Epidemiology of Respiratory Pathogens
This summary presents the key findings from the 2023 national respiratory virus surveillance report produced by the Centre for Respiratory Diseases and Meningitis at the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS). Drawing on three national syndromic surveillance programmes across South Africa’s public and private healthcare sectors, it highlights trends in major respiratory pathogens and their implications for public health monitoring and response.
The content in this summary is intended as an overview and does not replace the original report. The Medical Education Network encourages readers to review the full report before forming clinical opinions or making decisions. While every effort has been made to represent the findings accurately, any errors are unintentional, and the Medical Education Network cannot be held liable for inaccuracies or omissions.
The report draws on data from three national syndromic surveillance programmes operating concurrently across South Africa’s public and private healthcare sectors during 2023. The surveillance systems and participating sites included are outlined below.
| Programme | Scope & Setting | Coverage | Active Since |
|---|---|---|---|
| PSP Pneumonia Surveillance Programme |
Hospital-based inpatients with severe respiratory illness. Tests influenza, RSV, pertussis and SARS-CoV-2. | 14 hospitals across 6 provinces: Gauteng, North West, KZN, Eastern Cape, Western Cape, Mpumalanga | 2009 |
| ILI-PHC Primary Health Clinic Surveillance |
Outpatient public sector ILI and suspected pertussis. Tests all four pathogens. | 5 clinics across 4 provinces: KZN, North West, Mpumalanga, Western Cape | 2012 |
| ILI-VW Viral Watch |
Private general practitioner network. Tests influenza, RSV and SARS-CoV-2. | 8 provinces: EC, Free State, Limpopo, Mpumalanga, Northern Cape, Gauteng, North West, Western Cape | 1984 |
Understanding the timing of each pathogen is as clinically valuable as knowing the burden. This timeline maps 2023 activity across all 12 months, enabling proactive preparation rather than reactive response.
Peak: early June
Peak: late March. Year-round low.
Heaviest in first half of year.
No seasonal pattern.
Influenza — Full Return to Pre-Pandemic Pattern
The 2023 season confirmed that South African influenza patterns have fully returned to pre-pandemic norms for the second consecutive year. After profound disruption during 2020–2021 — when non-pharmaceutical interventions suppressed global circulation — the bi-phasic seasonal pattern re-established itself.
- Season ran from Week 17 (27 April) to Week 27 (10 July) — 11 weeks total
- Dominant subtype: Influenza A(H3N2) — 90.3% of PSP positives, 82.0% of Viral Watch positives
- Community transmission reached HIGH levels (ILI-PHC). Healthcare system impact: MODERATE (PSP)
- Detection in children under 15 at PHC: 16.7%. Adults 15+ at PHC: 9.9%. Private practice (Viral Watch): 26.7%
- In-hospital adult mortality across all severe respiratory admissions: 10.3% in adults aged 15 and older
- Influenza B/Victoria was detected mainly at the tail end of the season (5.4% of PSP positives)
Why was A(H3N2) so dominant? This was the first post-pandemic year in which H3N2 predominated. A residual population immunity gap — the result of suppressed natural infection and disrupted vaccination during 2020–2022 — likely amplified transmission. The same pattern was documented in Europe, Australia, and New Zealand. This immunity debt effect may persist into 2025–2026 in under-vaccinated populations, making pre-season vaccination more important than ever.
The season starts in late April. Vaccinate risk groups in March at the latest. Do not wait for the first positive result. A(H3N2) disproportionately affects older adults and those with comorbidities.
RSV — The Defining Paediatric Pathogen
RSV is the most significant respiratory pathogen for young children in South Africa. The 2023 data are unambiguous: RSV was the leading cause of hospitalisation in children under five, with detection rates that dwarf all other pathogens in this age group.
