Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa

Nature

Volumn 524, Issue 7563, 2015, Pages 97-101

  Carroll, Miles W ^a,b,c   Matthews, David A ^d   Hiscox, Julian A ^e   Elmore, Michael J ^a   Pollakis, Georgios ^e   Rambaut, Andrew ^f,g   Hewson, Roger ^a,b,h   García Dorival, Isabel ^e   Bore, Joseph Akoi ^b,i,j   Koundouno, Raymond ^b,i,j   Abdellati, Saïd ^b,k   Afrough, Babak ^a,b   Aiyepada, John ^b,l   Akhilomen, Patience ^b,l   Asogun, Danny ^b,l   Atkinson, Barry ^a,b   Badusche, Marlis ^b,m   Bah, Amadou ^b,n   Bate, Simon ^a,b   Baumann, Jan ^b   Becker, Dirk ^b,m,o   Becker Ziaja, Beate ^b,m   Bocquin, Anne ^b,p,q   Borremans, Benny ^b,r   Bosworth, Andrew ^a,b,e   Boettcher, Jan Peter ^b,s   Cannas, Angela ^b,t   Carletti, Fabrizio ^b,t   Castilletti, Concetta ^b,t   Clark, Simon ^a,b   Colavita, Francesca ^b,t   Diederich, Sandra ^b,m,u   Donatus, Adomeh ^b,l   Duraffour, Sophie ^b,v   Ehichioya, Deborah ^b,w   Ellerbrok, Heinz ^b,s   Fernandez Garcia, Maria Dolores ^b,x   Fizet, Alexandra ^b,p,y   Fleischmann, Erna ^b,m,z   Gryseels, Sophie ^b,r   Hermelink, Antje ^b,s   Hinzmann, Julia ^b,s   Hopf Guevara, Ute ^b,s   Ighodalo, Yemisi ^b,l   Jameson, Lisa ^a,b   Kelterbaum, Anne ^b,m,o   Kis, Zoltan ^b,aa   Kloth, Stefan ^b,s   Kohl, Claudia ^b,s   Korva, Miša ^b,ab   Kraus, Annette ^b,ac   Kuisma, Eeva ^a,b   Kurth, Andreas ^b,s   Liedigk, Britta ^b,m   Logue, Christopher H ^a,b   Lüdtke, Anja ^b,m,ad   Maes, Piet ^b,v   McCowen, James ^a,b   Mély, Stéphane ^b,p,q   Mertens, Marc ^b,m,u   Meschi, Silvia ^b,t   Meyer, Benjamin ^b,m,ae   Michel, Janine ^b,s   Molkenthin, Peter ^b,m,z   Muñoz Fontela, César ^b,m,ad   Muth, Doreen ^b,m,ae   Newman, Edmund N C ^a,b   Ngabo, Didier ^a,b   Oestereich, Lisa ^b,m   Okosun, Jennifer ^b,l   Olokor, Thomas ^b,l   Omiunu, Racheal ^b,l   Omomoh, Emmanuel ^b,l   Pallasch, Elisa ^b,m   Pályi, Bernadett ^b,aa   Portmann, Jasmine ^b,af   Pottage, Thomas ^a,b   Pratt, Catherine ^a,b   Priesnitz, Simone ^b,ag   Quartu, Serena ^b,t   Rappe, Julie ^b,ah   Repits, Johanna ^b,ai   Richter, Martin ^b,s   Rudolf, Martin ^b,m   Sachse, Andreas ^b,s   Schmidt, Kristina Maria ^b,s   Schudt, Gordian ^b,m,o   Strecker, Thomas ^b,m,o   Thom, Ruth ^a,b   Thomas, Stephen ^a,b   Tobin, Ekaete ^b,l   Tolley, Howard ^a,b   Trautner, Jochen ^b,aj   Vermoesen, Tine ^b,k   Vitoriano, Inês ^a,b   Wagner, Matthias ^b,m,z   Wolff, Svenja ^b,m,o   Yue, Constanze ^b,s   Capobianchi, Maria Rosaria ^b,t   Kretschmer, Birte ^ak   Hall, Yper ^a   Kenny, John G ^e   Rickett, Natasha Y ^e   Dudas, Gytis ^f   Coltart, Cordelia E M ^al   Kerber, Romy ^b,m   Steer, Damien ^d   Wright, Callum ^d   Senyah, Francis ^a   Keita, Sakoba ^am   Drury, Patrick ^an   Diallo, Boubacar ^an   De Clerck, Hilde ^ao   Van Herp, Michel ^ao   Sprecher, Armand ^ao   Traore, Alexis ^ap   Diakite, Mandiou ⁱ   Konde, Mandy Kader ^aq   Koivogui, Lamine ^j   Magassouba, NâFaly ⁱ   AvšiÄ Aupanc, Tatjana ^b,ab   Nitsche, Andreas ^b,s   Strasser, Marc ^b,af   Ippolito, Giuseppe ^b,t   Becker, Stephan ^b,m,o   Stoecker, Kilian ^b,m,z   Gabriel, Martin ^b,m   Raoul, Hervé ^b,q   Di Caro, Antonino ^b,t   Wölfel, Roman ^b,m,z   Formenty, Pierre ^an   Günther, Stephan ^b,m   more..

