Q2 2026
West African Wastewater Surveillance
Country profile · Q2 2026

South Africa

Largest WES footprint of the five. NICD-led, but operating without a national policy mandate. Research-to-routine transition stalled.

At a glance · today
30–40
Active sites
35%
Population coverage
35%
Sewered coverage
$99
Cost / sample
11
Pathogens tracked
80+
5-yr target sites
Trajectory

Today vs the 5-year target

Today
Active sites
30–40
Provinces covered
9 / 9
Population coverage
35%
Cost / sample
$99
5-year target
Active sites
80+
Provinces covered
9 / 9
Population coverage
55%
Cost / sample
—

~30–40% urban sewered

Pathogens monitored

What is being tracked today

  • Poliovirus integrated
  • SARS-CoV-2 integrated
  • Mpox surveyed
  • Influenza surveyed
  • Measles researched
  • Rubella researched
  • Hepatitis A/E researched
  • Antimicrobial Resistance (AMR) researched
  • ESKAPE pathogens researched
  • Tuberculosis researched
  • HIV researched
Cost economics · per sample

What it costs to monitor

$99
cost per sample, today
Panel A · By cost type
$85 Total $99
  • Direct recurrent$85 · 86%
  • Direct capital$5 · 5%
  • Indirect$9 · 9%
Panel B · By activity
Sample collection: $5 (6%)Sample transport: $12 (13%)Sample processing: $14 (16%)Sample analysis: $56 (62%)Outreach & communication: $3 (3%)Activity$90
  • Sample collection6%$5
  • Sample transport13%$12
  • Sample processing16%$14
  • Sample analysis62%$56
  • Outreach & communication3%$3
Panel C · Cost drivers
  • Staff (high-skilled)$4442%
  • Reagents$1716%
  • Transport (private)$1413%
  • Utilities & overheads$99%
  • Consumable supplies$55%
  • Non-consumable supplies$55%
  • Staff (low-skilled)$44%
  • Lab equipment & other$44%
  • Transport (government)$22%
Capability

Strengths and challenges

Capability scorecard
  • Sewer coverage
    Moderate
  • Logistics
    Rarely
  • Testing capacity
    High
  • Use of information
    High
  • Cost & value
    High
Inside the system
Operational and institutional factors
Strengths
Infrastructure & Capacity
  • Advanced technical and laboratory ecosystems with significant existing WES capacity across public, academic, and private sectors (NICD, NHLS, SAMRC, WRC, Waterlab, multiple universities). This breadth of capacity means scale-up does not require building from scratch.
  • Waterlab provides an ISO 17025-accredited private laboratory provides speed, flexibiliy, and a logistics capacity that neither government or public labs can replicate. It is a valuable commercial partner for a scale-up.
  • More advanced than most African countries in adapting WES to non-conventional sewage intrastructure. Passive samplers have been validated as more sensitive than grab samples for low viral loads, and alternative sampling methods have been explored for non-sewered communities.
Coordination & Integration
  • The NICD's DPHSR division provides an establised institutional bridge between WES science and public health action. WES data currently has a functional pathway into decision-making through governement incident management teams that the data is shared with. The NICD also has epidemiologists in all 9 provinces that can anchor WES data within routine surviellance architecture.
  • Standardised Coordination Mechanism - SAMRC's Pandemic Fund programme is actively re-establishing coordinated national WES with standardised methodology across 6 partner laboratories. This enables comparability.
Data & Methodology
  • Integrated Public Dashboard - The NICD has developed a public-facing integrated WES and clinical surveillance dashboard that integerates environmental and clinical data for real-time transparency.
Financial Resources
  • The WRC provides catalytic seed funding to de-risk WES research before handing it to government or implementing partners. The model used, "pilot, prove, transition", has previously been used to establish multiple WES programmes and is an important pipeline for new pathogen surveillance and non-sewered community methods.
Challenges
Policy & Governance
  • No standardised national protocols exist across the multiple insitutions doing WES. This makes cross-institutional comparability of results difficult. The SAMRC stanardises within its own 6-lab network, but no agreed frameowkr beyong this network exists. Waterlab proposed the NICD lead a national proficiency testing scheme as a pragmatic first step for full ISO accreditation.
Coordination & Integration
  • WES data is not yet systematically integrated with clinical surveillance data for most pathogens. Outside of emergencies, translating WES hotspots and signals into actionable public health responses is not yet systematic.
  • Previous coordinated national WES network (SACCESS) collapsed when funding ended, demonstrating the fragility of coordination structures built around time-limited project funding. Currently, coordination remained fragmented across multiple entities, each with differing priorities, pathogens and methods.
Financial Resources
  • High operational costs - A reliance on imported reagents and high sequencing costs creates financial vulnerabilities for lab groups. Waterlab proposed a 2-step concentration/extraction then PCR approach to reduce setup costs for outlying labs.
Infrastructure & Capacity
  • Scale-up into non-sewered and rural areas is technically and logistically significantly more complex than metro-based WWTW sampling, and approx 40% of South Africans are not served by public sewage system. Cold chain and transport logistics from remote sites are a major cost and quality driver.
External environment
Political, economic and ecosystem factors
Strengths
Financial Resources
  • The Pandemic Fund is providing active multi-institutional coordination funding across the NDoH, WHO, UNICEF, FAO, NICD, and SAMRC under a 'One Health' framework. This aligns with WES' scale-up needs.
  • Established and functioning public budgeting pathway for health entities to access treasury funding, including the possibility of direct submissions from public entities like NICD/NHLS to National Treasury.
  • High International profile in disease surveillance and its role as the NICD reference lab for several African countries strengthens the case for international doner investment in WES, as benefits extend beyond national borders.
Coordination & Integration
  • A strong civil society, a private sector, and multiple academic institutions are already engaged in WES. This provides a diverse stakeholder base that can advocate for sustained investment.
Challenges
Policy & Governance
  • No formal national policy or legislation mandating WES as a routine public healh function. WES is entirely dependent on project-based funding and institution's willingness to prioritise it. Without a policy mandate, entities have no obligations to participate in, fund or share data for WES.
  • Widely perceived as a research activity rather than a core public health surveillance function. Researcher seek competitive grants rather than operational budgets.
  • Inter-governmental fragmentation is a structural barrier to scale-up. WES spans multiple uncoordinated government departments, all with different budget cycles, planning processes, and accountability structures.
Financial Resources
  • The National Treasury has maintained the formal position of no additional budget allocations. Any new domestic WES funding must come from reprioritisation within existing budgets.
  • The World Bank has not been mandated to engage with WES in South Africa, removing a likely multilateral development bank funding routes. This reduces available external funding landscape.
  • Domestic government funding for WES is entirely absent as a dedicated line item. Most funding is through international donors (Gates Foundation, US CDC) and competitive research grants. Additionally, NHLS and NDoH funding not directed towards WES.
Infrastructure & Capacity
  • Municipalities own and operate most wastewater treatment infrastructure and face severe capacity constraints. Without a regulatory directive from the Department of Water and Sanitation or the Department of Health, voluntary participation is unlikely at scale.
Financing landscape

