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Dadonaite B, Ahn JJ, Ort JT, Yu J, Furey C, Dosey A, Hannon WW, Baker AV, Webby RJ, King NP, Liu Y, Hensley SE, Peacock TP, Moncla LH, Bloom JD. Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595634. [PMID: 38826368 PMCID: PMC11142178 DOI: 10.1101/2024.05.23.595634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
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.
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2
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Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex. Immunity 2024:S1074-7613(24)00319-4. [PMID: 39013466 DOI: 10.1016/j.immuni.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of the Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we used pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affected cell entry and antibody neutralization. Our experiments defined functional constraints throughout GPC. We quantified how GPC mutations affected neutralization with a panel of monoclonal antibodies. All antibodies tested were escaped by mutations that existed among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid the design of therapeutics and vaccines.
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Affiliation(s)
- Caleb R Carr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jared G Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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3
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Wheeler NE, Carter SR, Alexanian T, Isaac C, Yassif J, Millet P. Developing a Common Global Baseline for Nucleic Acid Synthesis Screening. APPLIED BIOSAFETY 2024; 29:71-78. [PMID: 39131178 PMCID: PMC11313551 DOI: 10.1089/apb.2023.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Introduction Nucleic acid synthesis is a powerful tool that has revolutionized the life sciences. However, the misuse of synthetic nucleic acids could pose a serious threat to public health and safety. There is a need for international standards for nucleic acid synthesis screening to help prevent the misuse of this technology. Methods We outline current barriers to the adoption of screening, which include the cost of developing screening tools and resources, adapting to existing commercial practices, internationalizing screening, and adapting screening to benchtop nucleic acid synthesis devices. To address these challenges, we then introduce the Common Mechanism for DNA Synthesis Screening, which was developed in consultation with a technical consortium of experts in DNA synthesis, synthetic biology, biosecurity, and policy, with the aim of addressing current barriers. The Common Mechanism software uses a variety of methods to identify sequences of concern, identify taxonomic best matches to regulated pathogens, and identify benign genes that can be cleared for synthesis. Finally, we describe outstanding challenges in the development of screening practices. Results The Common Mechanism is a step toward ensuring the safe and responsible use of synthetic nucleic acids. It provides a baseline capability that overcomes challenges to nucleic acid synthesis screening and provides a solution for broader international adoption of screening practices. Conclusion The Common Mechanism is a valuable tool for preventing the misuse of synthetic nucleic acids. It is a critical step toward ensuring the safe and responsible use of this powerful technology.
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Affiliation(s)
- Nicole E. Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | | | - Tessa Alexanian
- International Biosecurity and Biosafety Initiative for Science (IBBIS), Geneva, Switzerland
| | | | | | - Piers Millet
- International Biosecurity and Biosafety Initiative for Science (IBBIS), Geneva, Switzerland
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4
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Larsen BB, McMahon T, Brown JT, Wang Z, Radford CE, Crowe JE, Veesler D, Bloom JD. Functional and antigenic landscape of the Nipah virus receptor binding protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589977. [PMID: 38659959 PMCID: PMC11042328 DOI: 10.1101/2024.04.17.589977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and is a major target of neutralizing antibodies. Here we use deep mutational scanning to measure how all amino-acid mutations to the RBP affect cell entry, receptor binding, and escape from neutralizing antibodies. We identify functionally constrained regions of the RBP, including sites involved in oligomerization, along with mutations that differentially modulate RBP binding to its two ephrin receptors. We map escape mutations for six anti-RBP antibodies, and find that few antigenic mutations are present in natural Nipah strains. Our findings offer insights into the potential for functional and antigenic evolution of the RBP that can inform the development of antibody therapies and vaccines.
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Affiliation(s)
- Brendan B. Larsen
- Basic Sciences Division and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA 98109, USA
| | - Teagan McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA 98109, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Caelan E. Radford
- Basic Sciences Division and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA 98109, USA
| | - James E. Crowe
- Department of Pathology Microbiology and Immunology, The Vanderbilt Vaccine Center, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutch Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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5
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Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579020. [PMID: 38370709 PMCID: PMC10871245 DOI: 10.1101/2024.02.05.579020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.
