Gain-of-Function Research: Science, Risk, and Governance
In 2012, two research groups demonstrated that just five mutations could make H5N1 avian influenza airborne-transmissible between mammals. The same virus that kills 50-60% of human cases but rarely spreads person-to-person could become a respiratory pathogen. The studies sparked immediate controversy. Critics called it a recipe for a pandemic. Defenders argued the knowledge was essential for surveillance and vaccine development. More than a decade later, the scientific community remains divided on whether we can safely create pandemic threats to prevent them.
- Understand what gain-of-function (GOF) research is and why it’s controversial
- Evaluate the H5N1 ferret transmissibility studies that sparked the 2012 debate
- Analyze the 2014-2017 U.S. moratorium and the P3CO framework
- Assess the scientific benefits versus biosecurity risks of GOF research
- Identify alternatives to GOF research (field surveillance, reverse genetics, computational modeling)
- Recognize the ethical and policy challenges in regulating dual-use research
This chapter discusses biosecurity risks at a conceptual level appropriate for education and policy analysis. Consistent with responsible information practices:
- Omitted: Actionable protocols, specific synthesis routes, exact pathogen sequences
- Included: Risk frameworks, governance mechanisms, policy recommendations
For detailed biosafety protocols, consult your Institutional Biosafety Committee and relevant regulatory guidance.
Introduction
Gain-of-function research represents biosecurity’s most contentious debate. The scientific question is straightforward: if we understand what mutations make a virus pandemic-capable, can we better prepare for natural emergence? The biosecurity question is equally clear: if we create those mutations in a lab, have we just handed malicious actors a blueprint?
This debate has evolved since the 2011 H5N1 ferret studies. Respected colleagues stand on opposite sides. Some argue GOF provides irreplaceable insights into pandemic threats. Others contend the risks are catastrophic and the benefits overstated. Both sides cite science, ethics, and public health. Neither is obviously wrong.
This chapter covers what GOF research actually is, the H5N1 controversy that brought it to public attention, the regulatory responses (2014 moratorium, P3CO framework, 2024 policy), the scientific case for and against GOF, and alternatives that might provide similar knowledge with lower risk.
Full disclosure: the analysis leans toward skepticism about high-risk GOF research, but both sides are presented fairly. The goal is to equip readers to evaluate the arguments themselves.
Gain-of-Function Research Defined
Definition
Gain-of-function (GOF) research involves genetically altering organisms to give their gene products new or enhanced capabilities. In the biosecurity context, GOF specifically refers to experiments that enhance a pathogen’s:
- Transmissibility: Making it spread more easily (e.g., airborne transmission)
- Virulence: Increasing disease severity or lethality
- Host range: Enabling infection of new species (e.g., making avian virus infect mammals)
Not all GOF research is controversial. Enhancing antibiotic resistance in E. coli to study resistance mechanisms doesn’t raise biosecurity alarm. The concern focuses on potential pandemic pathogens (PPPs), organisms that could cause widespread, uncontrollable human disease.
Technical Approaches
GOF experiments use standard molecular biology techniques:
Serial passage: Growing virus repeatedly in target host (e.g., ferrets). Each passage selects for variants better adapted to that host. After enough passages, virus gains new capabilities.
Reverse genetics: Directly introducing specific mutations into viral genome to test their effects. Allows precise control over which changes are made.
Reassortment: Combining gene segments from different viruses (for segmented viruses like influenza). Can create hybrids with enhanced properties.
Directed evolution: Systematically testing many variants to find ones with desired traits (enhanced binding, increased replication).
These are legitimate research tools. The question is whether applying them to create enhanced pandemic threats is justified.
The H5N1 Controversy: Spark That Ignited the Debate
Background: H5N1 Avian Influenza
H5N1 highly pathogenic avian influenza emerged in 1996. Key characteristics:
- In birds: Spreads efficiently, devastates poultry flocks
- In humans: Case fatality rate of 50-60% (WHO) in confirmed cases (one of highest for any infectious disease)
- Transmission barrier: Rare human infections, almost always from direct bird contact. Limited human-to-human spread
The nightmare scenario: What if H5N1 evolved to spread efficiently between humans while maintaining its high lethality? You’d have a disease more transmissible than seasonal flu with lethality rivaling Ebola.
The Fouchier and Kawaoka Studies (2012)
In late 2011, two independent research groups announced they’d made H5N1 transmissible between mammals via respiratory route.
