Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa

Brett N Archer,Stefano Tempia,Cheryl Cohen,Marcello Pagano,Laura F White

doi:10.1371/journal.pone.0049482

Abstract

Background/ObjectiveDescribing 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.MethodsWe 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.Results12,360 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).ConclusionsTransmissibility 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.

Highlights

During 2009, the emergence and worldwide spread of influenza A(H1N1)pdm09 was observed [1]
While a rapid and timely estimation of the transmission parameters of this novel virus played an important role in informing transmission potential and mitigation interventions during the 2009 pandemic period, the post-pandemic documentation of these parameters is important as many previous estimates were established from analyses conducted during the early stages of epidemics and often from preliminary data [2,3]
When estimating initial reproductive number (Rt), we focus our analysis on the exponential growth phase of the epidemic in South Africa

Summary

Introduction

During 2009, the emergence and worldwide spread of influenza A(H1N1)pdm (pH1N1) was observed [1]. Enhancing our knowledge of past pandemics assists in providing greater insight to prepare and respond in future outbreaks. Four key measures are typically used to describe the transmissibility of an infectious disease. The secondary attack rate (SAR) describes the proportion of susceptible contacts that acquire infection from an infectious person. The basic reproductive number (R0) is defined as the average number of secondary cases per primary case in an idealised entirely susceptible population in the absence of control measures. The effective reproductive number (Rt) at any given time point represents the actual average number of secondary cases per primary case observed in a population. Rt reflects the impact of control measures and the depletion of susceptible persons over time. The initial Rt may approximate R0 in pandemic situations. The initial Rt may approximate R0 in pandemic situations. [2,3,4,5]

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Discussion

Conclusion