^a PUBLIC HEALTH ENGLAND   (United Kingdom)

^b BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

^c UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

^e UNIVERSITY OF LIVERPOOL   (United Kingdom)

^f UNIVERSITY OF EDINBURGH   (United Kingdom)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

^h LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

ⁱ Université Gamal Abdel Nasser de Conakry   (Guinea)

^j INSTITUT NATIONAL DE SANTÉ PUBLIQUE   (Guinea)

^k INSTITUTE OF TROPICAL MEDICINE   (Belgium)

^l IRRUA SPECIALIST TEACHING HOSPITAL   (Nigeria)

^m HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

ⁿ UNIVERSITY OF BASEL   (Switzerland)

^o PHILIPPS UNIVERSITY MARBURG   (Germany)

^p National Reference Center for Viral Hemorrhagic Fevers   (France)

^q INSERM   (France)

^r UNIVERSITY OF ANTWERP   (Belgium)

^s ROBERT KOCH INSTITUTE   (Germany)

^t NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

^u FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^v REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^w REDEEMER S UNIVERSITY   (Nigeria)

^x INSTITUTO DE SALUD CARLOS III   (Spain)

^y Institut Pasteur   (France)

^z BUNDESWEHR INSTITUTE OF MICROBIOLOGY   (Germany)

^aa NATIONAL CENTER FOR EPIDEMIOLOGY   (Hungary)

^ab UNIVERSITY OF LJUBLJANA   (Slovenia)

^ac SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^ad LEIBNIZ INSTITUTE FOR EXPERIMENTAL VIROLOGY   (Germany)

^ae UNIVERSITY OF BONN   (Germany)

^af SPIEZ LABORATORY   (Switzerland)

^ag Bundeswehr Hospital Hamburg   (Germany)

^ah INSTITUTE OF VIROLOGY AND IMMUNOLOGY   (Switzerland)

^ai JanssenCilag AB   (Sweden)

^aj Thünen Institute   (Germany)

^ak Eurice European Research and Project Office GmbH   (Germany)

^al UNIVERSITY COLLEGE LONDON   (United Kingdom)

^am Ministry of Health Guinea   (Guinea)

^an WORLD HEALTH ORGANIZATION   (Switzerland)

^ao Médecins Sans Frontiè Res   (Belgium)

^ap Section Prevention et Lutte Contre la Maladie A la Direction Prefectorale de la Sante de Gueckedou   (Guinea)

^aq Health and Sustainable Development Foundation   (Guinea)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DEVELOPING WORLD; HEALTH RISK; HEALTH SERVICES; NUMERICAL MODEL; PUBLIC HEALTH; SPATIOTEMPORAL ANALYSIS; VIRAL DISEASE;

