeys. J. Virol., 86, 11434-11440.
65. Letourneau, S., Im, E.J., Mashishi, T. et al. (2007) Design and preclinical evaluation of a universal HIV-1 vaccine. PLoS One, 2, e984.
66. Flyak, A.I., Shen, X., Murin, C.D. et al. (2016) Cross-reactive and potent neutralizing antibody responses in human survivors of natural ebolavirus infection. Cell, 164, 392-405.
67. Grant-Klein, R.J., Altamura, L.A., Badger, C.V. et al. (2015) Codon-optimized filovirus DNA vaccines delivered by intramuscular electroporation protect cynomolgus macaques from lethal Ebola and Marburg virus challenges. Hum. Vaccin. Immunother., 11, 1991-2004.
68. Holtsberg, F.W., Shulenin, S., Vu, H. et al. (2015) Pan-ebolavirus and Pan-filovirus mouse monoclonal antibodies: protection against Ebola and Sudan Viruses. J. Virol., 90, 266-278.