Q2 2026
West African Wastewater Surveillance
Country profile · Q2 2026

Mozambique

Polio-led WES at INS Maputo with growing multi-pathogen pilot. Sewerage coverage and decentralisation are the key constraints.

At a glance · today
9–10
Active sites
3%
Population coverage
3%
Sewered coverage
$110
Cost / sample
6
Pathogens tracked
56+
5-yr target sites
Trajectory

Today vs the 5-year target

Today
Active sites
9–10
Provinces covered
4 / 11
Population coverage
3%
Cost / sample
$110
5-year target
Active sites
56+
Provinces covered
11 / 11
Population coverage
20%
Cost / sample
—

~3% nationally; ~10% Maputo

Pathogens monitored

What is being tracked today

  • Poliovirus integrated
  • Cholera surveyed
  • SARS-CoV-2 surveyed
  • Influenza surveyed
  • Salmonella Typhi surveyed
  • Mpox researched
Cost economics · per sample

What it costs to monitor

$110
cost per sample, today
Panel A · By cost type
$90 Total $110
  • Direct recurrent$90 · 82%
  • Direct capital$10 · 9%
  • Indirect$10 · 9%
Panel B · By activity
Sample collection: $17 (17%)Sample processing: $29 (29%)Sample analysis: $46 (46%)Outreach & communication: $8 (8%)Activity$100
  • Sample collection17%$17
  • Sample processing29%$29
  • Sample analysis46%$46
  • Outreach & communication8%$8
Panel C · Cost drivers
  • Staff (high-skilled)$3331%
  • Reagents$3331%
  • Consumable supplies$1817%
  • Utilities & overheads$109%
  • Lab equipment & other$76%
  • Transport (government)$66%
  • Staff (low-skilled)$11%
Capability

Strengths and challenges

Capability scorecard
  • Sewer coverage
    High
  • Logistics
    High
  • Testing capacity
    Moderate
  • Use of information
    Moderate
  • Cost & value
    Moderate
Inside the system
Operational and institutional factors
Strengths
Infrastructure & Capacity
  • INS has a dedicated, experienced WES team with hands-on implementation knowledge, rapid mobilisation capacity and multi-pathogen experience.
  • INS has a strong genomic sequencing capacity at national level, making it one of the better-equipped institutions in the region for pathogen characterisation from wastwater data.
  • Established and functional network of regional and provincial public health laboratories, providing a platform for future decentralised WES testing.
  • INS has negotiated deal with the national airline (LAM) to transport WES samples and supplies free of charge, reducing one of the most significant operational costs.
Coordination & Integration
  • IDS-MOSS integrated disease surveillance framework, developed by INS and endorsed by the Gates Foundation, positions Mozambique as a model for integrated WES surveillance.
  • Cross-border strong technical partnership with NICD (South Africa) for polio testing and quality assurance that allows Mozambique to operate a functional polio WES programme wihout domestic accreditation but ensuring quality anchor.
Policy & Governance
  • Actively working towards domestic polio testing accreditation, which would reduce turnaround time and transport costs.
Challenges
Infrastructure & Capacity
  • No dedicated WES staff, resulting in quality and consistency gaps as the same personnel completing the field work are also handling laboratory processing. Passive sampler traps have strict 24-hour placing and collection windows.
  • Sample transport from central and northern provinces to the INS lab in Maputo is logistically difficult and risks compromising sample quality. Unable to locally test samples yet in these provinces.
Data & Methodology
  • Methods for collection, concentration, storage, and PCR are not standardised across pathogesns (polio, cholera, SARS-CoV-2, and typhoid).
  • Wastewater data handling remains largely manual (procesed by LNHAA) without a laboratory information management system, with results being communicated informally to the NDPH rather than through a structured digital reporting system.
Coordination & Integration
  • WES data not yet intergrated into Ministry of Health (MoH) decision-making, aside from polio. No routine reporting of wastewater data to the MoH exists, and there is no formal feedback loop between surveillance results and public health response for non-polio pathogens.
  • Institutional fragmentation between INS and the Faculty of Medicine, which currently hosts the polio WES, creates barriers to scale-up. WHO-AFRO has been a blockage to providing training and reagents directly to INS for polio testing
Policy & Governance
  • No national WES strategy exists outside of polio.
External environment
Political, economic and ecosystem factors
Strengths
Policy & Governance
  • Growing post-COVID-19 interest and awareness among partners and government stakeholders in the use of wastewater as an early-warning tool.
  • Mozambique's high burden of epidemic-prone diseases makes the WES value proposition attractive to donors. The country sufers fron annual polio outbreaks, recurent polio risks, and Mpox, making it a natural candidate for sustained international WES investment.
Financial Resources
  • Active donor landscape. Gates Foundation, Global Fund, WHO, GAVI, and Belgian Development Agency, are all either funding or have shown interest in WES expansion.
Coordination & Integration
  • Intersectoral coordination committee already exists that brings together health, water, and public works stakeholders. This provides a platform for aligning WES with WASH priorities.
Challenges
Infrastructure & Capacity
  • Very low sewage network coverage limits WES representativeness. Only ~10% of Maputo city's population is connected to the sewage system. This restricts the population that can be reached through conventional WES methods.
Policy & Governance
  • WES is not a priority within the MoH and domestic government funding is minimal and does not fund operational WES activities. Not seen as a health system priority, just as a research activity.
Financial Resources
  • High cost of reagents and complex costly customs clearance for laboratory inputs. This has previously prevented INS from testing in some provinces.
  • Limited access to and exchange rate volatility of foreign currency nake it difficult to plan and execute purchases of imported laboratory supplies. This makes reagent procurement unpredictable and can lead to disruptions to programme continuity.
  • Weak budget execution - Government institutions (such as LNHAA) often struggle to effectively spend and manage awarded donor funds.
  • US government funding disruptions and cuts (PEPFAR/USAID) have affected the broader health system's capacity to support WES by reducing bandwidth for non-emergency surveillance activities.
Financing landscape