Fouchier et al. (Erasmus Medical Center): Published in Science, June 2012. Ron Fouchier’s team took an H5N1 virus from Indonesia and serially passaged it through ferrets. After 10 passages, the virus gained airborne transmissibility. Genetic analysis showed just 5 mutations: - 4 amino acid changes in hemagglutinin (HA) protein - 1 change in polymerase basic 2 (PB2) protein
Note: For detailed coverage of the publication controversy and NSABB review process, see Dual-Use Research of Concern.
Ferrets infected via aerosol showed illness but didn’t die. The modified virus was transmissible but had reduced lethality compared to parent strain.
Kawaoka et al. (University of Wisconsin / University of Tokyo): Published in Nature, May 2012. Yoshihiro Kawaoka’s group used reverse genetics to introduce specific HA mutations into H5N1, then combined these with genes from 2009 H1N1 pandemic virus (reassortment). The hybrid virus transmitted between ferrets via respiratory droplets.
Both studies used ferrets because they’re the standard animal model for human influenza. Transmissibility in ferrets strongly predicts human transmissibility.
Critics argued these studies created a step-by-step manual for making a pandemic virus. The identified mutations could theoretically be introduced into circulating H5N1 strains by someone with moderate molecular biology skills and access to a BSL-3 lab. Defenders countered that the information was critical for surveillance (monitoring natural H5N1 for these mutations) and vaccine development. This tension between open science benefiting public health and information security preventing misuse has no clean resolution.
The Publication Controversy
Before publication, both manuscripts went to the U.S. National Science Advisory Board for Biosecurity (NSABB) for review. NSABB initially recommended redacting key experimental details: publish the findings, but not the methods.
Outcry from scientific community: redaction would undermine peer review, reproducibility, and scientific progress. After further review and researchers providing additional context, NSABB reversed its recommendation. Both papers published in full.
The voluntary 60-day moratorium in early 2012 by 39 influenza researchers (including Fouchier and Kawaoka) demonstrated scientific community’s awareness of the controversy. Moratorium letter stated they would pause research to allow time for discussion of benefits and risks.
The 2014-2017 U.S. Funding Pause
Trigger: Biosafety Incidents
In October 2014, the U.S. government implemented a funding pause (HHS announcement) on new GOF research involving influenza, MERS, and SARS viruses.
Immediate triggers were biosafety lapses at federal facilities: - CDC anthrax exposure incident (June 2014) - Discovery of forgotten smallpox vials at NIH (July 2014) - CDC cross-contamination of H5N1 samples (July 2014)
These incidents raised concerns: if federal BSL-3/BSL-4 labs had safety problems, were we confident about oversight of enhanced pathogen research across all institutions?
Scope of the Pause
The moratorium targeted research “reasonably anticipated to”: - Enhance pathogenicity or transmissibility of influenza, MERS, or SARS viruses - Make these viruses transmissible via respiratory route in mammals
Key limitation: applied only to new federally funded research. Ongoing projects could continue. Non-federally-funded research wasn’t covered.
The pause aimed to provide time for: - Risk-benefit analysis of GOF research - Development of comprehensive federal policy - Assessment of adequate oversight mechanisms
The Three-Year Wait
From October 2014 to December 2017, no new federal funding for covered GOF research. Scientists conducting this work either: - Pivoted to non-GOF projects - Found non-federal funding - Waited for policy resolution
Critics argued the pause was too long and stifled important research. Defenders said three years was necessary for thorough deliberation on managing catastrophic risks.
The P3CO Framework (2017-2025)
HHS P3CO: Enhanced Potential Pandemic Pathogens
In December 2017, HHS released the Framework for Guiding Funding Decisions about Proposed Research Involving Enhanced Potential Pandemic Pathogens (P3CO = Potential Pandemic Pathogen Care and Oversight).
Enhanced PPP (ePPP) definition: A pathogen that has been enhanced to be: 1. Highly transmissible: Likely highly transmissible and capable of wide, uncontrollable spread in human populations 2. Highly virulent: Likely to cause significant morbidity and/or mortality in humans
If proposed research is “reasonably anticipated” to create, transfer, or use an ePPP, it triggers P3CO review before funding.
