Rethinking biosafety in research on potential pandemic pathogens

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

H5 influenza is considered a potential pandemic threat. Recently, H5 viruses belonging to clade 2.3.4.4b have caused large outbreaks in avian and multiple nonhuman mammalian species. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to pandemic potential in humans, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. However, prior experimental work has only measured how these phenotypes are affected by a handful of the >10,000 different possible amino-acid mutations to HA. Here, we use pseudovirus deep mutational scanning to measure how all mutations to a 2.3.4.4b H5 HA affect each phenotype. We identify mutations that allow HA to better bind α2-6-linked sialic acids and show that some viruses already carry mutations that stabilize HA. We also measure how all HA mutations affect neutralization by sera from mice and ferrets vaccinated against or infected with 2.3.4.4b H5 viruses. These antigenic maps enable rapid assessment of when new viral strains have acquired mutations that may create mismatches with candidate vaccine virus, and we show that a mutation present in some recent H5 HAs causes a large antigenic change. Overall, the systematic nature of deep mutational scanning combined with the safety of pseudoviruses enables comprehensive measurements of the phenotypic effects of mutations that can inform real-time interpretation of viral variation observed during surveillance of H5 influenza.

Bridging biosafety and biosecurity gaps: DURC and ePPP policy insights from U.S. institutions

Overview

This study provides empirical data on the knowledge and practices of biosafety and biosecurity professionals and researchers involved in research on enhanced Potential Pandemic Pathogens (ePPPs) and Dual Use Research of Concern (DURC) within various U.S. sectors. The goal is to improve public health interventions and oversight for DURC and ePPP, contributing valuable insights for policy development. A notable finding was the association between larger biosafety/biosecurity teams and a higher likelihood of conducting high-risk biological research.

Methods

A survey of 541 biosafety and biosecurity professionals was conducted between March 8 and 10 April 2024, with results analyzed using SAS at a significance level of 0.05. The study received approval from the Institutional Review Boards (IRBs) at Arizona State University and the University of Nevada, Reno.

Results

Government organizations were more likely to conduct DURC compared to other sectors (e.g., Academic, Commercial, Consulting). Public institutions reviewed more experiments outside the scope of the U.S. DURC Policy than private for-profit institutions. Institutions with larger biosafety/biosecurity teams reported greater research activity and more effective non-compliance reporting mechanisms (e.g., anonymous hotlines, reporting forms). Additionally, financial support and the challenges of policy implementation varied significantly across sectors.

Discussion

The findings emphasize the need for appropriate staffing and resource allocation for high-risk biosafety and biosecurity research. A differentiated regulatory approach and equitable distribution of resources are essential for effective oversight. Moreover, robust non-compliance reporting systems are critical to mitigating the risks associated with DURC and ePPP research.

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

H5 influenza is a potential pandemic threat. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to pandemic risk, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. Here we use pseudovirus deep mutational scanning to measure how all mutations to a clade 2.3.4.4b H5 HA affect each phenotype. We identify mutations that allow HA to better bind a2-6-linked sialic acids, and show that some viruses already carry mutations that stabilize HA. We also identify recent viral strains with reduced neutralization to sera elicited by candidate vaccine virus. Overall, the systematic nature of deep mutational scanning combined with the safety of pseudoviruses enables comprehensive characterization of mutations to inform surveillance of H5 influenza.

Biosafety, biosecurity, and bioethics

The COVID-19 pandemic has highlighted the importance of biosafety in the biomedical sciences. While it is often assumed that biosafety is a purely technical matter that has little to do with philosophy or the humanities, biosafety raises important ethical issues that have not been adequately examined in the scientific or bioethics literature. This article reviews some pivotal events in the history of biosafety and biosecurity and explores three different biosafety topics that generate significant ethical concerns, i.e., risk assessment, risk management, and risk distribution. The article also discusses the role of democratic governance in the oversight of biosafety and offers some suggestions for incorporating bioethics into biosafety practice, education, and policy.

