In- and Out-of-hospital Mortality Associated with Seasonal and Pandemic Influenza and Respiratory Syncytial Virus in South Africa, 2009–2013

BACKGROUND: Estimates of influenza- and respiratory syncytial virus (RSV)-associated mortality burden are important to guide policy for control. Data are limited on the contribution of out-of-hospital deaths to this mortality. METHODS: We modeled excess mortality attributable to influenza and RSV infection by applying regression models to weekly deaths from national vital statistics from 2009 through 2013, using influenza and RSV laboratory surveillance data as covariates. We fitted separate models for in- and out-of-hospital deaths. RESULTS: There were 509791 average annual deaths in South Africa, of which 44% (95% confidence interval [CI] 43%–45%) occurred out-of-hospital. Seasonal influenza and RSV all-cause mortality rates were 23.0 (95% CI 11.0–30.6) and 13.2 (95% CI 6.4–33.8) per 100000 population annually (2.3% [95%CI 2.3%–2.4%] and 1.3% [95% CI 1.2%–1.4%] of all deaths respectively). The peak mortality rate was in individuals aged ≥75 years (386.0; 95% CI 176.5–466.3) for influenza and in infants (143.4; 95% CI 0–194.8) for RSV. Overall, 63% (95% CI 62%–-65%) of seasonal influenza and 48% (95% CI 47%–49%) of RSV-associated deaths occurred out-of-hospital. Among children aged <5 years, RSV-associated deaths were more likely to occur in-hospital, whereas influenza-associated deaths were more likely to occur out-of-hospital. The mortality rate was 6.7 (95% CI 6.4–33.8) in the first influenza A(H1N1)pdm09 wave in 2009 and 20.9 (95% CI 6.4–33.8) in the second wave in 2011, with 30% (95% CI 29%–32%) of A(H1N1)pdm09-associated deaths in 2009 occurring out-of-hospital. DISCUSSION: More than 45% of seasonal influenza- and RSV-associated deaths occur out-of-hospital in South Africa. These data suggest that hospital-based studies may substantially underestimate mortality burden.