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Su H, Lin J. Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:109. [PMID: 37400889 DOI: 10.1186/s13068-023-02340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023]
Abstract
Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.
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Affiliation(s)
- Haifeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, The Ministry of Natural and Resources, Xian, 710075, Shanxi, China
| | - JiaFu Lin
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
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2
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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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3
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Shinomiya N, Minari J, Yoshizawa G, Dando M, Shang L. Reconsidering the need for gain-of-function research on enhanced potential pandemic pathogens in the post-COVID-19 era. Front Bioeng Biotechnol 2022; 10:966586. [PMID: 36091454 PMCID: PMC9458934 DOI: 10.3389/fbioe.2022.966586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The dual-use risk of infectious disease research using enhanced potential pandemic pathogens (ePPP), particularly gain-of-function (GOF) research, has been debated since 2011. As of now, research is supported on the condition that the research plan is reviewed and the actual experiment is supervised. However, the kinds of research conducted and what benefits they have brought to our society have not been adequately verified. Nevertheless, due to the COVID-19 pandemic that began at the end of 2019 and caused numerous deaths and wide economic disruption, the importance of infectious disease control from an international perspective has been recognized. Although complete control of the pandemic is still far off, positive signs include generating epidemiological trends based on genome analysis, therapeutic drug and vaccine development, clinical patient management, and public health policy interventions. In this context, the time has come to reconsider the true significance of GOF research on ePPP and the state of research governance in the post-COVID-19 era. In particular, the risks of such research are clearer than before, whereas its benefits seem less apparent. In this paper, we summarize the history of discussions on such GOF research, its significance in the light of the current COVID-19 pandemic, and the direction we shall take in the future.
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Affiliation(s)
- Nariyoshi Shinomiya
- National Defense Medical College, Saitama, Japan
- *Correspondence: Nariyoshi Shinomiya,
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Go Yoshizawa
- Innovation System Research Center, Kwansei Gakuin University, Hyogo, Japan
| | - Malcolm Dando
- Section of Peace Studies and International Development, University of Bradford, Bradford, United Kingdom
| | - Lijun Shang
- School of Human Sciences, London Metropolitan University, London, United Kingdom
- Biological Security Research Center, London Metropolitan University, London, United Kingdom
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4
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Velardo F, Prudhomme J, Temime L, Jean K. [Dual-use research on modified pathogens in the laboratory: What framework for what issue?]. Med Sci (Paris) 2022; 38:303-308. [PMID: 35333169 DOI: 10.1051/medsci/2022026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Technological advances in synthetic biology have made in vitro modification, or even creation, of viruses easier and more affordable. Several research studies using synthesis of potential pandemic pathogens led to controversies in the 2010's. More recently, the hypothesis that Covid-19 pandemics could originate from a lab escape is still under debate. In France, a legislative vacuum remains concerning the synthesis of modified pathogens. Initiating a collective reflection process towards setting of a legal framework on this type of work is timely so that research continues to provide profit to society rather than hazard.
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Affiliation(s)
- Fanny Velardo
- École Pasteur, Conservatoire national des Arts et Métiers (Cnam) de Santé publique, 292 rue Saint-Martin, 75141 Paris Cedex 03, France
| | - Julie Prudhomme
- École Pasteur, Conservatoire national des Arts et Métiers (Cnam) de Santé publique, 292 rue Saint-Martin, 75141 Paris Cedex 03, France
| | - Laura Temime
- Laboratoire MESuRS, Conservatoire national des Arts et Métiers (Cnam), Paris, France
| | - Kévin Jean
- Laboratoire MESuRS, Conservatoire national des Arts et Métiers (Cnam), Paris, France
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5
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Van der Walt R. Implications of evolutionary unpredictability for gain-of-function research. Postgrad Med J 2022; 99:postgradmedj-2022-141612. [PMID: 35273121 DOI: 10.1136/postgradmedj-2022-141612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Riaan Van der Walt
- Department of Philosophy, Practical and Systematic Theology, University of South Africa, Pretoria, Gauteng, South Africa
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6
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Carlson CJ, Farrell MJ, Grange Z, Han BA, Mollentze N, Phelan AL, Rasmussen AL, Albery GF, Bett B, Brett-Major DM, Cohen LE, Dallas T, Eskew EA, Fagre AC, Forbes KM, Gibb R, Halabi S, Hammer CC, Katz R, Kindrachuk J, Muylaert RL, Nutter FB, Ogola J, Olival KJ, Rourke M, Ryan SJ, Ross N, Seifert SN, Sironen T, Standley CJ, Taylor K, Venter M, Webala PW. The future of zoonotic risk prediction. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200358. [PMID: 34538140 PMCID: PMC8450624 DOI: 10.1098/rstb.2020.0358] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 01/26/2023] Open
Abstract
In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoe Grange
- Public Health Scotland, Glasgow G2 6QE, UK
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, NY 12545, USA
| | - Nardus Mollentze
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alexandra L. Phelan
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Angela L. Rasmussen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - Bernard Bett
- Animal and Human Health Program, International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - David M. Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Evan A. Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C. Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sam Halabi
