Reproductive number and serial interval of the first wave of influenza A(H1N1)pdm09 virus in South Africa

Abstract

Background/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.

Figure 1. Epidemic curve of laboratory-confirmed influenza A(H1N1)pdm09 cases, South Africa, June 12 to September 30, 2009.

Bars show original recorded data applying date of symptom onset where available (n = 758) and substitute by date of specimen collection where onset was unavailable (total n = 12,526). The line shows imputed data where date of symptom onset for missing case-based data was obtained by multiple imputations adjusted by provincial location of specimen collection and the occurrence of a case on a weekend day (n = 12,491).

Figure 2. Distribution of serial interval and initial effective reproductive number (R_t) across 100 simulations for the influenza A(H1N1)pdm09 epidemic in South Africa using the likelihood-based simultaneous estimation method (method 1).

Figure 3. Distribution of the initial effective reproduction number (R_t) across 100 simulations for the pandemic influenza A(H1N1)pdm09 epidemic in South Africa, assuming known serial interval (SI) estimates derived from (A) confirmed secondary cases only (SI: 2.3 days) and (B) confirmed plus suspected secondary cases (SI: 2.7 days) in the transmission chain (method 2).

Figure 4. Temporal variation in the mean effective reproductive number () of influenza A(H1N1)pdm09 in South Africa, June 15 to October 4, 2009 (method 3).