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Affiliation(s)
- Caleb R. Carr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Katharine H. D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jared G. Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh K. Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A. Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead contact
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Liang C, Wagstaff J, Aharony N, Schmit V, Manheim D. Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance. Health Secur 2023; 21:34-45. [PMID: 36629860 PMCID: PMC9940815 DOI: 10.1089/hs.2022.0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for "widespread metagenomic monitoring" to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.
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Affiliation(s)
- Chelsea Liang
- Chelsea Liang is an Independent Researcher, University of New South Wales, School of Biotechnology and Biomolecular Sciences, Sydney, Australia
| | - James Wagstaff
- James Wagstaff, PhD, is a Research Fellow, Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Noga Aharony
- Noga Aharony, MS, is a PhD Student, Department of Systems Biology, Columbia University, New York, NY
| | - Virginia Schmit
- Virginia Schmit, PhD, is Director of Research, 1DatSooner, DE, and a Policy Specialist, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - David Manheim
- David Manheim, PhD, is Head of Policy and Research, ALTER, Rehovot, Israel; Lead Researcher, 1DaySooner, Claymont, DE,Visiting Researcher, Humanities and Arts Department, Technion – Israel Institute of Technology, Haifa, Israel.,Address correspondence to: David B. Manheim, 8734 First Avenue, Silver Spring, MD 20910
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7
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Trump B, Cummings C, Klasa K, Galaitsi S, Linkov I. Governing biotechnology to provide safety and security and address ethical, legal, and social implications. Front Genet 2023; 13:1052371. [PMID: 36712887 PMCID: PMC9873990 DOI: 10.3389/fgene.2022.1052371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
The field of biotechnology has produced a wide variety of materials and products which are rapidly entering the commercial marketplace. While many developments promise revolutionary benefits, some of them pose uncertain or largely untested risks and may spur debate, consternation, and outrage from individuals and groups who may be affected by their development and use. In this paper we show that the success of any advanced genetic development and usage requires that the creators establish technical soundness, ensure safety and security, and transparently represent the product's ethical, legal, and social implications (ELSI). We further identify how failures to address ELSI can manifest as significant roadblocks to product acceptance and adoption and advocate for use of the "safety-by-design" governance philosophy. This approach requires addressing risk and ELSI needs early and often in the technology development process to support innovation while providing security and safety for workers, the public, and the broader environment. This paper identifies and evaluates major ELSI challenges and perspectives to suggest a methodology for implementing safety-by-design in a manner consistent with local institutions and politics. We anticipate the need for safety-by-design approach to grow and permeate biotechnology governance structures as the field expands in scientific and technological complexity, increases in public attention and prominence, and further impacts human health and the environment.
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Affiliation(s)
- Benjamin Trump
- Engineering Research and Development Center, United States Army Corps of Engineers, Vicksburg, MS, United States
| | - Christopher Cummings
- Engineering Research and Development Center, United States Army Corps of Engineers, Vicksburg, MS, United States,Genetic Engineering and Society, North Carolina State University, Raleigh, NC, United States,Gene Edited Foods Project, Iowa State University, Ames, IA, United States,*Correspondence: Christopher Cummings,
| | - Kasia Klasa
- Department of Healthcare Management and Policy, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Stephanie Galaitsi
- Engineering Research and Development Center, United States Army Corps of Engineers, Vicksburg, MS, United States
| | - Igor Linkov
- Engineering Research and Development Center, United States Army Corps of Engineers, Vicksburg, MS, United States,Department of Engineering and Public Policy, Carnegie Mellon University, Pittsburgh, PA, United States
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8
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Greene D, Palmer MJ, Relman DA. Motivating Proactive Biorisk Management. Health Secur 2023; 21:46-60. [PMID: 36633603 PMCID: PMC9940813 DOI: 10.1089/hs.2022.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 01/13/2023] Open
Abstract
Scholars and practitioners of biosafety and biosecurity (collectively, biorisk management or BRM) have argued that life scientists should play a more proactive role in monitoring their work for potential risks, mitigating harm, and seeking help as necessary. However, most efforts to promote proactive BRM have focused on training life scientists in technical skills and have largely ignored the extent to which life scientists wish to use them (ie, their motivation). In this article, we argue that efforts to promote proactive BRM would benefit from a greater focus on life scientists' motivation. We review relevant literature on life scientists' motivation to practice BRM, offer examples of successful interventions from adjacent fields, and outline ideas for possible interventions to promote proactive BRM, along with strategies for iterative development, testing, and scaling.
