Global Surveillance Equity: LMIC Capacity as Collective Security

South Africa detected and transparently reported the Omicron variant in November 2021. Their reward: travel bans from over 40 countries and over $63 million in documented tourism cancellations, despite Omicron already circulating in Europe. This creates perverse incentives where countries that invest in surveillance and report rapidly face punishment while those that delay or lack capacity face no consequences.

Learning Objectives
  • Understand why surveillance capacity in low- and middle-income countries (LMICs) is a global biosecurity priority, not just a development issue
  • Analyze how current incentive structures (travel bans, economic punishment) discourage transparent outbreak reporting
  • Evaluate the WHO Joint External Evaluation (JEE) framework and its findings on global capacity gaps
  • Describe initiatives like the Africa Pathogen Genomics Initiative and their role in building regional capacity
  • Apply equity-security frameworks to biosurveillance policy discussions

The Core Argument: Surveillance blind spots anywhere create risk everywhere. Treating LMIC capacity gaps as “their problem” is strategically wrong.

The Evidence:

Fact Implication
Omicron was detected in South Africa because they HAD sequencing capacity Many variants likely emerged in regions with NO sequencing and were never detected
In 2019, only 7 African countries could conduct basic genomic sequencing Surveillance blind spots covered most of the continent
By 2024, 46 African countries have some sequencing capacity Investment works, but gaps remain

The Perverse Incentives:

South Africa’s reward for transparent, rapid Omicron reporting: travel bans from 40+ countries and over $63 million (R1 billion) in documented cancellations according to FEDHASA/SATSA industry surveys. This creates rational incentives to delay or conceal outbreak information.

The Framework:

The WHO Pandemic Influenza Preparedness (PIP) Framework, adopted in 2011 after Indonesia’s “viral sovereignty” dispute, established benefit-sharing as a principle. But it applies only to influenza and did not prevent punitive responses to transparent COVID-19 reporting.

Bottom Line: Surveillance equity is biosecurity infrastructure. Investment in LMIC genomic capacity, data sharing agreements that do not penalize transparency, and benefit-sharing frameworks are not charity. They are collective security measures that protect everyone.

Introduction: Reframing the Problem

The standard framing treats surveillance gaps in low- and middle-income countries as a development challenge. Countries with weak health systems need capacity-building. This is true, but incomplete.

The biosecurity framing is different: surveillance blind spots anywhere create risk everywhere.

When a novel pathogen emerges in a region without sequencing capacity, it spreads undetected. By the time cases appear in countries with stronger surveillance, the pathogen has already seeded transmission chains globally. The delay between emergence and detection can be weeks or months, the difference between containable outbreak and global pandemic.

This chapter argues that LMIC surveillance capacity is not primarily a humanitarian issue. It is a collective security issue. Investment in global surveillance infrastructure protects high-income countries as much as it protects the countries receiving that investment.

The Capacity Gap: What the Data Show

WHO Joint External Evaluations

The WHO Joint External Evaluation (JEE) is a voluntary assessment tool measuring country capacity across 19 technical areas relevant to International Health Regulations (IHR) compliance.

As of 2022, over 115 JEEs have been completed, including every country in Africa. The findings reveal substantial gaps:

Common weaknesses identified:

  • Laboratory diagnostics (especially molecular and genomic capacity)
  • Trained epidemiology and bioinformatics workforce
  • Real-time surveillance data systems
  • Integration between human and animal health surveillance (One Health)
  • Sustainable financing beyond donor-dependent programs

The pattern: High-income countries score well. Low-income countries show systematic gaps, particularly in laboratory capacity, workforce, and sustainable financing.

Genomic Surveillance Capacity in Africa

The transformation of African genomic surveillance capacity illustrates both the gap and what investment can achieve.

2019 baseline: Only 7 African countries could conduct basic genomic sequencing in their public health laboratories.

2024 status: 46 African countries have some sequencing capacity, enabled by the Africa Pathogen Genomics Initiative (Africa PGI).

The Africa PGI, launched in October 2020 as a $100 million partnership, built a continental network of 13 sequencing centers of excellence. These hubs provide genomic sequencing, data analysis, and technical support to neighboring countries.

COVID-19 impact: African SARS-CoV-2 sequences in GISAID increased from approximately 5,000 in early 2020 to over 120,000 by late 2022, representing samples from 53 African Union Member States.

This work includes contributions through involvement with Africa CDC’s genomic surveillance efforts. The infrastructure that enabled Omicron detection in South Africa was built through years of deliberate investment, not accident.

The Blind Spot Problem

Regions without surveillance capacity are not regions without pathogens. They are regions where pathogens circulate undetected.

What we know: Omicron was detected in South Africa in November 2021 because South African laboratories had the capacity to identify unusual sequences, the expertise to recognize significance, and the commitment to share data immediately.

What we do not know: How many variants emerged in regions without similar capacity and spread globally without detection? Retrospective genomic analysis has found SARS-CoV-2 variants circulating weeks or months before their “official” detection, often in locations far from where they were first identified.

