Background: Invasive meningococcal disease (IMD) is a devastating illness with high mortality. Like influenza, endemic IMD is seasonal peaking in winter. Studies suggest that circulation of influenza virus may influence timing and magnitude of IMD winter peaks.

Methods: This ecological study used weekly data from two nationwide surveillance programmes: Viral Watch (proportion of out-patient influenza-positive cases from throat/nasal swabs) and GERMS-SA (laboratory-confirmed cases of IMD) occurring across South Africa from 2003 through 2018 in all age-bands. A bivariate time-series analysis using wavelet transform was conducted to determine co-circulation of the diseases and the time lag between the peak seasons. We modelled excess meningococcal disease cases attributable to influenza co-circulation using univariate regression spline models. Stata and R statistical packages were used for the analysis.

Results: 5256 laboratory-confirmed IMD cases were reported, with an average annual incidence of 0.23 episodes per 100 000 population and a mean seasonal peak during week 32 (+3 weeks). Forty-two percent (10 421/24 741) of swabs were positive for influenza during the study period. The mean peak for all influenza occurred at week 26 (+4 weeks). There was an average lag-time of 5 weeks between annual influenza and IMD seasons. Overall, 5% (1-9%) of meningococcal disease can be attributable to influenza co-circulation with, on average, 17 excess IMD cases per year attributable to influenza.

Conclusion: A quantifiable proportion of meningococcal disease in South Africa is associated with influenza co-circulation, therefore seasonal influenza vaccination may have an effect on preventing a small portion of meningococcal disease in addition to preventing influenza.