Review Process
P3CO established multi-level review:
Institutional level: - Institutional biosafety committees (IBCs) review protocols - Assess biosafety and biosecurity measures - Determine if research meets ePPP criteria
Federal level: - HHS conducts department-level multidisciplinary review - Scientific merit assessment - Public health benefit evaluation - Biosafety and biosecurity risk assessment - Mitigation strategy review - Final funding decision by HHS
Criteria for approval: Research must demonstrate: - Significant scientific and public health benefits - Risks can be adequately mitigated - No reasonable alternatives exist that pose less risk
Limitations of P3CO
Opacity: Critics noted the review process lacked transparency. Which projects were reviewed? Which approved or denied? Minimal public reporting.
HHS-only: Only HHS developed GOF review process. Other agencies funding life sciences research (DOD, DHS, USDA) had no equivalent framework.
Voluntary for non-federal: Private or foreign-funded research not covered.
Narrow scope: Focused on specific pathogens (influenza, MERS, SARS coronaviruses). What about other potential pandemic pathogens?
The 2024 Policy: Superseding P3CO
In May 2024, a new U.S. government policy for oversight of Dual Use Research of Concern and Pathogens with Enhanced Pandemic Potential was released by the White House Office of Science and Technology Policy.
This policy aimed to address P3CO limitations by: - Broadening scope beyond original three pathogen families - Expanding to all federally funded research (multi-agency) - Increasing transparency in review process - Clarifying Enhanced PPP (now called PEPP) definitions
May 2025 update: Executive Order 14292, “Improving the Safety and Security of Biological Research,” paused implementation of the 2024 policy just before its scheduled May 6, 2025 effective date. The EO defines “dangerous gain-of-function research” as “scientific research on an infectious agent or toxin with the potential to cause disease by enhancing its pathogenicity or increasing its transmissibility.” OSTP and National Security Advisor directed to develop new policy within 120 days. In interim, previous DURC policies and HHS P3CO Framework remain in effect.
The Scientific Case FOR Gain-of-Function Research
Argument 1: Anticipating Natural Evolution
Proponents argue GOF research identifies mutations that could arise naturally, allowing preemptive action.
Example: The H5N1 ferret studies showed specific HA mutations enable mammalian transmission. Surveillance programs can now monitor wild bird populations for these exact mutations (NIH statement). If they appear, triggers immediate response (culling, vaccine development, travel restrictions).
Without GOF research, we’d only discover dangerous combinations after human pandemic begins.
Argument 2: Vaccine and Therapeutic Development
Understanding mechanisms of virulence and transmission accelerates countermeasure development.
Vaccine targets: GOF studies identify which viral proteins are critical for pandemic potential. Target vaccines at those proteins.
Animal models: Enhanced viruses that can infect standard lab animals (mice, ferrets) enable testing vaccines and drugs that otherwise couldn’t be evaluated (since natural virus doesn’t infect these species efficiently).
Historical precedent: Many successful vaccines (polio, measles) involved modifying viruses, some through processes classifiable as GOF (attenuating by passage, introducing mutations).
Argument 3: Basic Science Value
Fundamental understanding of host-pathogen interactions, immune evasion, and viral evolution has applications beyond specific pandemic threats.
Insights from influenza GOF inform coronaviruses, and vice versa. General principles of viral adaptation benefit entire field.
The Scientific Case AGAINST Gain-of-Function Research
Argument 1: Lab Accidents Happen
Even with best practices, biosafety incidents occur. CDC, USAMRIID, and other elite facilities have documented lapses.
Risk calculation: Quantitative risk modeling by biosecurity researchers estimates laboratory accident probabilities. If even a conservative 0.3% annual escape probability exists for an enhanced pandemic pathogen, cumulative risk over 10 years exceeds 3%. A single escape of airborne-transmissible H5N1 could cause millions of deaths.
Gryphon Scientific’s 2016 risk assessment commissioned during the moratorium found significant uncertainties in both risk and benefit estimates, noting that benefits were often overstated while risks were underappreciated.
Critics argue: we’re creating risks nature hasn’t yet produced, in settings (urban research labs) where release impacts dense populations.
Argument 2: Overstated Benefits
Surveillance argument weak: Monitoring for specific lab-generated mutations assumes pandemic will follow that evolutionary path. Nature might take completely different route. Individual H5N1 ferret study mutations have occasionally appeared in circulating strains, but all five together have not been detected in wild bird populations after 12+ years of surveillance. Was the research predictive, or did it create a threat that doesn’t match natural evolution?
Vaccine development alternatives: Reverse genetics can create safer vaccine candidates without enhancing pandemic potential. Field surveillance of circulating strains provides real-world data better than lab-generated threats.
Animal model assumption: Just because a virus transmits in ferrets doesn’t mean it will in humans. Ferret models are proxy, not proof.
