Can year-round respiratory surveillance improve South Africa’s response to seasonal and emerging respiratory diseases?

Respiratory pathogens remain a major public health concern, causing seasonal outbreaks and severe illness, particularly among young children, older adults, and people with underlying health conditions. Understanding when these pathogens circulate, who is most affected, and how they evolve is essential for guiding prevention and control measures. While routine clinical surveillance provides valuable information, systematic sentinel surveillance offers a more comprehensive picture of disease trends, seasonality, and the populations most at risk.

In South Africa, the National Institute for Communicable Diseases coordinates three respiratory illness surveillance programmes: the hospital-based Pneumonia Surveillance Programme, the Influenza-like Illness Primary Healthcare Clinic Surveillance Programme, and the Viral Watch Programme conducted through private general practitioners. Together, these programmes monitor the circulation of key respiratory pathogens, including influenza viruses, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Bordetella pertussis, while also generating data to characterise circulating strains and identify groups at increased risk of severe disease.

The following report describes the epidemiology of respiratory pathogens detected through South Africa’s influenza-like illness and pneumonia surveillance programmes during 2024. It examines seasonal patterns, pathogen circulation, genetic characterisation, and demographic trends, providing evidence to support public health preparedness, inform vaccination strategies, and strengthen the prevention and management of respiratory diseases in South Africa.

Methods

Mid-turbinate nasal swabs from ILI-PHC and PSP sites were tested for four pathogens: influenza, respiratory syncytial virus (RSV), Bordetella pertussis, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ILI-VW specimens were tested for influenza, RSV, and SARS-CoV-2 only.

The CRDM laboratory at the NICD tested specimens for influenza A and B, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using a commercial multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assay (Allplex™ SARS-CoV-2/FluA/FluB/RSV PCR kit, Seegene Inc., Seoul, South Korea). 

Results

In the ILI-PHC surveillance programme, influenza was the most frequently detected pathogen among individuals under 15 years old, with a detection rate of 19% (170/880), followed by RSV at 8% (70/880), SARS CoV-2 at 2% (20/880), and B. pertussis at 0.9% (8/879).

In the PSP surveillance programme, RSV was the most frequently detected pathogen among individuals younger than 15 years, with a detection rate of 24% (677/2 801), followed by influenza at 6% (177/2 801), SARS-CoV-2 at 2% (61/2 801), and B. pertussis at 2%.

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