The absence of evidence is not evidence of absence. Surveillance blind spots mean we do not know what we do not know.

The Incentive Problem: Punishing Transparency

The Omicron Case Study

On November 25, 2021, South Africa reported a new SARS-CoV-2 variant to the World Health Organization. Within 24 hours, the European Union banned travel from seven southern African countries. The United States and other high-income countries followed.

The economic impact:

  • Documented tourism cancellations exceeded $63 million in the December-March season, according to industry association surveys
  • At peak, over 40 countries had imposed travel restrictions on South Africa

The epidemiological reality:

  • Omicron was already circulating in Europe before South African scientists identified it
  • Travel bans did not prevent Omicron spread; the variant became dominant globally within weeks
  • Similar restrictions were not applied to European countries where Omicron was subsequently detected

The message received:

South Africa’s National Assembly Speaker stated that travel bans were “essentially a punishment for world-class science and responsible global citizenship, as well as transparency and openness.”

UN Secretary-General Antonio Guterres called the travel bans “travel apartheid”, noting the inequity of countries being “condemned to a lockout when they were the ones that revealed the existence of a new variant.”

The Rational Response to Perverse Incentives

From a game theory perspective, South Africa’s experience creates rational incentives for delayed or concealed reporting:

Action Outcome for Reporting Country
Rapid, transparent reporting Travel bans, economic losses, international stigma
Delayed reporting Variant spreads before detection elsewhere; blame diffused
No sequencing capacity Cannot detect variants; no reporting obligation triggered

This incentive structure is catastrophically misaligned with collective security interests. Countries that invest in surveillance and report transparently face punishment. Countries that lack capacity or delay reporting face no consequences.

Historical Precedent: Indonesia and Viral Sovereignty

The tension between surveillance transparency and national interest is not new.

In 2007, Indonesia’s Health Minister announced that Indonesia would no longer share H5N1 avian influenza virus samples with the WHO Global Influenza Surveillance Network. The argument: Indonesia provided virus samples that were used by pharmaceutical companies in high-income countries to develop vaccines Indonesia could not afford to purchase.

This “viral sovereignty” dispute led to four years of negotiations, culminating in the WHO Pandemic Influenza Preparedness (PIP) Framework, adopted in May 2011.

PIP Framework provisions:

  • Established benefit-sharing as a principle equal to virus-sharing
  • Created Standard Material Transfer Agreements requiring vaccine manufacturers to provide pandemic supplies to WHO
  • Established annual partnership contributions for pandemic preparedness capacity-building

PIP Framework limitations:

  • Applies only to influenza viruses with pandemic potential
  • Did not establish precedent that prevented punitive travel bans for COVID-19 reporting
  • Benefit-sharing mechanisms proved inadequate during COVID-19 vaccine distribution (high-income countries secured supplies first)

Building Equitable Surveillance Infrastructure

The Africa Pathogen Genomics Initiative Model

The Africa PGI demonstrates what sustained investment can achieve:

Structure:

  • $100 million, four-year partnership launched October 2020
  • Led by African Union Commission through Africa CDC
  • Partners include Bill & Melinda Gates Foundation, US CDC, Microsoft, and others
  • 13 sequencing centers of excellence serving as regional hubs

Achievements:

  • Sequencing capacity expanded from 7 to 46 African countries
  • Over 120,000 SARS-CoV-2 sequences generated from the continent
  • Training programs for laboratory technicians and bioinformaticians
  • AGARI platform launched for continental genomic data sharing

Sustainability challenges:

  • Dependence on external funding (what happens when grants end?)
  • Workforce retention (trained bioinformaticians may seek opportunities elsewhere)
  • Equipment maintenance and reagent supply chains
  • Integration with routine public health operations beyond emergency response

Investment Priorities

If we accept that LMIC surveillance capacity is collective security infrastructure, what investments matter most?

Tier 1: Foundation (essential)

  • Sequencing equipment and laboratory infrastructure
  • Basic bioinformatics training and computational resources
  • Sample collection and transport systems
  • Data sharing platforms and GISAID accounts

Tier 2: Sustainability (critical)

  • Career pathways for trained personnel (preventing brain drain)
  • Domestic funding mechanisms beyond donor dependence
  • Integration with routine surveillance (not just emergency response)
  • Regional reference laboratory networks

Tier 3: Enabling environment (often neglected)

  • Data sharing agreements that protect contributor interests
  • Non-punitive response frameworks for transparent reporting
  • Benefit-sharing mechanisms for vaccines and therapeutics
  • Political insulation of surveillance from interference

Policy Reforms Needed

1. Non-punitive response to transparent reporting

Travel restrictions imposed as punishment for transparent reporting undermine the surveillance system. Policy alternatives:

  • Differentiated responses based on epidemiological evidence, not reporting country
  • Economic support mechanisms for countries facing outbreak-related losses
  • International agreements establishing reporting country protections