- Season: Week 6 (6 February) to Week 21 (22 May) — preceded the influenza season by approximately 10 weeks
- Detection in hospitalised children under 5: 21.7% — the highest of any pathogen in any paediatric group
- Detection in infants under 2 months (hospital): 41.2% — this single figure represents the most acute vulnerability in the data set
- 61% of all paediatric RSV cases occurred in infants under 12 months of age
- RSV subgroup A predominated: 74.1% of positive hospital samples
- ICU admission for RSV-positive children: 1.6%. In-hospital paediatric mortality: 0.5%
- Year-round low-level detection confirmed across all three surveillance programmes
The intervention imperative: Both maternal RSV vaccination and the long-acting monoclonal antibody nirsevimab are now approved and available. WHO and CDC data consistently demonstrate 50–80% reduction in infant hospitalisations in the first 3–6 months of life. Given a 41.2% detection rate in the most vulnerable infants, the argument for inclusion in South Africa's national immunisation programme is overwhelming. Every antenatal consult is an opportunity that cannot be missed.
RSV season starts in early February. Young infants presenting with poor feeding, apnoea, or subtle tachypnoea should trigger early assessment — classic cough and wheeze are often absent in the youngest patients.
Bordetella Pertussis — A Neonatal Emergency
Pertussis is resurgent in South Africa and the age distribution is deeply concerning. This is not a childhood illness in the classical sense — it is a neonatal emergency occurring in infants who have not yet completed their primary immunisation series.
- Total 2023 cases across PSP and ILI-PHC: 210 (detection rate: 2.3%). Year-round circulation confirmed
- Peak months: January, March and May — concentrated in the first half of the year
- 69.6% of all paediatric pertussis cases occurred in infants aged 0–2 months
- In-hospital mortality for pertussis in children under 15: 3.5% — the highest case fatality of any pathogen in the paediatric group
- ICU admission rate: 3.1% in children with pertussis
- Provincial concentration: Gauteng (37.5%), Mpumalanga (15.9%), North West (15.9%)
- Context: Sharp national resurgence began in 2022, particularly in the Western Cape (42% of cases). 2023 confirmed nationwide sustained circulation
The Tdap opportunity: Maternal Tdap vaccination at 27–36 weeks of gestation transfers passive immunity to the neonate at the most critical window. South Africa included this in its national immunisation schedule in 2024. Uptake in antenatal settings is the critical implementation gap. For infants presenting with apnoea, paroxysmal cough, or poor feeding in the first two months, consider pertussis regardless of maternal vaccination history.
Year-round, peaking Jan–May. In infants under 3 months, apnoea alone qualifies as a case definition. Do not wait for the classic whoop. Hospitalise early.
SARS-CoV-2 — Endemic Phase Confirmed
SARS-CoV-2 circulated at consistently low, non-seasonal levels throughout 2023 — a pattern now documented across multiple international surveillance systems, including the United Kingdom, United States, and Australia. South Africa's data align with the global picture of viral endemicity.
- Overall detection rate: 4.7% across all three surveillance programmes (513/10,817 tests)
- No seasonality observed. Detections remained sporadic throughout the year
- Omicron was the only variant detected (99.7% of sequenced samples)
- XBB.1.5 (clade 23A) dominated the first half of 2023; BA.2.86 (clade 23I) rose in the second half
- Higher detection in private Viral Watch cohort (10.1%) vs public PHC (4.3%) and hospital (3.7%) — likely reflecting testing behaviour rather than true burden differences
- Suspected COVID-19 was removed from ILI and SRI case definitions from 1 November 2023, reflecting the transition to endemic management
Clinical recalibration: COVID-19 is no longer driving major respiratory illness surges. The appropriate clinical response is integration — SARS-CoV-2 should be included in standard respiratory differential workups alongside influenza, RSV and pertussis. Genomic surveillance must continue to detect variant evolution early, but emergency-era acute protocols are no longer warranted by the current data.
De-escalate separate COVID pathways. Integrate into standard respiratory workup. Continue monitoring NICD weekly reports for variant signals — XBB.1.5 → BA.2.86 transition happened within a single calendar year.
The surveillance data identify four distinct groups where respiratory disease outcomes are disproportionately severe. Clinical and vaccine counselling should be prioritised accordingly at every contact.