Biological Containment for African Swine Fever (ASF) Laboratories and Animal Facilities: The Italian Challenge in Bridging the Present Regulatory Gap and Enhancing Biosafety and Biosecurity Measures

The African Swine Fever Virus (ASFV) is a DNA virus of the Asfarviridae family, Asfivirus genus. It is responsible for massive losses in pig populations and drastic direct and indirect economic impacts. The ever-growing handling of ASFV pathological material in laboratories, necessary for either diagnostic or research activities, requires particular attention to avoid accidental virus release from laboratories and its detrimental economic and environmental effects. Recently, the Commission Delegated Regulation (EU) 2020/689 of 17 December 2019 repealed the Commission Decision of 26 May 2003 reporting an ASF diagnostic manual (2003/422/EC) with the minimum and supplementary requirements for ASF laboratories. This decision generated a regulatory gap that has not been addressed yet. This paper aims to describe the Italian National Reference Laboratory (NRL) efforts to develop an effective and reliable biological containment tool for ASF laboratories and animal facilities. The tool consists of comprehensive and harmonized structural and procedural requirements for ASF laboratories and animal facilities that have been developed based on both current and repealed legislation, further entailing a risk assessment and internal audit as indispensable tools to design, adjust, and improve biological containment measures.

Integrating evolutionary aspects into dual-use discussion: the cases of influenza virus and enterohemorrhagic Escherichia coli

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential.

A machine learning toolkit for genetic engineering attribution to facilitate biosecurity

The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed 'genetic engineering attribution', would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype data can reach 70% attribution accuracy in distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.

Rethinking Gain-of-Function Experiments in the Context of the COVID-19 Pandemic

Proponents of the use of gain-of-function (GOF) experiments with pathogens with pandemic potential (PPP) have argued that such experiments are necessary because they reveal important facets of pathogenesis and can be performed safely. Opponents of GOF experiments with PPP have argued that the risks outweigh the knowledge gained. The COVID-19 pandemic demonstrates the vulnerability of human societies to a new PPP, while also validating some arguments of both camps, questioning others, and suggesting the need to rethink how we approach this class of experiments.

Proponents of the use of gain-of-function (GOF) experiments with pathogens with pandemic potential (PPP) have argued that such experiments are necessary because they reveal important facets of pathogenesis and can be performed safely. Opponents of GOF experiments with PPP have argued that the risks outweigh the knowledge gained. The COVID-19 pandemic demonstrates the vulnerability of human societies to a new PPP, while also validating some arguments of both camps, questioning others, and suggesting the need to rethink how we approach this class of experiments.

Public awareness, acceptability and risk perception about infectious diseases dual-use research of concern: a cross-sectional survey

OBJECTIVES

In this study, we aimed to measure the awareness, acceptability and perceptions of current issues in biosecurity posed by infectious diseases dual-use research of concern (DURC) in the community. DURC is conducted today in many locations around the world for the benefit of humanity but may also cause harm through either a laboratory accident or deliberate misuse. Most DURC is approved by animal ethics committees, which do not typically consider harm to humans. Given the unique characteristics of contagion and the potential for epidemics and pandemics, the community is an important stakeholder in DURC.

DESIGN

Self-administered web-based cross-sectional survey.

PARTICIPANTS

Participants over the age of 18 in Australia and 21 in the USA were included in the survey. A total of 604 participants completed the study. The results of 52 participants were excluded due to potential biases about DURC stemming from their employment as medical researchers, infectious diseases researchers or law enforcement professionals, leaving 552 participants. Of those, 274 respondents resided in Australia and 278 in the USA.

OUTCOMES

Baseline awareness, acceptability and perceptions of current issues surrounding DURC. Changes in perception from baseline were measured after provision of information about DURC.