AFRICA; ARTICLE; BIOGEOGRAPHY; EBOLA HEMORRHAGIC FEVER; EBOLAVIRUS; EPIDEMIC; EVOLUTIONARY RATE; FEMALE; GENE SEQUENCE; GENETIC CONSERVATION; GUINEA; HUMAN; MAJOR CLINICAL STUDY; MALE; MEDICAL GEOGRAPHY; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIERRA LEONE; SPATIOTEMPORAL ANALYSIS; VIRUS GENOME; VIRUS LOAD; AMINO ACID SUBSTITUTION; GENETICS; HEMORRHAGIC FEVER, EBOLA; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; LIBERIA; MALI; MOLECULAR GENETICS; PHYLOGENY; STATISTICS AND NUMERICAL DATA; TRANSMISSION; VIROLOGY;

WEST AFRICA;

EBOLA VIRUS;

AMINO ACID SUBSTITUTION; DISEASE OUTBREAKS; EBOLAVIRUS; EVOLUTION, MOLECULAR; FEMALE; GUINEA; HEMORRHAGIC FEVER, EBOLA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIBERIA; MALE; MALI; MOLECULAR SEQUENCE DATA; PHYLOGENY; SIERRA LEONE; SPATIO-TEMPORAL ANALYSIS;

EID: 84937234767     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14594     Document Type: Article

References (20)

1. Schieffelin, J. S. et al. Clinical illness and outcomes in patients with Ebola in Sierra Leone. N. Engl. J. Med. 371, 2092-2100 (2014).
2. Baize, S. et al. Emergence of Zaire Ebola virus disease in Guinea. N. Engl. J. Med. 371, 1418-1425 (2014).
3. Gatherer, D. The unprecedented scale of the West African Ebola virus disease outbreak is due to environmental and sociological factors, not special attributes of the currently circulating strain of the virus. Evid. Based Med. 20, 28 (2015).
4. Dowall, S. D. et al. Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity. Genome Biol. 15, 540 (2014).
5. Wynne, J. W. et al. Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis. Genome Biol. 15, 532 (2014).
6. Gire, S. K. et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369-1372 (2014).
7. Ho, S. Y., Phillips, M. J., Cooper, A. & Drummond, A. J. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 22, 1561-1568 (2005).
8. Mateo, M. et al. VP24 is amolecular determinant of Ebola virus virulence in guinea pigs. J. Infect. Dis. 204 (Suppl 3), S1011-S1020 (2011).
9. García-Dorival, I. et al. Elucidation of the Ebola virus VP24 cellular interactome and disruption of virus biology through targeted inhibitionof host-cell protein function. J. Proteome Res. 13, 5120-5135 (2014).
10. Basler, C. F. & Amarasinghe, G. K. Evasion of interferon responses by Ebola and Marburg viruses. J. Interferon Cytokine Res. 29, 511-520 (2009).
11. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542 (2012).
12. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359 (2012).
13. Topfer, A. et al. Probabilistic inference of viral quasispecies subject to recombination. J. Comput. Biol. 20, 113-123 (2013).
14. Goecks, J., Nekrutenko, A., Taylor, J. & Galaxy, T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
15. Hoenen, T. et al. Mutation rate and genotype variation of Ebola virus fromMali case sequences. Science, (2015).
16. Tavaré, S. Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences in Lectures onMathematics in the Life Sciences Vol. 17 (ed.Muira, R. M.) Some Mathematical Questions in Biology: DNA Sequence Analysis (American Mathematical Society, 1986).
17. Yang, Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximatemethods. J. Mol. Evol. 39, 306-314 (1994).
18. Drummond, A. J., Suchard, M. A., Xie, D.&Rambaut, A.Bayesianphylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973 (2012).
19. Drummond, A. J., Ho, S. Y., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).
20. Gill, M. S. et al. Improving Bayesian population dynamics inference: a coalescentbased model for multiple loci. Mol. Biol. Evol. 30, 713-724 (2013).