How can sentinel surveillance uncover patterns of respiratory infections and guide public health responses?
Respiratory viruses are a major cause of illness affecting both the upper and lower respiratory tracts, with seasonal peaks typically observed during the autumn and winter months. Pathogens such as influenza, respiratory syncytial virus (RSV), and SARS-CoV-2 continue to contribute substantially to morbidity and mortality, placing pressure on health systems through increased outpatient visits, hospitalisations, and deaths.
Clinical presentation can range from mild symptoms, including fever, cough, sore throat, and fatigue, to more severe disease characterised by pneumonia and other serious lower respiratory tract infections. The wide spectrum of illness and variation in healthcare-seeking behaviour can make it challenging to accurately estimate disease burden using routine clinical data alone.
Surveillance programmes are therefore essential for monitoring respiratory disease patterns, identifying seasonal changes, and characterising the epidemiology of affected populations. Sentinel syndromic surveillance, in particular, plays a critical role by systematically enrolling patients who meet standardised case definitions, regardless of disease severity. This approach allows for consistent monitoring of trends over time and supports early detection of changes in pathogen circulation.
Data generated through sentinel surveillance contribute to estimates of disease burden, identification of groups at higher risk of severe outcomes, and evaluation of vaccine effectiveness. These findings provide an evidence base for policymakers and public health stakeholders responsible for designing, implementing, and assessing prevention and control strategies.
In South Africa, systematic syndromic respiratory illness surveillance is conducted by the Centre for Respiratory Diseases and Meningitis (CRDM) at the National Institute for Communicable Diseases, a division of the National Health Laboratory Service. Surveillance activities include the hospital-based Pneumonia Surveillance Programme (PSP) and two Influenza-like Illness (ILI) programmes: ILI surveillance at public sector primary healthcare clinics (ILI-PHC) and the Viral Watch programme (ILI-VW) at private general practitioner practices.
This report outlines the epidemiology of key respiratory pathogens in South Africa during 2023, providing data to support evidence-based policies and strategies for the prevention, control, and management of respiratory infections.
Materials and Methods
Mid-turbinate nasal swabs collected from participants enrolled at ILI-PHC and PSP sites were tested for influenza, RSV, Bordetella pertussis, and SARS-CoV-2. Specimens from ILI-VW sites were tested for influenza, RSV, and SARS-CoV-2.
In the PSP and ILI-PHC programmes, surveillance officers screened patients and enrolled those meeting case definitions after informed consent. Case investigation forms were completed and uploaded to the NICD database, and specimens were transported under cold-chain conditions for laboratory testing within 72 hours of collection.
Results
In the 2023 ILI-PHC surveillance programme, influenza was the most frequently detected pathogen among individuals younger than 15 years, with a detection rate of 16.7%, followed by RSV (6.8%), SARS-CoV-2 (3.2%), and Bordetella pertussis (2.0%).
In the 2023 PSP surveillance programme, RSV was the most commonly detected pathogen among individuals under 15 years of age, with a detection rate of 21.7%. This was followed by influenza (4.4%), Bordetella pertussis (3.8%), and SARS-CoV-2 (3.1%).
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