2. Benefit-sharing by default

The PIP Framework model (benefit-sharing as a condition of virus access) should extend beyond influenza:

  • Pathogen access agreements including technology transfer provisions
  • Advance purchase commitments reserving supplies for countries providing surveillance data
  • Manufacturing capacity development in regions currently dependent on imports

3. Sustainable financing

Surveillance infrastructure requires sustained funding, not just emergency surge capacity:

  • Domestic budget allocations for genomic surveillance (not just donor projects)
  • Regional pooled financing mechanisms
  • Integration with broader health system strengthening

The Equity-Security Nexus

Why This Framing Matters

Framing LMIC surveillance as charity positions it as discretionary spending, subject to political winds and donor fatigue. Framing it as collective security positions it as essential infrastructure, like military preparedness or critical infrastructure protection.

The evidence supports the security framing:

  • Novel pathogens disproportionately emerge in regions with high biodiversity and human-animal interface (many are LMICs)
  • Early detection and containment is vastly cheaper than pandemic response
  • Surveillance blind spots benefit no one, including high-income countries

Addressing Counterarguments

“Countries should fund their own surveillance.”

True in principle, but unrealistic in practice. Many LMICs face competing priorities (food security, basic healthcare, education) with limited fiscal space. Waiting for domestic capacity to develop organically means accepting decades of surveillance blind spots. The collective security interest justifies external investment.

“Aid dependency creates unsustainable systems.”

A legitimate concern. The solution is not to withhold investment but to design programs that build toward sustainability: domestic budget integration, regional cost-sharing, workforce retention strategies.

“We cannot force countries to share data.”

Correct. Data sharing must be incentivized, not mandated. Benefit-sharing frameworks, protection from punitive responses, and recognition of contributor interests create positive incentives. Coercion does not work.

Case Studies in Surveillance Equity

Success: South African Genomic Surveillance

South Africa’s detection of Beta (November 2020) and Omicron (November 2021) variants demonstrated functional surveillance infrastructure:

Enabling factors:

  • Established sequencing capacity at multiple academic and public health laboratories
  • Trained bioinformatics workforce
  • Strong scientific networks enabling rapid collaboration
  • Commitment to transparent international reporting

The cost of success:

Despite saving potentially millions of lives through early variant detection, South Africa faced economic punishment. This tension remains unresolved.

Partial Success: Sequencing Capacity Expansion in Africa

The Africa PGI dramatically expanded continental sequencing capacity (7 to 46 countries). However:

  • Capacity remains uneven (some countries have multiple sequencing centers; others have minimal capability)
  • Sustainability depends on continued external funding
  • Integration with routine surveillance beyond COVID-19 is incomplete

Ongoing Gap: Southeast Asia and Other Regions

While Africa received substantial genomic surveillance investment during COVID-19, other regions with biosecurity significance (parts of Southeast Asia, Central Asia, parts of South America) have received less attention. Surveillance blind spots persist.

The Bottom Line

A surveillance system that punishes transparency is a surveillance system that will fail. Building equitable global surveillance infrastructure requires both technical investment (sequencing capacity, bioinformatics training, data platforms) and policy reform (non-punitive response frameworks, benefit-sharing, sustainable financing).

This is not altruism. It is self-interested collective security. Every surveillance blind spot is a place where the next pandemic can emerge undetected.

Why is LMIC surveillance capacity a global biosecurity priority?

Surveillance blind spots anywhere create risk everywhere. Novel pathogens disproportionately emerge in regions with high biodiversity and human-animal interfaces, many of which are LMICs. When a pathogen emerges in a region without sequencing capacity, it spreads undetected until cases appear in countries with stronger surveillance. Early detection and containment is vastly cheaper than pandemic response.

What happened after South Africa reported the Omicron variant?

South Africa faced travel bans from over 40 countries and lost over $63 million in documented tourism cancellations during peak holiday season, despite Omicron already circulating in Europe before detection. Travel bans did not prevent Omicron spread, as the variant became dominant globally within weeks. This creates rational incentives to delay or conceal outbreak reporting.

What is the Africa Pathogen Genomics Initiative?

A $100 million, four-year partnership launched in October 2020 that expanded genomic sequencing capacity from 7 to 46 African countries. It established 13 sequencing centers of excellence serving as regional hubs, trained laboratory technicians and bioinformaticians, and generated over 120,000 SARS-CoV-2 sequences from the continent.

What is the WHO PIP Framework and why does it matter?

The Pandemic Influenza Preparedness Framework, adopted in 2011 after Indonesia’s viral sovereignty dispute, established benefit-sharing as a principle equal to virus-sharing. However, it applies only to influenza and did not prevent punitive travel bans for COVID-19 reporting, demonstrating the need for broader protections.

This chapter is part of The Biosecurity Handbook. For related content, see Outbreak Detection and Surveillance, Digital Biosurveillance, and Policy Frameworks for AI-Bio Convergence.