title: A new framework and software to estimate time-varying reproduction numbers during epidemics.
abstract: The quantification of transmissibility during epidemics is essential to designing and adjusting public health responses. Transmissibility can be measured by the reproduction number R, the average number of secondary cases caused by an infected individual. Several methods have been proposed to estimate R over the course of an epidemic; however, they are usually difficult to implement for people without a strong background in statistical modeling. Here, we present a ready-to-use tool for estimating R from incidence time series, which is implemented in popular software including Microsoft Excel (Microsoft Corporation, Redmond, Washington). This tool produces novel, statistically robust analytical estimates of R and incorporates uncertainty in the distribution of the serial interval (the time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases). We applied the method to 5 historical outbreaks; the resulting estimates of R are consistent with those presented in the literature. This tool should help epidemiologists quantify temporal changes in the transmission intensity of future epidemics by using surveillance data.
authors.forename: Anne
authors.initials: A
authors.lastname: Cori
authors.forename: Neil M
authors.initials: NM
authors.lastname: Ferguson
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
authors.forename: Simon
authors.initials: S
authors.lastname: Cauchemez
mesh_terms: D058872:Epidemics / Q000706:statistics & numerical data*; D006801:Humans; D015994:Incidence; D015233:Models, Statistical; D012984:Software; D013997:Time Factors; D014777:Virus Diseases / Q000453:epidemiology* / Q000635:transmission*
keywords: SARS; incidence; influenza; measles; reproduction number; smallpox; software
references.citation: Am J Epidemiol. 2006 Sep 15;164(6):591-7
references.pmid: 16887892
references.citation: Emerg Infect Dis. 2006 Jan;12(1):110-3
references.pmid: 16494726
references.citation: Science. 2009 Jun 19;324(5934):1557-61
references.pmid: 19433588
references.citation: Science. 2006 Nov 17;314(5802):1150-3
references.pmid: 17110580
references.citation: Epidemiology. 2010 Nov;21(6):842-6
references.pmid: 20805752
references.citation: PLoS One. 2010 Jun 28;5(6):e11341
references.pmid: 20596536
references.citation: Lancet. 2000 Apr 1;355(9210):1131-7
references.pmid: 10791375
references.citation: PLoS One. 2008 May 14;3(5):e2185
references.pmid: 18478118
references.citation: Nature. 2006 Jul 27;442(7101):448-52
references.pmid: 16642006
references.citation: Am J Epidemiol. 2011 Sep 1;174(5):505-14
references.pmid: 21749971
references.citation: Epidemiol Infect. 2004 Dec;132(6):1139-49
references.pmid: 15635973
references.citation: Euro Surveill. 2010 Jun 17;15(24):
references.pmid: 20576236
references.citation: Ann Intern Med. 2004 Nov 2;141(9):662-73
references.pmid: 15520422
references.citation: Vaccine. 2011 Jan 29;29(5):896-904
references.pmid: 20580742
references.citation: Science. 2003 Jun 20;300(5627):1966-70
references.pmid: 12766207
references.citation: Science. 1982 Feb 26;215(4536):1053-60
references.pmid: 7063839
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12637-42
references.pmid: 16894173
references.citation: Nature. 2001 Oct 4;413(6855):542-8
references.pmid: 11586365
references.citation: Science. 2003 Jun 20;300(5627):1961-6
references.pmid: 12766206
references.citation: Int J Epidemiol. 2007 Aug;36(4):881-9
references.pmid: 17517812
references.citation: Nature. 2001 Dec 13;414(6865):748-51
references.pmid: 11742399
references.citation: Lancet. 1952 Sep 20;2(6734):549-54
references.pmid: 12981903
references.citation: Am J Epidemiol. 2004 Sep 15;160(6):509-16
references.pmid: 15353409
references.citation: N Engl J Med. 2003 May 15;348(20):1986-94
references.pmid: 12682352
references.citation: Lancet. 2003 May 24;361(9371):1767-72
references.pmid: 12781535
references.citation: PLoS One. 2007 Aug 22;2(8):e758
references.pmid: 17712406
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6146-51
references.pmid: 15071187
references.citation: Euro Surveill. 2010 Jul 22;15(29):
references.pmid: 20667300
references.citation: PLoS One. 2008 Jan 30;3(1):e1498
references.pmid: 18231585
references.citation: Nature. 2005 Sep 8;437(7056):209-14
references.pmid: 16079797
references.citation: Influenza Other Respir Viruses. 2011 Sep;5(5):306-16
references.pmid: 21668690
references.citation: J Infect Dis. 2010 May 15;201(10):1509-16
references.pmid: 20377412
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2825-30
references.pmid: 21282645
references.citation: Am J Epidemiol. 2003 Jul 15;158(2):110-7
references.pmid: 12851223
references.citation: J Epidemiol Biostat. 2000;5(3):161-8
references.pmid: 11051112
references.citation: PLoS Comput Biol. 2009 Aug;5(8):e1000471
references.pmid: 19696879
references.citation: Math Biosci Eng. 2009 Apr;6(2):261-82
references.pmid: 19364152