Where the funding could come from

Domestic public
  • Domestic government expenditure
    unlikely

    Staff salaries only. LNHAA budget execution very low.

Multilateral development banks
  • World Bank IDA
    possible

    $201M Health Emergency Preparedness (2025–30). WES component possible at mid-term review.

  • European Investment Bank
    possible

    Possible if framed around supply chain or local commodity production.

Global health funds
  • Pandemic Fund
    possible

    Eligible for single or multi-country grants. Strong alignment with INS integrated surveillance agenda.

  • IPSN (WHO Pathogen Surveillance Network)
    possible

    INS has sequencing platforms. IPSN could support integration of WES genomic data into the global network, strengthening Mozambique's surveillance architecture.

  • The Global Fund
    possible

    Historic relationship (Project Stellar 2022–23). Inclusion in PES is the key precondition.

Bilateral & philanthropic
  • Gates Foundation
    likely

    Currently funding $4M IDS-MOSS (2025–2027). Continued engagement likely if proof-of-concept delivers.

  • Rotary Foundation
    possible

    Long-term surveillance post-eradication is a compelling framing for Rotary.

  • Bilateral GHS donors
    possible

    Belgian Development Agency already expressing interest in WES and air surveillance in Mozambique.

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. Formalise a national WES strategy document — a prerequisite for Global Fund eligibility and for WES inclusion in PES (national health strategic plan).
    Cost: low Timeline: immediate
  2. Achieve domestic polio testing accreditation at INS Maputo — reduce dependence on NICD South Africa for confirmation, cutting turnaround from weeks to days.
    Cost: medium Timeline: immediate
  3. Establish dedicated WES field staff — separate collection team from laboratory staff to address the dual-role bottleneck and ensure 24-hour passive sampler windows.
    Cost: medium Timeline: immediate
  4. Formally integrate cholera WES data into MoH surveillance reporting — establish a data-to-action pathway linking WES results to outbreak response decisions.
    Cost: low Timeline: immediate
Medium term · 2–4 years
  1. Decentralise concentration and PCR capacity to Sofala (Beira) and Nampula provincial labs — eliminating costly air freight of samples to Maputo.
    Cost: high Timeline: medium
  2. Add Influenza A&B and Rubella to the INS WES programme across all 38 current sites — leveraging existing infrastructure for incremental pathogen expansion.
    Cost: medium Timeline: short
  3. Submit WES to Global Fund as a component of the next national health grant — requires PES inclusion as the enabling precondition.
    Cost: high Timeline: short
  4. Formalise the Intersectoral Working Committee (MoH, Public Works, municipalities) as the standing WES governance body with a formal secretariat at INS.
    Cost: medium Timeline: short
Long term · 4–6 years
  1. Expand to 56 sites (+2 per province) including peri-urban and WASH-priority communities — using adapted pit-latrine and tanker-effluent sampling where sewage is absent.
    Cost: high Timeline: long
  2. Secure stable foreign currency access for reagent procurement via MoF agreement — classify WES reagents as essential health commodities under existing FX frameworks.
    Cost: medium Timeline: long
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