title: Insights into the early epidemic spread of ebola in sierra leone provided by viral sequence data.
abstract: METHODS
  The current Ebola virus epidemic in West Africa has been spreading at least since December 2013. The first confirmed case of Ebola virus in Sierra Leone was identified on May 25. Based on viral genetic sequencing data from 72 individuals in Sierra Leone collected between the end of May and mid June, we utilize a range of phylodynamic methods to estimate the basic reproductive number (R0). We additionally estimate the expected lengths of the incubation and infectious periods of the virus. Finally, we use phylogenetic trees to examine the role played by population structure in the epidemic.
  
  
  RESULTS
  The median estimates of R0 based on sequencing data alone range between 1.65-2.18, with the most plausible model yielding a median R0 of 2.18 (95% HPD 1.24-3.55). Importantly, our results indicate that, at least until mid June, relief efforts in Sierra Leone were ineffective at lowering the effective reproductive number of the virus. We estimate the expected length of the infectious period to be 2.58 days (median; 95% HPD 1.24-6.98). The dataset appears to be too small in order to estimate the incubation period with high certainty (median expected incubation period 4.92 days; 95% HPD 2.11-23.20). While our estimates of the duration of infection tend to be smaller than previously reported, phylodynamic analyses support a previous estimate that 70% of cases were observed and included in the present dataset. The dataset is too small to show a particular population structure with high significance, however our preliminary analyses suggest that half the population is spreading the virus with an R0 well above 2, while the other half of the population is spreading with an R0 below 1.
  
  
  CONCLUSIONS
  Overall we show that sequencing data can robustly infer key epidemiological parameters. Such estimates inform public health officials and help to coordinate effective public health efforts. Thus having more sequencing data available for the ongoing Ebola virus epidemic and at the start of new outbreaks will foster a quick understanding of the dynamics of the pathogen.
authors: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
authors: Tanja
authors: T
authors: Stadler
authors: Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
authors: Denise
authors: D
authors: Kühnert
authors: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
authors: David A
authors: DA
authors: Rasmussen
authors: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
authors: Louis
authors: L
authors: du Plessis
keywords: EBOV; birth-death; coalescent; ebola; phylodynamics
references: PLoS Comput Biol. 2014 Dec 04;10(12):e1003919
references: 25474353
references: PLoS Negl Trop Dis. 2014 Jul 31;8(7):e3056
references: 25079231
references: J Infect Dis. 1999 Feb;179 Suppl 1:S170-6
references: 9988181
references: J Infect Dis. 1999 Feb;179 Suppl 1:S8-10
references: 9988156
references: Genetics. 2012 Jan;190(1):187-201
references: 22042576
references: J R Soc Interface. 2014 Feb 26;11(94):20131106
references: 24573331
references: Philos Trans R Soc Lond B Biol Sci. 2013 Feb 04;368(1614):20120198
references: 23382421
references: J Infect Dis. 1999 Feb;179 Suppl 1:S1-7
references: 9988155
references: PLoS Comput Biol. 2014 Apr 10;10(4):e1003537
references: 24722319
references: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6187-92
references: 21444816
references: Euro Surveill. 2014 Sep 11;19(36):null
references: 25232919
references: PLoS Curr. 2014 Sep 18;6:null
references: 25642357
references: Biometrics. 2006 Dec;62(4):1170-7
references: 17156292
references: N Engl J Med. 2014 Oct 16;371(16):1481-95
references: 25244186
references: Mol Biol Evol. 2012 Jan;29(1):347-57
references: 21890480
references: J Infect Dis. 1999 Feb;179 Suppl 1:S28-35
references: 9988162
references: Epidemiol Infect. 2007 May;135(4):610-21
references: 16999875
references: Syst Biol. 2011 Oct;60(5):676-84
references: 21482552
references: PLoS Curr. 2014 Sep 02;6:null
references: 25642360
references: J Infect Dis. 1999 Feb;179 Suppl 1:S76-86
references: 9988168
references: Mol Biol Evol. 2016 Aug;33(8):2102-16
references: 27189573
references: PLoS Curr. 2014 Sep 02;6:null
references: 25642364
references: N Engl J Med. 2014 Sep 25;371(13):1183-5
references: 25140856
references: Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33
references: 23248286
references: J Infect Dis. 1999 Feb;179 Suppl 1:S87-91
references: 9988169
references: PLoS Curr. 2014 Sep 08;6:null
references: 25642358
references: N Engl J Med. 2014 Sep 25;371(13):1180-3
references: 25140855
references: Science. 2014 Sep 12;345(6202):1369-72
references: 25214632
references: J Theor Biol. 2004 Jul 7;229(1):119-26
references: 15178190
references: J Theor Biol. 2009 Nov 7;261(1):58-66
references: 19631666