Quantifying the epidemic spread of ebola virus (Ebov) in sierra leone using phylodynamics

Virulence

Volumn 5, Issue 8, 2014, Pages 825-827

  Alizon, Samuel ^a   Lion, Sebastien ^b   Murall, Carmen Lía ^a,b   Abbate, Jessica L ^b  

^a University de Montpellier   (France)

^b CENTRE D ECOLOGIE FONCTIONNELLE ET EVOLUTIVE   (France)

Author keywords

Bayesian inference; Ebola virus (EBOV); Epidemiology; Phylogenetics; R0

Indexed keywords

ARTICLE; BASIC REPRODUCTION NUMBER; DISEASE DURATION; EBOLA HEMORRHAGIC FEVER; EBOLA VIRUS; EFFECTIVE REPRODUCTION NUMBER; EPIDEMIOLOGICAL DATA; GENE SEQUENCE; HUMAN; INFECTION CONTROL; NONHUMAN; PHYLOGENY; PUBLIC HEALTH; SIERRA LEONE; SUSCEPTIBLE POPULATION; VIRUS GENOME; VIRUS MUTATION; EBOLAVIRUS; EPIDEMIC; GENETICS; HEMORRHAGIC FEVER, EBOLA; MIXED INFECTION;

EBOLA VIRUS;

COINFECTION; DISEASE OUTBREAKS; EBOLAVIRUS; EPIDEMICS; GENOME, VIRAL; HEMORRHAGIC FEVER, EBOLA; HUMANS; PHYLOGENY; SIERRA LEONE;

EID: 84921934974     PISSN: 21505594     EISSN: 21505608     Source Type: Journal    
DOI: 10.4161/21505594.2014.976514     Document Type: Article

References (20)

1. Fauci AS. Ebola – underscoring the global disparities in health care resources. N Engl J Med 2014; 371:1084-6; PMID:25119491; http://dx.doi.org/10.1056/NEJMp1409494
2. Pourrut X, Kumulungui B, Wittmann T, Moussavou G, Delicat A, Yaba P, Nkoghe D, Gonzalez JP, Leroy EM. The natural history of Ebola virus in Africa. Microbes Infect 2005; 7:1005-14; PMID:16002313; http://dx.doi.org/10.1016/j.micinf.2005.04.006
3. Groseth A, Feldmann H, Strong JE. The ecology of Ebola virus. Trends Microbiol 2007; 15(9):408-16; PMID:17698361; http://dx.doi.org/10.1016/j.tim.2007.08.001
4. Baize S, Pannetier D, Oestreich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keita S, De Clerck H. Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med 2014; 371 (15):1418-25; PMID:24738640; http://dx.doi.org/10.1056/NEJMoa1404505
5. World Health Organization (WHO). Ebola Response Roadmap Update. 2014. Sept. 22; 4 pp.; http://apps.who.int/iris/bitstream/10665/134449/1/roadmapupdate22sept14_eng.pdf?uaD1
6. Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014; 345(6202):1369-72; PMID:25214632; http://dx.doi.org/10.1126/science.1259657
7. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, Mumford JA, Holmes EC, et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 2004; 303(5656):327-32; PMID:14726583;http://dx.doi.org/10.1126/science.1090727
8. Volz EM, Koelle K, Bedford T. Viral phylodynamics. PLoS Comput Biol 2013; 9(3):1002947; PMID:23555203; http://dx.doi.org/10.1371/journal.pcbi.1002947
9. Stadler T, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, et al. Estimating the basic reproductive number from viral sequence data. Mol Biol Evol 2012; 29(1):347-57; PMID:21890480; http://dx.doi.org/10.1093/molbev/msr217
10. Bouchaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014; 10(4): 1003537; PMID:24722319; http://dx.doi.org/10.1371/journal.pcbi.1003537
11. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005; 22(5):1185-1192; PMID:15703244; http://dx.doi.org/10.1093/molbev/msi103
12. Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T. Using an epidemiological model for phylogenetic inference reveals density dependence in hiv transmission. Mol Biol Evol 2014; 31:6-17; PMID:24085839;http://dx.doi.org/10.1093/molbev/mst172
13. Bwaka MA, Bonnet MJ, Calain P, Colebunders R, De Roo A, Guimard Y, Katwiki KR, Kibadi K, Kipasa MA, Kuvula KJ, et al. Ebola hemorrhagic fever in Kikwit, Democratic Republic of the Congo: clinical observations in 103 patients. J Infect Dis 1999; 179:S1-S7; PMID:9988155; http://dx.doi.org/10.1086/514308
14. Aylward B, Barboza P, Bawo L, Bertherat E, Bilivogui P, Blake I, et al; The WHO Ebola Response Team. Ebola virus disaease in West Africa – The first 9 months of the epidemic and forward projections. N Engl J Med2014; 371:1481-1495; PMID:24678955
15. Althaus CL. Estimating the Reproduction Number of Ebola Virus (EBOV) During the 2014 Outbreak in West Africa. Plos Curr Outbreaks 2014. Sep 2. Edition 1. doi:10.1371/currents.outbreaks.91afb5e0f279e7f29e7056095255b288
16. House T. Epidemiological dynamics of Ebola outbreaks. Elife 2014; 3; PMID:25217532; http://dx.doi.org/10.7554/eLife.03908
17. Nishiura H, Chowell G. Early transmission dynamics of Ebola virus disease (EVD), West Africa, March to August 2014. Euro Surveill 2014; 19(36):20894;PMID:25232919
18. Chowell G, Hengartner NW, Castillo-Chavez C, Fenimore PW, Hyman JM. The basic reproductive number of Ebola and the effects of public health measures: the cases of Congo and Uganda. J Theor Biol 2004; 229 (1):119-26; PMID:15178190; http://dx.doi.org/10.1016/j.jtbi.2004.03.006
19. Rasmussen DA, Ratmann O, Koelle K. Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comput Biol 2011; 7(8): 1002136; PMID:21901082; http://dx.doi.org/10.1371/journal.pcbi.1002136
20. Stadler T, Kühnert D, Rasmussen DA, du Plessis L. Insights into the early epidemic spread of ebola in Sierra Leone provided by viral sequence data. PLoS Currents Outbreaks; 2014 Oct 6.; Edition 1; doi:10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f