The 2026 influenza season ended in week 39 (week ending 27 September 2026). In South Africa, the influenza season typically begins around mid-to-late April and ends around late August to mid-September. The 2026 season began in week 11 (week starting 9 March 2026), when the influenza detection rate among patients enrolled in inpatient pneumonia surveillance at public hospitals exceeded the seasonal threshold and remained above it for two consecutive weeks. This was earlier than most previous seasons but similar to 2025, when the season started in week 13 (week starting 24 March 2025). Influenza activity subsequently increased and peaked in week 20 (week starting 11 May 2026). The detection rate subsequently dropped below the seasonal threshold from week 40 (week starting 28 September 2026) and remained below the threshold for two consecutive weeks.
From 29 December 2025 to 11 October 2026 across the three sentinel surveillance systems (outpatient influenza-like-illness (ILI) surveillance at public primary health care clinics, outpatient ILI surveillance at private general practitioner practices, and inpatient pneumonia surveillance at public hospitals), influenza was detected in 1029 of 6212 specimens tested (16.6%) . Among the cases for which a subtype could be determined (97.1%; 999/1029), 44.0% (453/1029) were influenza A(H3N2), 32.6% (335/1029) were influenza A(H1N1)pdm09 and 20.5% (211/1029) were influenza B (211/1029; 20.5%). Additionally, seven dual infections were detected: one case of A(H1N1) and A(H3N2), one case of A(H3N2) and influenza B, two cases of A(H1N1) and influenza B, and three cases of an inconclusive influenza A subtype and influenza B. Before routine lineage subtyping of influenza B was discontinued in June 2026, 100% (111/111) of tested influenza B samples were B/Victoria.
Message to clinicians
Influenza is an acute respiratory infection caused by influenza viruses. It spreads easily between people through respiratory droplets and causes seasonal epidemics. Most people recover without treatment, but influenza can cause severe illness or death, especially in people at high risk of severe influenza illness or complications.
Although the 2026 influenza season has ended, sporadic influenza infections may continue to occur outside the defined seasonal period. Clinicians should therefore continue to consider influenza in the differential diagnosis of patients presenting with respiratory illness and in patients with highly suggestive symptoms. High-risk groups include pregnant women, individuals living with HIV, those with chronic conditions such as diabetes, lung disease, tuberculosis, heart disease, renal disease, and obesity, older individuals (≥65 years), and children under two years old.
Where to find updated data
Weekly reports documenting respiratory pathogen circulation in South Africa, including influenza, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Bordetella pertussis, human adenovirus, human metapneumovirus, human parainfluenza virus and human rhinovirus, are available on the NICD website here.