Argument 3: Dual-Use Information Risk
Publishing GOF methods provides: - Step-by-step protocols - Identification of key mutations - Validation that approach works
A sophisticated state bioweapons program or well-funded terrorist group could replicate. The information is inherently dual-use. It can’t benefit public health without also informing malicious actors.
Argument 4: Alternatives Exist
Field surveillance, computational modeling, reverse genetics for vaccine development, and pseudovirus systems can provide significant pandemic preparedness benefits without creating enhanced pathogens.
Many influenza experts argue that basic epidemiology and veterinary monitoring of animal reservoirs would do more for pandemic prevention than lab-created threats.
The 2001 anthrax attacks originated from a U.S. biodefense lab, not external terrorists. The perpetrator was a microbiologist with authorized access to select agents. GOF research creates new threats and trains researchers in how to create them. Even with perfect biosafety, insider threats are harder to mitigate. Background checks, personnel reliability programs, and security culture help but can’t eliminate risk from someone with legitimate access and specialized knowledge who decides to cause harm.
Alternatives to Gain-of-Function Research
Field Surveillance and Genomic Epidemiology
Monitor naturally circulating viruses in animal reservoirs and humans:
Advantages: - Studies real-world evolution, not lab artifacts - Identifies actual threats, not hypothetical ones - Lower biosafety risk (studying natural isolates at BSL-2 or BSL-3, not enhanced versions at BSL-3 or BSL-4)
Examples: - GISAID database tracking influenza and coronavirus evolution globally - Veterinary surveillance of avian influenza in wild birds and poultry - Syndromic surveillance detecting unusual respiratory disease patterns
Limitations: - Reactive rather than anticipatory - Requires extensive global infrastructure - May miss rare combinations that could emerge
Reverse Genetics for Vaccine Development
Use reverse genetics to create attenuated vaccine strains without enhancing pandemic potential:
Approach: - Take pathogen sequence - Introduce mutations that reduce virulence or replication - Test safety and immunogenicity - Develop as vaccine candidate
This is GOF in reverse: gain-of-attenuation rather than gain-of-danger.
Advantages: - Directly produces public health tool (vaccine) - Lower biosecurity risk (making pathogens less dangerous, not more) - Established regulatory pathway
Computational Modeling and Bioinformatics
Analyze sequence databases to predict: - Which mutations likely increase transmissibility - Host receptor binding changes - Immune escape variants
Advantages: - No wet lab work, no biosafety risk - Can analyze thousands of hypothetical variants rapidly - Increasingly accurate with AI/ML advances (AlphaFold for structure prediction)
Limitations: - Predictions need experimental validation - Models only as good as training data (which comes from… experimental research) - Can’t fully replace empirical biology
Pseudovirus Systems
Create replication-defective viral particles that mimic aspects of target virus:
How it works: - Take envelope proteins from pathogen of interest (e.g., H5N1 HA) - Package into replication-incompetent vector backbone (e.g., VSV, lentivirus) - Resulting particle has target virus’s surface but can’t reproduce beyond one infection cycle
Advantages: - Safe to work with (BSL-2 instead of BSL-3/4) - Can study receptor binding, entry mechanisms, antibody neutralization - No risk of creating transmissible pandemic virus
Limitations: - Doesn’t fully recapitulate real virus behavior - Can’t study replication, immune evasion beyond entry, or transmission
Ethical and Policy Challenges
The Dual-Use Dilemma
GOF research perfectly embodies dual-use: same information benefits public health and enables harm. You can’t selectively publish; either knowledge is open (benefiting both good and bad actors) or restricted (limiting scientific progress and global health capacity).
Open science tradition: Reproducibility, peer review, and cumulative knowledge require sharing methods and data.
Security imperative: Some information may be too dangerous to disseminate widely.
No consensus on how to balance these values.
Global Governance Gaps
P3CO and 2024 U.S. policy only cover federally funded U.S. research. GOF experiments can occur: - In other countries with different (or no) oversight - With private funding - In academic-industry partnerships
Pandemic threats don’t respect borders. A lab accident in any country affects the world. But national sovereignty limits international regulation.
Biological Weapons Convention prohibits bioweapons but has no verification mechanism and doesn’t explicitly cover GOF research.
Scientific Freedom vs. Public Safety
Researchers argue for autonomy in choosing research questions and methods. Governments and publics expect protection from catastrophic risks created by research.
