[Source: PLoS ONE, full text: (LINK). Abstract, edited.]
Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa
Brett N. Archer1, Stefano Tempia2, Laura F. White3, Marcello Pagano4, Cheryl Cohen1,5*
1 National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Gauteng, South Africa, 2 United States Centers for Disease Control and Prevention, Attaché to the National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Gauteng, South Africa, 3 Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, United States of America, 4 School of Public Health, Harvard University, Cambridge, Massachusetts, United States of America, 5 School of Public Health, University of Witwatersrand, Johannesburg, Gauteng, South Africa
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 Rt) and the temporal variation of Rt.
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 Rt and the SI; estimate initial Rt from SI distributions established from prior field studies (method 2); and the Wallinga and Teunis method (method 3) to model the temporal variation of Rt.
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 Rt 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 Rt of 1.43 (95% CI: 1.38–1.49) (method 2). The mean Rt peaked at 2.91 (95% CI: 0.85–2.91) on June 21, as the epidemic commenced, and Rt>1 was sustained until August 22 (method 3).
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.
Citation: Archer BN, Tempia S, White LF, Pagano M, Cohen C (2012) Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa. PLoS ONE 7(11): e49482. doi:10.1371/journal.pone.0049482
Editor: Benjamin J. Cowling, University of Hong Kong, Hong Kong
Received: June 11, 2012; Accepted: October 9, 2012; Published: November 16, 2012
Copyright: © 2012 Archer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was partly supported by the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS). Laboratory testing and influenza surveillance activities at the NICD are funded, in part, by an unrestricted grant from the United States Centers for Disease Control and Prevention (CDC) [grant number 5U51/IP000155]. Dr. White and Dr. Pagano were supported by the National Institute of General Medical Sciences (NIGMS) [award number U54GM088558]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NICD, NHLS, US CDC, NIGMS, NIH or the affiliated universities. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: firstname.lastname@example.org