RESULTS

Presurvey, 77% of respondents were unaware of DURC and 64% found it unacceptable or were unsure. Two-thirds of respondents did not change their views. The baseline perception of high risk for laboratory accidents (29%) and deliberate bioterrorism (34%) was low but increased with increasing provision of information (42% and 44% respectively, p<0.001), with men more accepting of DURC (OR=1.79, 95% CI 1.25 to 2.57, p=0.002). Postsurvey, higher education predicted lower risk perception of laboratory accidents (OR=0.56, 95% CI 0.34 to 0.93, p=0.02) and bioterrorism (OR=0.48, 95% CI 0.29 to 0.80, p=0.004).

CONCLUSION

The community is an important stakeholder in infectious diseases DURC but has a low awareness of this kind of research. Only a minority support DURC, and this proportion decreased with increasing provision of knowledge. There were differences of opinion between age groups, gender and education levels. The community should be informed and engaged in decisions about DURC.

Improved Biosafety and Biosecurity Measures and/or Strategies to Tackle Laboratory-Acquired Infections and Related Risks

Herein, we reviewed laboratory-acquired infections (LAIs) along with their health-related biological risks to provide an evidence base to tackle biosafety/biosecurity and biocontainment issues. Over the past years, a broad spectrum of pathogenic agents, such as bacteria, fungi, viruses, parasites, or genetically modified organisms, have been described and gained a substantial concern due to their profound biological as well as ecological risks. Furthermore, the emergence and/or re-emergence of life-threatening diseases are of supreme concern and come under the biosafety and biosecurity agenda to circumvent LAIs. Though the precise infection risk after an exposure remains uncertain, LAIs inspections revealed that Brucella spp., Mycobacterium tuberculosis, Salmonella spp., Shigella spp., Rickettsia spp., and Neisseria meningitidis are the leading causes. Similarly, the human immunodeficiency virus (HIV) as well as hepatitis B (HBV) and C viruses (HCV), and the dimorphic fungi are accountable for the utmost number of viral and fungal-associated LAIs. In this context, clinical laboratories at large and microbiology, mycology, bacteriology, and virology-oriented laboratories, in particular, necessitate appropriate biosafety and/or biosecurity measures to ensure the safety of laboratory workers and working environment, which are likely to have direct or indirect contact/exposure to hazardous materials or organisms. Laboratory staff education and training are indispensable to gain an adequate awareness to handle biologically hazardous materials as per internationally recognized strategies. In addition, workshops should be organized among laboratory workers to let them know the epidemiology, pathogenicity, and human susceptibility of LAIs. In this way, several health-related threats that result from the biologically hazardous materials can be abridged or minimized and controlled by the correct implementation of nationally and internationally certified protocols that include proper microbiological practices, containment devices/apparatus, satisfactory facilities or resources, protective barriers, and specialized education and training of laboratory staffs. The present work highlights this serious issue of LAIs and associated risks with suitable examples. Potential preventive strategies to tackle an array of causative agents are also discussed. In this respect, the researchers and scientific community may benefit from the lessons learned in the past to anticipate future problems.

Transcriptional response to a prime/boost vaccination of chickens with three vaccine variants based on HA DNA and Pichia-produced HA protein

Highly pathogenic avian influenza causes severe economic losses and is a potential threat to public health. Better knowledge of the mechanisms of chicken response to the novel types of vaccines against avian influenza might be helpful in their successful implementation into poultry vaccination programs in different countries. This work presents a comprehensive analysis of gene expression response elicited in chicken spleens by a combined DNA/recombinant protein prime/boost vaccination compared to DNA/DNA and protein/protein regimens. All groups of vaccinated chickens displayed changes in spleen transcriptomes in comparison to the control group with 423, 375 and 212 identified differentially expressed genes in protein/protein, DNA/DNA and DNA/protein group, respectively. Genes with most significantly changed expression belong to immune-related categories. Depending on a group, a fraction of 15-34% of up-regulated and a fraction of 15-42% of down-regulated immune-related genes are shared by all groups. Interestingly, the most upregulated genes encode β-defensins, short peptides with antimicrobial activity and immunomodulatory functions. Microarray results were validated with RT-qPCR method, which confirmed differential regulation of the selected immune-related genes. Immune-related differentially expressed genes and metabolic pathways identified in this work are compared to the available literature data on gene expression changes in vaccinated and non-vaccinated chickens after influenza infection.