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Affiliation(s)
- Daniel Greene
- Daniel Greene, PhD, is a Senior Analyst, Biosafety, Biosecurity & Emerging Technologies, Gryphon Scientific, Takoma Park, MD. Daniel Greene is also a Postdoctoral Fellow, Center for International Security and Cooperation; Stanford University, Stanford, CA
| | - Megan J. Palmer
- Megan J. Palmer, PhD, is Executive Director, Bio Policy & Leadership Initiatives, and an Adjunct Professor, Department of Bioengineering; Stanford University, Stanford, CA
| | - David A. Relman
- David A. Relman, MD, is a Senior Fellow, Center for International Security and Cooperation; Stanford University, Stanford, CA. David A. Relman is also the Thomas C. and Joan M. Merigan Professor, Departments of Medicine, and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
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9
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Manheim D, Lewis G. High-risk human-caused pathogen exposure events from 1975-2016. F1000Res 2022; 10:752. [PMID: 35903214 PMCID: PMC9274012 DOI: 10.12688/f1000research.55114.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 11/20/2022] Open
Abstract
Biological agents and infectious pathogens have the potential to cause very significant harm, as the natural occurrence of disease and pandemics makes clear. As a way to better understand the risk of Global Catastrophic Biological Risks due to human activities, rather than natural sources, this paper reports on a dataset of 71 incidents involving either accidental or purposeful exposure to, or infection by, a highly infectious pathogenic agent. There has been significant effort put into both reducing the risk of purposeful spread of biological weapons, and biosafety intended to prevent the exposure to, or release of, dangerous pathogens in the course of research. Despite these efforts, there are incidents of various types that could potentially be controlled or eliminated by different lab and/or bioweapon research choices and safety procedures. The dataset of events presented here was compiled during a project conducted in 2019 to better understand biological risks from anthropic sources. The events which are listed are unrelated to clinical treatment of naturally occurring outbreaks, and are instead entirely the result of human decisions and mistakes. While the events cover a wide range of cases, the criteria used covers a variety of events previously scattered across academic, policy, and other unpublished or not generally available sources.
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Affiliation(s)
| | - Gregory Lewis
- Future of Humanity Institute, University of Oxford, Oxford, UK
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10
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Abstract
The risk of accidental or deliberate misuse of biological research is increasing as biotechnology advances. As open science becomes widespread, we must consider its impact on those risks and develop solutions that ensure security while facilitating scientific progress. Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. Increasing the availability of computational tools, datasets, and protocols could increase risks from research with misuse potential. For instance, in the context of viral engineering, open code, data, and materials may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. While preprints accelerate dissemination of findings, their increased use could challenge strategies for risk mitigation at the publication stage. This highlights the importance of oversight earlier in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research. Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.
