title: Reproductive number and serial interval of the first wave of influenza A(H1N1)pdm09 virus in South Africa.
abstract: OBJECTIVE
  Describing transmissibility parameters of past pandemics from diverse geographic sites remains critical to planning responses to future outbreaks. We characterize the transmissibility of influenza A(H1N1)pdm09 (hereafter pH1N1) in South Africa during 2009 by estimating the serial interval (SI), the initial effective reproductive number (initial R(t)) and the temporal variation of R(t).
  
  
  METHODS
  We make use of data from a central registry of all pH1N1 laboratory-confirmed cases detected throughout South Africa. Whenever date of symptom onset is missing, we estimate it from the date of specimen collection using a multiple imputation approach repeated 100 times for each missing value. We apply a likelihood-based method (method 1) for simultaneous estimation of initial R(t) and the SI; estimate initial R(t) from SI distributions established from prior field studies (method 2); and the Wallinga and Teunis method (method 3) to model the temporal variation of R(t).
  
  
  RESULTS
  12,360 confirmed pH1N1 cases were reported in the central registry. During the period of exponential growth of the epidemic (June 21 to August 3, 2009), we simultaneously estimate a mean R(t) of 1.47 (95% CI: 1.30-1.72) and mean SI of 2.78 days (95% CI: 1.80-3.75) (method 1). Field studies found a mean SI of 2.3 days between primary cases and laboratory-confirmed secondary cases, and 2.7 days when considering both suspected and confirmed secondary cases. Incorporating the SI estimate from field studies using laboratory-confirmed cases, we found an initial R(t) of 1.43 (95% CI: 1.38-1.49) (method 2). The mean R(t) peaked at 2.91 (95% CI: 0.85-2.91) on June 21, as the epidemic commenced, and R(t)>1 was sustained until August 22 (method 3).
  
  
  CONCLUSIONS
  Transmissibility characteristics of pH1N1 in South Africa are similar to estimates reported by countries outside of Africa. Estimations using the likelihood-based method are in agreement with field findings.
authors.affiliation: National Institute for Communicable Diseases-NICD, National Health Laboratory Service-NHLS, Johannesburg, Gauteng, South Africa.
authors.forename: Brett N
authors.initials: BN
authors.lastname: Archer
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
authors.forename: Laura F
authors.initials: LF
authors.lastname: White
authors.forename: Marcello
authors.initials: M
authors.lastname: Pagano
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004196:Disease Outbreaks; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000502:physiology*; D007251:Influenza, Human / Q000453:epidemiology* / Q000635:transmission; D015233:Models, Statistical; D058873:Pandemics; D012042:Registries; D013019:South Africa / Q000453:epidemiology