CRDM coordinates the following syndromic surveillance programmes: pneumonia surveillance, influenza-like illness (ILI) (2 programmes: systematic ILI at public health clinics and viral watch) and the respiratory morbidity surveillance system).

Pneumonia surveillance

Pneumonia is a leading cause of hospitalisation and death in children and adults in South Africa. The National Pneumonia Surveillance Programme (NPSP), started in 2009, includes sentinel syndromic surveillance for severe respiratory illness (SRI) irrespective of duration of symptoms and testing for core pathogens of public health importance, namely, influenza, respiratory syncytial virus (RSV) and Bordetella pertussis. Surveillance is operational in five provinces. In addition, at three of the surveillance sites, surveillance for Streptococcus pneumoniae is included. Data from this surveillance programme provides policy makers, clinicians and the general medical community with regular updates on seasonality, trends and the burden of pathogens associated with pneumonia. It also provides strategic information to support planning and monitoring of pneumonia prevention and control activities.

Influenza-like illness surveillance

Surveillance for influenza-like illness (ILI) is ongoing at outpatient clinics at three provinces, with plans to expand to cover all provinces with existing pneumonia surveillance sites. In addition, CRDM has a long- standing ILI programme (since 1984), The Viral Watch sentinel surveillance programme. The surveillance programmes provide data to describe the timing and severity of the influenza and RSV seasons, characterisation of circulating influenza virus strains to guide decisions around Southern Hemisphere influenza vaccine composition, annual estimates of influenza vaccine effectiveness and detect outbreaks caused by the pathogens included as part of surveillance.

Respiratory morbidity surveillance system tracks trends in the number of pneumonia and influenza hospitalizations, using anonymised data from a private hospital group.

CRDM houses a World Health Organisation (WHO)-designated National Influenza Centre (NIC). This is 1 of 142 NICs in 113 countries that form part of the WHO’s Global Influenza Surveillance and Response System (GISRS). The South African NIC works closely with the stakeholders from the National Department of Health and the WHO Collaborating Centres to monitor of the emergence of novel, emerging or resistant influenza virus strains through surveillance activities. The NIC also performs preliminary genotypic and phenotypic characterization of influenza virus specimens circulating in South Africa and ships representative clinical specimens and isolated viruses to WHO Collaborating Centres for advanced antigenic and genetic analysis. The results form the basis for WHO recommendations on the composition of the Northern and Southern hemisphere influenza vaccine each year.

Since 1999, CRDM has conducted national laboratory-based, population-based active surveillance for invasive disease caused by S. pneumoniae, H. influenzae and N. meningitidis. Enhanced surveillance occurs at 26 hospital sites (at least one in every South African province) where additional clinical data are collected on each patient with invasive disease. Surveillance data contribute to the evaluation and understanding of the impact of both the pneumococcal conjugate vaccine (PCV) and the Haemophilus influenzae serotype b conjugate vaccine (Hib CV). CRDM also contribute data on numbers and serogroups of Neisseria meningitidis and support diagnostic testing and outbreak response for suspected cases of meningococcal meningitis. The data allow for descriptive epidemiology of invasive disease and emergence of resistance in these three pathogens.

The Invasive Pneumococcal Disease (IPD) cumulative graphs report provides a summary of the total number of IPD cases reported to GERMS-SA to date, and if vaccine or non-vaccine serotypes of Streptococcus pneumoniae were identified. GERMS-SA is a national, active, laboratory-based surveillance system initiated in 2003 and this report is updated on a quarterly basis. 

Invasive Pneumococcal Disease (IPD) cumulative graphs report (31 July 2021)

CRDM serves as a regional reference laboratory (RRL) for the WHO Regional Office (WHO/AFRO), Immunization and Vaccine Development Cluster, which is part of the WHO/AFRO (VP-IBD) surveillance network. Cerebrospinal fluid samples are submitted from eleven countries (mostly SADC) for molecular detection and serotyping/grouping of S. pneumoniae, H. influenzae and N. meningitidis. Data are reported back to countries and WHO AFRO. Training and site assessments are also provided to improve surveillance capacity in these 11 countries.

CRDM partners with the Outbreak Response Unit (Public Health Surveillance and Response Division/NICD). They are tasked with providing technical support for all aspects of communicable disease outbreak investigation and control in the nine provinces of South Africa, with special emphasis on optimising the role of laboratory services during these events. The Unit ensures constant communication with stakeholders such as the Department of Health, medical practitioners, media and the general public.

CRDM partners with the national Notifiable Medical Conditions (NMC) surveillance system, which is tasked with providing timely, accurate data of diseases that are of public health importance. These diseases may pose significant public health risks that can result in disease outbreaks or epidemics with high case fatality rates both nationally and internationally.