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Affiliation(s)
- James Andrew Smith
- Botnar Research Centre and Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
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11
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Vennis IM, Schaap MM, Hogervorst PAM, de Bruin A, Schulpen S, Boot MA, van Passel MWJ, Rutjes SA, Bleijs DA. Dual-Use Quickscan: A Web-Based Tool to Assess the Dual-Use Potential of Life Science Research. Front Bioeng Biotechnol 2021; 9:797076. [PMID: 34957083 PMCID: PMC8696162 DOI: 10.3389/fbioe.2021.797076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/03/2021] [Indexed: 12/02/2022] Open
Abstract
Research on pathogenic organisms is crucial for medical, biological and agricultural developments. However, biological agents as well as associated knowledge and techniques, can also be misused, for example for the development of biological weapons. Potential malicious use of well-intended research, referred to as “dual-use research”, poses a threat to public health and the environment. There are various international resources providing frameworks to assess dual-use potential of the research concerned. However, concrete instructions for researchers on how to perform a dual-use risk assessment is largely lacking. The international need for practical dual-use monitoring and risk assessment instructions, in addition to the need to raise awareness among scientists about potential dual-use aspects of their research has been identified over the last years by the Netherlands Biosecurity Office, through consulting national and international biorisk stakeholders. We identified that Biorisk Management Advisors and researchers need a practical tool to facilitate a dual-use assessment on their specific research. Therefore, the Netherlands Biosecurity Office developed a web-based Dual-Use Quickscan (www.dualusequickscan.com), that can be used periodically by researchers working with microorganisms to assess potential dual-use risks of their research by answering a set of fifteen yes/no questions. The questions for the tool were extracted from existing international open resources, and categorized into three themes: characteristics of the biological agent, knowledge and technology about the biological agent, and consequences of misuse. The results of the Quickscan provide the researcher with an indication of the dual-use potential of the research and can be used as a basis for further discussions with a Biorisk Management Advisor. The Dual-Use Quickscan can be embedded in a broader system of biosafety and biosecurity that includes dual-use monitoring and awareness within organizations. Increased international attention to examine pathogens with pandemic potential has been enhanced by the current COVID-19 pandemic, hence monitoring of dual-use potential urgently needs to be encouraged.
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Affiliation(s)
- Iris M Vennis
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Mirjam M Schaap
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Petra A M Hogervorst
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Arnout de Bruin
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Sjors Schulpen
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Marijke A Boot
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Mark W J van Passel
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Saskia A Rutjes
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Diederik A Bleijs
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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12
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Principles of synthetic biology. Essays Biochem 2021; 65:791-811. [PMID: 34693448 PMCID: PMC8578974 DOI: 10.1042/ebc20200059] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 09/05/2021] [Accepted: 09/24/2021] [Indexed: 12/18/2022]
Abstract
In synthetic biology, biological cells and processes are dismantled and reassembled to make novel systems that do useful things. Designs are encoded by deoxyribonucleic acid (DNA); DNA makes biological (bio-)parts; bioparts are combined to make devices; devices are built into biological systems. Computers are used at all stages of the Design-Build-Test-Learn cycle, from mathematical modelling through to the use of robots for the automation of assembly and experimentation. Synthetic biology applies engineering principles of standardisation, modularity, and abstraction, enabling fast prototyping and the ready exchange of designs between synthetic biologists working around the world. Like toy building blocks, compatible modular designs enable bioparts to be combined and optimised easily; biopart specifications are shared in open registries. Synthetic biology is made possible due to major advances in DNA sequencing and synthesis technologies, and through knowledge gleaned in the field of systems biology. Systems biology aims to understand biology across scales, from the molecular and cellular, up to tissues and organisms, and describes cells as complex information-processing systems. By contrast, synthetic biology seeks to design and build its own systems. Applications of synthetic biology are wide-ranging but include impacting healthcare to improve diagnosis and make better treatments for disease; it seeks to improve the environment by finding novel ways to clean up pollution, make industrial processes for chemical synthesis sustainable, and remove the need for damaging farming practices by making better fertilisers. Synthetic biology has the potential to change the way we live and help us to protect the future of our planet.
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13
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Musunuri S, Sandbrink JB, Monrad JT, Palmer MJ, Koblentz GD. Rapid Proliferation of Pandemic Research: Implications for Dual-Use Risks. mBio 2021; 12:e0186421. [PMID: 34663091 PMCID: PMC8524337 DOI: 10.1128/mbio.01864-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 pandemic has demonstrated the world's vulnerability to biological catastrophe and elicited unprecedented scientific efforts. Some of this work and its derivatives, however, present dual-use risks (i.e., potential harm from misapplication of beneficial research) that have largely gone unaddressed. For instance, gain-of-function studies and reverse genetics protocols may facilitate the engineering of concerning SARS-CoV-2 variants and other pathogens. The risk of accidental or deliberate release of dangerous pathogens may be increased by large-scale collection and characterization of zoonotic viruses undertaken in an effort to understand what enables animal-to-human transmission. These concerns are exacerbated by the rise of preprint publishing that circumvents a late-stage opportunity for dual-use oversight. To prevent the next global health emergency, we must avoid inadvertently increasing the threat of future biological events. This requires a nuanced and proactive approach to dual-use evaluation throughout the research life cycle, including the conception, funding, conduct, and dissemination of research.