The dual use of research ethics committees: why professional self-governance falls short in preserving biosecurity

Background

Dual Use Research of Concern (DURC) constitutes a major challenge for research practice and oversight on the local, national and international level. The situation in Germany is shaped by two partly competing suggestions of how to regulate security-related research: The German Ethics Council, as an independent political advisory body, recommended a series of measures, including national legislation on DURC. Competing with that, the German National Academy of Sciences and the German Research Foundation, as two major professional bodies, presented a strategy which draws on the self-control of science and, inter alia, suggests expanding the scope of research ethics committees (RECs) to an evaluation of DURC.

Main body

This situation is taken as an occasion to further discuss the scope and limits of professional self-control with respect to security-related research. The role of RECs as professional bodies of science is particularly analyzed, referring to the theoretical backgrounds of professionalism. Two key sociological features of professionalism – ethical orientation and professional self-control – are discussed with respect to the practice of biomedical science. Both attributes are then analyzed with respect to the assessment of DURC by RECs.

Conclusion

In conclusion, it is stated that issues of biosecurity transcend the boundaries of the scientific community and that a more comprehensive strategy should be implemented encompassing both professional self-control and legal oversight.

A New Approach to Evaluating the Risk-Benefit Equation for Dual-Use and Gain-of-Function Research of Concern

In the twenty-first century, biology faces a problem that has previously vexed other disciplines such as physics, namely the prospect that its knowledge domain could be used to generate biological agents with altered properties that enhanced their weapon potential. Biological weapons bring the additional dimension that these could be self-replicating, easy to manufacture and synthesized with commonly available expertise. This resulted in increasing concern about the type of research done and communicated, despite the fact that such research often has direct societal benefits, bringing the dual-use dilemma to biology. The conundrum of dual use research of concern was crystallized by the so-called "gain-of-function" type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. After more than a decade of intensive discussion and controversy involving biological experiments with dual-use potential, there is no consensus on the issue except for the need to carry out such experiments in the safest conditions possible. In this essay, we review the topic with the hindsight of several years and suggest that instead of prescribing prohibitions and experimental limitations the focus should be on the importance of scientific questions at hand. We posit that the importance of a scientific question for medical and scientific progress provides a benchmark to determine the acceptable level of risk in biological experimentation.

Does influenza pandemic preparedness and mitigation require gain-of-function research?

The risk and benefits of gain‐of‐function studies on influenza A have been widely debated since 2012 when the methods to create two respiratory transmissible H5N1 mutant isolates were published. Opponents of gain‐of‐function studies argue the biosecurity risk is unacceptable, while proponents cite potential uses for pandemic surveillance, preparedness and mitigation. In this commentary, we provide an overview of the background and applications of gain‐of‐function research and argue that the anticipated benefits have yet to materialize while the significant risks remain.

Zika Virus Focuses the Gain-of-Function Debate

This year, the National Science Advisory Board for Biosecurity (NSABB) will be making recommendations to the U.S. Government regarding the ongoing saga of gain-of-function (GOF) experiments with highly infectious respiratory pathogens, such as influenza virus, severe acute respiratory syndrome (SARS) coronavirus, and Middle East respiratory syndrome (MERS) coronavirus.

