Background

The first laboratory-confirmed SARS-CoV-2 case in South Africa was reported 5 March 2020. Followed by the implementation of varying SARS-CoV-2 containment measures, resulting in a lack of the typical seasonal influenza in 2020 and 2021, on a background of four SARS-COV-2 infection waves. We determined the change in invasive pneumococcal disease (IPD) cases during this time.

Methods

National, laboratory-based IPD data from an established surveillance system was used to perform interrupted time series analysis to compare IPD diagnoses pre-(2012-2019) and during the SARS-CoV-2 pandemic (2020-2021) overall, by PCV13 serotype and age group.

Results

During 2012-2021 we enrolled 23,759 IPD cases, ranging from 3,223 in 2012 to 1,241 in 2020. Compared to 2012-2019 trends, IPD diagnoses in South Africa reduced by 42% (95%CI 40%-44%) in 2020 and 23% (95%CI 22%-25%) in 2021. Except for children aged 2-4 years in 2021, all age groups saw a reduction of IPD diagnoses. The highest reductions were seen in adults aged ≥65 years (53% [95%CI 46%-58%] in 2020 and 50% [95%CI 45%-54%] in 2021). There were similar reductions in PCV13 and non-PCV13 serotype IPD (41%, [95%CI 38%-44%] vs 46%, [95%CI 43%-48%]).

Figure. Observed IPD cases (grey), trend (black) and predicted (red)

Conclusions

We observed a marked reduction in IPD diagnoses during the SARS-CoV-2 pandemic, with larger reductions in the first year of the pandemic where restrictions were more stringent compared to the second. Reductions may be attributed to the introduction of non-pharmaceutical interventions that reduced transmission of pneumococcus, reduced healthcare-seeking behaviour, or reduced sample collection for diagnosis.