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Affiliation(s)
| | - Jonas B. Sandbrink
- Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
- Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Joshua Teperowski Monrad
- Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Health Policy, London School of Economics, London, United Kingdom
| | - Megan J. Palmer
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Center for International Security and Cooperation (CISAC), Stanford University, Stanford, California, USA
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Fairfax, Virginia, USA
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14
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Abstract
PURPOSE OF REVIEW Due to the impact of the COVID-19 pandemic this past year, we have witnessed a significant acceleration in the science, technology, and policy of global health security. This review highlights important progress made toward the mitigation of Zika, Ebola, and COVID-19 outbreaks. These epidemics and their shared features suggest a unified policy and technology agenda that could broadly improve global health security. RECENT FINDINGS Molecular epidemiology is not yet in widespread use, but shows promise toward informing on-the-ground decision-making during outbreaks. Point-of-care (POC) diagnostics have been achieved for each of these threats; however, deployment of Zika and Ebola diagnostics lags behind those for COVID-19. POC metagenomics offers the possibility of identifying novel viruses. Vaccines have been successfully approved for Ebola and COVID-19, due in large part to public-private partnerships and advance purchase commitments. Therapeutics trials conducted during ongoing epidemics have identified effective antibody therapeutics for Ebola, as well as steroids (both inhaled and oral) and a broad-spectrum antiviral for COVID-19. SUMMARY Achieving global health security remains a challenge, though headway has been made over the past years. Promising policy and technology strategies that would increase resilience across emerging viral pathogens should be pursued.
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Affiliation(s)
| | - Michele Barry
- School of Medicine
- Center for Innovation in Global Health, Stanford University, Stanford, California, USA
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Sandberg A, Nelson C. Who Should We Fear More: Biohackers, Disgruntled Postdocs, or Bad Governments? A Simple Risk Chain Model of Biorisk. Health Secur 2020; 18:155-163. [PMID: 32522112 DOI: 10.1089/hs.2019.0115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The biological risk landscape continues to evolve as developments in synthetic biology and biotechnology offer increasingly powerful tools to a widening pool of actors, including those who may consider carrying out a deliberate biological attack. However, it remains unclear whether it is the relatively large numbers of low-resourced actors or the small handful of high-powered actors who pose a greater biosecurity risk. To answer this question, this paper introduces a simple risk chain model of biorisk, from actor intent to a biological event, where the actor can successfully pass through each of N steps. Assuming that actor success probability at each independent step is sigmoidally distributed and actor power follows a power-law distribution, if a biorisk event were to occur, this model shows that the expected perpetrator would likely be highly powered, despite lower-powered actors being far more numerous. However, as the number of necessary steps leading to a biological release scenario decreases, lower-powered actors can quickly overtake more powerful actors as the likely source of a given event. If steps in the risk chain are of unequal difficulty, this model shows that actors are primarily limited by the most difficult step. These results have implications for biosecurity risk assessment and health security strengthening initiatives and highlight the need to consider actor power and ensure that the steps leading to a biorisk event are sufficiently difficult and not easily bypassed.
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Affiliation(s)
- Anders Sandberg
- Anders Sandberg, PhD, is a Senior Research Fellow; Cassidy Nelson, MBBS, MPH, is a Research Scholar; both are at the Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Cassidy Nelson
- Anders Sandberg, PhD, is a Senior Research Fellow; Cassidy Nelson, MBBS, MPH, is a Research Scholar; both are at the Future of Humanity Institute, University of Oxford, Oxford, UK
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