Where the funding could come from

Domestic public
  • Domestic government expenditure
    possible

    ~R10M/yr already reprioritised. Direct Treasury submission pathway confirmed. Depends on NDoH endorsement.

Multilateral development banks
  • World Bank IDA
    unlikely

    IBRD-eligible only (not IDA). World Bank confirmed no WES mandate in SA.

  • European Investment Bank
    likely

    SA's private sector infrastructure (Waterlab) and PPP-readiness aligns well with EIB's operating model.

Global health funds
  • Pandemic Fund
    unlikely

    South Africa is already implementing WES work through a PF grant. It is probably best to make progress with this before bidding for more - budget allocated to WES = 1M

  • IPSN (WHO Pathogen Surveillance Network)
    likely

    NICD is Africa's leading pathogen genomics hub. SA already contributes to global surveillance networks. IPSN partnership would formalise WES genomic data sharing and attract co-investment.

  • The Global Fund
    unlikely

    SA income level limits eligibility for new GF grants.

Bilateral & philanthropic
  • Gates Foundation
    likely

    Gates funding NICD/SAMRC WES work. Strong existing relationship. Continued engagement likely.

  • Rotary Foundation
    possible

    Possible for polio-linked WES. Less compelling given SA non-endemic status.

  • Bilateral GHS donors
    unlikely

    SA upper-middle income limits bilateral GHS access. PEPFAR withdrawal reduces this further.

Strategic pathway

What to do next

Phase 1 · 0–2 years
Immediate
Phase 2 · 2–4 years
Medium term
Phase 3 · 4–6 years
Long term
Immediate · 0–2 years
  1. Submit a formal WES investment brief to National Treasury — outside the normal budget cycle, framed around value for money and averted healthcare costs. Target the July 2026 MTEF guidelines window.
    Cost: low Timeline: immediate
  2. Re-establish the SACCESS-successor national coordination network under SAMRC/Pandemic Fund leadership — formalise with a steering committee, pathogen prioritisation framework, and quarterly meetings.
    Cost: medium Timeline: immediate
  3. Establish a national proficiency testing scheme for WES methods — propose NICD as the accreditation body; implement a round-robin scheme across the 6 SAMRC partner labs as a first step.
    Cost: medium Timeline: immediate
  4. Engage SALGA to formalise municipal access agreements for WWTW sites — draft a standard MOU template usable by all 8 metro municipalities.
    Cost: medium Timeline: immediate
Medium term · 2–4 years
  1. Develop and submit formal national WES policy/legislation to NDoH — framing WES as 'public health infrastructure', not research, to unlock operational budget classification.
    Cost: high Timeline: medium
  2. Integrate Mpox, Influenza, and Measles into the NICD national WES programme — moving these from the 'surveyed' tier to formally integrated, with dedicated budget lines.
    Cost: high Timeline: medium
  3. Submit value-for-money evidence to National Treasury before the July 2027 MTEF window — including cost per outbreak prevented and comparison with clinical surveillance costs.
    Cost: medium Timeline: short
  4. Expand SAMRC lab network from 6 to 12 partner universities — targeting previously disadvantaged institutions in Eastern Cape, KZN, and Limpopo.
    Cost: high Timeline: medium
Long term · 4–6 years
  1. Achieve national WES policy enactment — establish a legal mandate requiring municipalities above 500k population to participate in WES with data shared to the NICD.
    Cost: high Timeline: long
  2. Scale to 80+ sites covering all 9 provinces including non-sewered communities (pit latrines, river run-off, tanker effluent) — using alternative sampling methods validated by SAMRC.
    Cost: high Timeline: long
  3. Transition AMR/ESKAPE WES to routine surveillance integrated with GEMS-SA — creating a nationally representative antimicrobial resistance environmental monitoring system.
    Cost: high Timeline: long
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