BACKGROUND: There is limited data on the epidemiology of influenza and few published estimates of influenza vaccine
effectiveness (VE) from Africa. In April 2009, a new influenza virus strain infecting humans was identified and rapidly spread
globally. We compared the characteristics of patients ill with influenza A(H1N1)pdm09 virus to those ill with seasonal
influenza and estimated influenza vaccine effectiveness during five influenza seasons (2005–2009) in South Africa.
METHODS : Epidemiological data and throat and/or nasal swabs were collected from patients with influenza-like illness (ILI) at
sentinel sites. Samples were tested for seasonal influenza viruses using culture, haemagglutination inhibition tests and/or
polymerase chain reaction (PCR) and for influenza A(H1N1)pdm09 by real-time PCR. For the vaccine effectiveness (VE)
analysis we considered patients testing positive for influenza A and/or B as cases and those testing negative for influenza as
controls. Age-adjusted VE was calculated as 1-odds ratio for influenza in vaccinated and non-vaccinated individuals.
RESULTS : From 2005 through 2009 we identified 3,717 influenza case-patients. The median age was significantly lower
among patients infected with influenza A(H1N1)pdm09 virus than those with seasonal influenza, 17 and 27 years
respectively (p,0.001). The vaccine coverage during the influenza season ranged from 3.4% in 2009 to 5.1% in 2006 and
was higher in the $50 years (range 6.9% in 2008 to 13.2% in 2006) than in the ,50 years age group (range 2.2% in 2007 to
3.7% in 2006). The age-adjusted VE estimates for seasonal influenza were 48.6% (4.9%, 73.2%); 214.2% (29.7%, 34.8%);
12.0% (270.4%, 55.4%); 67.4% (12.4%, 90.3%) and 29.6% (221.5%, 60.1%) from 2005 to 2009 respectively. For the
A(H1N1)pdm09 season, the efficacy of seasonal vaccine was 26.4% (293.5%, 43.3%).
CONCLUSION : Influenza vaccine demonstrated a significant protective effect in two of the five years evaluated. Low vaccine
coverage may have reduced power to estimate vaccine effectiveness.