Where’s the line? Who decides?
- Should review be institutional (scientists governing scientists)?
- Governmental (democratic accountability)?
- International (global risks require global oversight)?
No system satisfies everyone.
Current State and Future Outlook
As of late 2024, GOF research with potential pandemic pathogens continues under P3CO framework. Key research includes: - SARS-CoV-2 variant studies - Influenza reassortment experiments - Coronavirus host range investigations
In October 2022, Boston University researchers created a chimeric SARS-CoV-2 virus combining Omicron spike protein with ancestral strain backbone. In mice, the chimera caused 80% mortality (versus 0% for Omicron, 100% for ancestral strain). Media headlines claimed BU “created deadly COVID strain,” sparking controversy over:
- P3CO oversight: Did research require pre-approval? NIH found BU should have disclosed to them; BU believed institutional approval sufficient.
- Definitional ambiguity: Is this GOF if the chimera was less lethal than parent strain?
- Transparency: Preprint publication before NIH awareness raised questions about oversight effectiveness.
The incident highlighted continued gaps in P3CO framework application and fueled calls for clearer, mandatory oversight standards.
Transparency remains limited: Public doesn’t know how many GOF proposals are submitted, reviewed, approved, or denied. Lack of transparency fuels suspicion and hinders informed debate.
International landscape: China, Russia, and other countries conduct GOF research with varying levels of oversight. U.S. restrictions may simply shift research to less-regulated jurisdictions.
COVID-19 origins debate: Whether SARS-CoV-2 emerged from natural spillover or lab-related incident remains unresolved. The lab leak hypothesis (whether from GOF research or not) has intensified scrutiny of all laboratory pathogen research.
Technological change: Easier genetic engineering (CRISPR), cheaper DNA synthesis, AI-assisted design all make GOF experiments more accessible. Oversight mechanisms designed for 2017 technology may not adequately address 2024 capabilities.
Demonstrated (supported by published evidence):
- GOF experiments can create airborne-transmissible H5N1 in ferrets (Fouchier 2012, Kawaoka 2012)
- Enhanced pathogens can be created in BSL-3+ containment
- Laboratory biosafety incidents occur at documented rates across all biosafety levels
- P3CO framework provides enhanced oversight for federally funded U.S. research
- Alternatives (field surveillance, computational modeling, pseudovirus systems) provide some pandemic preparedness benefits
Contested (experts disagree):
- Whether GOF research provides unique pandemic preparedness benefits unavailable through alternatives
- Whether accident risks outweigh knowledge benefits
- Whether information hazards from publication are significant given other sources
- Whether ferret transmission results predict human pandemic potential
Unknown (insufficient evidence to assess):
- Total global GOF research activity (much is not publicly reported)
- Actual laboratory accident rates for GOF experiments (underreporting likely)
- Whether SARS-CoV-2 originated from laboratory research (origin remains unresolved)
- Effectiveness of P3CO framework in preventing concerning research
The GOF debate reflects genuine scientific uncertainty combined with value differences about acceptable risk. Neither “always safe” nor “never justified” captures the complexity.
What is gain-of-function research in biosecurity?
Gain-of-function (GOF) research enhances a pathogen’s transmissibility, virulence, or host range to study pandemic potential and develop countermeasures. The controversy focuses on experiments with potential pandemic pathogens that could cause catastrophic disease if released.
What were the H5N1 ferret studies and why were they controversial?
In 2012, Fouchier and Kawaoka independently created airborne-transmissible H5N1 avian influenza in ferrets. The studies showed just 5 mutations could enable mammalian transmission of a virus with 50-60% case fatality in humans, raising concerns about publishing a “pandemic recipe” while defenders argued the information was critical for surveillance and vaccine development.
What is the P3CO framework?
The HHS P3CO (Potential Pandemic Pathogen Care and Oversight) framework, implemented in 2017 after a 2014-2017 funding pause, provides multi-level review for research reasonably anticipated to create enhanced potential pandemic pathogens. It requires demonstration of significant public health benefits, adequate risk mitigation, and absence of reasonable lower-risk alternatives.
What are safer alternatives to gain-of-function research?
Alternatives include field surveillance of naturally circulating viruses, reverse genetics for vaccine development without enhancing pandemic potential, computational modeling using AI to predict dangerous mutations, pseudovirus systems that are replication-defective, and in vitro protein studies. These provide pandemic preparedness benefits with substantially lower biosecurity risks.
This chapter is part of The Biosecurity Handbook.