Biological Risks and Laboratory-Acquired Infections: A Reality That Cannot be Ignored in Health Biotechnology

Advances and research in biotechnology have applications over a wide range of areas, such as microbiology, medicine, the food industry, agriculture, genetically modified organisms, and nanotechnology, among others. However, research with pathogenic agents, such as virus, parasites, fungi, rickettsia, bacterial microorganisms, or genetic modified organisms, has generated concern because of their potential biological risk - not only for people, but also for the environment due to their unpredictable behavior. In addition, concern for biosafety is associated with the emergence of new diseases or re-emergence of diseases that were already under control. Biotechnology laboratories require biosafety measures designed to protect their staff, the population, and the environment, which may be exposed to hazardous organisms and materials. Laboratory staff training and education is essential, not only to acquire a good understanding about the direct handling of hazardous biological agents but also knowledge of the epidemiology, pathogenicity, and human susceptibility to the biological materials used in research. Biological risk can be reduced and controlled by the correct application of internationally recognized procedures such as proper microbiological techniques, proper containment apparatus, adequate facilities, protective barriers, and special training and education of laboratory workers. To avoid occupational infections, knowledge about standardized microbiological procedures and techniques and the use of containment devices, facilities, and protective barriers is necessary. Training and education about the epidemiology, pathogenicity, and biohazards of the microorganisms involved may prevent or decrease the risk. In this way, the scientific community may benefit from the lessons learned in the past to anticipate future problems.

A new synthesis for dual use research of concern

Michael Imperiale and Arturo Casadevall propose a path forward for life sciences research whose results could be misused to cause harm.

Ethical alternatives to experiments with novel potential pandemic pathogens

Please see later in the article for the Editors' Summary

Containing the accidental laboratory escape of potential pandemic influenza viruses

BACKGROUND

The recent work on the modified H5N1 has stirred an intense debate on the risk associated with the accidental release from biosafety laboratory of potential pandemic pathogens. Here, we assess the risk that the accidental escape of a novel transmissible influenza strain would not be contained in the local community.

METHODS

We develop here a detailed agent-based model that specifically considers laboratory workers and their contacts in microsimulations of the epidemic onset. We consider the following non-pharmaceutical interventions: isolation of the laboratory, laboratory workers' household quarantine, contact tracing of cases and subsequent household quarantine of identified secondary cases, and school and workplace closure both preventive and reactive.

RESULTS

Model simulations suggest that there is a non-negligible probability (5% to 15%), strongly dependent on reproduction number and probability of developing clinical symptoms, that the escape event is not detected at all. We find that the containment depends on the timely implementation of non-pharmaceutical interventions and contact tracing and it may be effective (>90% probability per event) only for pathogens with moderate transmissibility (reproductive number no larger than R₀ = 1.5). Containment depends on population density and structure as well, with a probability of giving rise to a global event that is three to five times lower in rural areas.

CONCLUSIONS

Results suggest that controllability of escape events is not guaranteed and, given the rapid increase of biosafety laboratories worldwide, this poses a serious threat to human health. Our findings may be relevant to policy makers when designing adequate preparedness plans and may have important implications for determining the location of new biosafety laboratories worldwide.

Highly pathogenic avian influenza A(H5N1) mutants transmissible by air are susceptible to human and animal neutralizing antibodies

A laboratory-generated reassortant H5 hemagglutinin (HA)/influenza A(H1N1) strain containing 4 mutations in influenza A(H5N1) HA has become transmissible by air among mammals. Here, we constructed 15 influenza A(H5N1) pseudoviruses containing a single mutation or a combination of mutations and showed that the pseudoviruses were susceptible to neutralizing antibodies from patients with influenza A(H5N1) infection and from mice immunized with a vaccine containing the conserved HA1 sequence of influenza A(H5N1). These results indicate that antibodies in patients currently infected by influenza A(H5N1) and antibodies induced by vaccines containing conserved sequences in HA1 of wild-type influenza A(H5N1) are highly effective in cross-neutralizing future influenza A(H5N1) mutants with airborne transmissibility, suggesting that human influenza pandemics caused by these influenza A(H5N1) variants can be prevented.