Infants under 6 months
RSV detection reaches 41.2% in infants under 2 months. Pertussis case fatality in children under 15 is 3.5%, with 69.6% of those cases in neonates too young for vaccination. Maternal vaccination is the only protective pathway available for this group before birth.
HIV-positive adults aged 25–44
64.2% HIV prevalence in the hospitalised respiratory cohort. In-hospital adult mortality reaches 10.3%. HIV co-infection amplifies severity across influenza, RSV and SARS-CoV-2. Respiratory vaccine counselling must become routine at every HIV care visit — not an optional extra.
Pregnant women
Dual vulnerability: increased influenza severity in pregnancy, plus the sole opportunity for passive neonatal protection. A single antenatal consultation is the opportunity to administer both RSV vaccine and Tdap — protecting mother and infant simultaneously before the season begins.
Adults ≥65 with chronic disease
Influenza detection reached 25.7% in adults 65 and older. Comorbidities including diabetes, chronic lung disease, heart disease, renal disease and obesity all compound severity. Annual influenza vaccination, timed before April, is the primary intervention for this group.
Direct practice and referral guidance derived from the 2023 surveillance data. Six actions, in order of impact.
Clinical Action Summary
For practice · referral · counselling
The 2023 data provide a stable post-pandemic epidemiological baseline. Four structural implications stand out for health system planning and clinical service delivery heading into 2026.
Seasonal respiratory burden is now predictable again
With influenza and RSV both returning to pre-pandemic seasonal patterns for two consecutive years, the uncertainty of 2020–2022 is resolved. Planning horizons can now be re-established: stock influenza vaccines for pre-April administration, prepare paediatric RSV admission capacity from February, and maintain pertussis surveillance year-round. The compressed February–July respiratory season should drive annual resource allocation decisions at facility and district level.
A window of vaccine opportunity is opening — and it is time-limited
Three newly available or newly scaled interventions — maternal RSV vaccination, nirsevimab (long-acting monoclonal antibody), and Tdap in pregnancy — represent the most significant development in paediatric respiratory prevention in a generation. The 2023 burden data make the clinical case overwhelming. The implementation challenge is reaching pregnant women in the public sector before their third trimester. Health systems that solve this problem by 2026 will see measurable reductions in neonatal and infant ICU admissions.
HIV and respiratory disease are structurally inseparable in the South African context
The 64.2% HIV prevalence in the hospitalised 25–44 respiratory cohort is not a surveillance artefact — it reflects the structural reality of South African public health. Any respiratory disease prevention strategy that does not explicitly integrate PLHIV management will fail to reach the highest-risk population. This has direct implications for where vaccination campaigns are conducted, which healthcare workers receive training, and how respiratory disease is prioritised within HIV care pathways.
SARS-CoV-2 surveillance must evolve, not disappear
The shift to endemic COVID-19 does not mean zero risk. Variant evolution — evidenced by the XBB.1.5 to BA.2.86 transition within 2023 alone — means genomic surveillance must continue at sufficient scale to provide early warning. The 2026 challenge is calibrating surveillance intensity appropriately: enough to detect a new variant of concern early, without maintaining emergency-era resource commitments that divert capacity from influenza and RSV programmes that now carry the primary respiratory burden.
- Vaccinate all influenza risk groups prior to the start of the season (before end of April). High-risk groups include PLHIV, pregnant women and those in the 6-week postpartum period, individuals with chronic conditions, adults 65 and older, and healthcare workers.
- Implement RSV prevention strategies for infants — including maternal immunisation and a single dose of long-acting monoclonal antibodies — as part of the standard of care for pregnant women.
- Vaccinate pregnant women with Tdap during the second or third trimester (27–36 weeks) to provide passive immunity to newborns who are at the highest risk of severe pertussis disease.
- Continue and expand syndromic respiratory surveillance to monitor disease trends, circulating strains, intervention effectiveness, and outbreak identification in real time.
- Maintain non-pharmaceutical interventions (masking, hand hygiene, staying home when symptomatic) during periods of high respiratory virus circulation, especially when in contact with vulnerable individuals.