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Charlotte C. Hammer
- Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Rebecca Katz
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
| | - Renata L. Muylaert
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | | | | | - Michelle Rourke
- Law Futures Centre, Griffith Law School, Griffith University, Nathan, Queensland 4111, Australia
| | - Sadie J. Ryan
- Department of Geography and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire J. Standley
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Kishana Taylor
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
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7
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Raybould A. New Frontiers in Biosafety and Biosecurity. Front Bioeng Biotechnol 2021; 9:727386. [PMID: 34368110 PMCID: PMC8334000 DOI: 10.3389/fbioe.2021.727386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022] Open
Affiliation(s)
- Alan Raybould
- Global Academy of Agriculture and Food Security and the Innogen Institute, Old Surgeons’ Hall, University of Edinburgh, Edinburgh, United Kingdom
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Wale N, Duffy MA. The Use and Underuse of Model Systems in Infectious Disease Ecology and Evolutionary Biology. Am Nat 2021; 198:69-92. [PMID: 34143716 DOI: 10.1086/714595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractEver since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based model systems have been important for developing and testing theory. Yet what EEID researchers mean by the term "model systems" and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID researchers are (and are not) using 10 key model systems. According to this definition, model systems in EEID are not being used to their fullest and, in fact, cannot even be considered model systems. Research using these systems consistently addresses only two of the three fundamental processes that underlie disease dynamics-transmission and disease, but not recovery. Furthermore, studies tend to focus on only a few scales of biological organization that matter for disease ecology and evolution. Moreover, the field lacks an infrastructure to perform comparative analyses. We aim to begin a discussion of what we want from model systems, which would further progress toward a thorough, holistic understanding of EEID.
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Application of a Biologically Contained Reporter System To Study Gain-of-Function H5N1 Influenza A Viruses with Pandemic Potential. mSphere 2020; 5:5/4/e00423-20. [PMID: 32848003 PMCID: PMC7449622 DOI: 10.1128/msphere.00423-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding how animal influenza viruses can adapt to spread in humans is critical to prepare for, and prevent, new pandemics. However, working safely with pathogens that have pandemic potential requires tight regulation and the use of high-level physical and biological risk mitigation strategies to stop accidental loss of containment. Here, we used a biological containment system for influenza viruses to study strains with pandemic potential. The system relies on deletion of the essential HA gene from the viral genome and its provision by a genetically modified cell line, to which virus propagation is therefore restricted. We show that this method permits safe handling of these pathogens, including gain-of-function variants, without the risk of generating fully infectious viruses. Furthermore, we demonstrate that this system can be used to assess virus sensitivity to both approved and experimental drugs, as well as the antigenic profile of viruses, important considerations for evaluating prepandemic vaccine and antiviral strategies. Natural adaptation of an antigenically novel avian influenza A virus (IAV) to be transmitted efficiently in humans has the potential to trigger a devastating pandemic. Understanding viral genetic determinants underlying adaptation is therefore critical for pandemic preparedness, as the knowledge gained enhances surveillance and eradication efforts, prepandemic vaccine design, and efficacy assessment of antivirals. However, this work has risks, as making gain-of-function substitutions in fully infectious IAVs may create a pathogen with pandemic potential. Thus, such experiments must be tightly controlled through physical and biological risk mitigation strategies. Here, we applied a previously described biological containment system for IAVs to a 2009 pandemic H1N1 strain and a highly pathogenic H5N1 strain. The system relies on deletion of the essential viral hemagglutinin (HA) gene, which is instead provided in trans, thereby restricting multicycle virus replication to genetically modified HA-complementing cells. In place of HA, a Renilla luciferase gene is inserted within the viral genome, and a live-cell luciferase substrate allows real-time quantitative monitoring of viral replication kinetics with a high dynamic range. We demonstrate that biologically contained IAV-like particles exhibit wild-type sensitivities to approved antivirals, including oseltamivir, zanamivir, and baloxavir. Furthermore, the inability of these IAV-like particles to genetically acquire the host-encoded HA allowed us to introduce gain-of-function substitutions in the H5 HA gene that promote mammalian transmissibility. Biologically contained “transmissible” H5N1 IAV-like particles exhibited wild-type sensitivities to approved antivirals, to the fusion inhibitor S20, and to neutralization by existing H5 monoclonal and polyclonal sera. This work represents a proof of principle that biologically contained IAV systems can be used to safely conduct selected gain-of-function experiments. IMPORTANCE Understanding how animal influenza viruses can adapt to spread in humans is critical to prepare for, and prevent, new pandemics. However, working safely with pathogens that have pandemic potential requires tight regulation and the use of high-level physical and biological risk mitigation strategies to stop accidental loss of containment. Here, we used a biological containment system for influenza viruses to study strains with pandemic potential. The system relies on deletion of the essential HA gene from the viral genome and its provision by a genetically modified cell line, to which virus propagation is therefore restricted. We show that this method permits safe handling of these pathogens, including gain-of-function variants, without the risk of generating fully infectious viruses. Furthermore, we demonstrate that this system can be used to assess virus sensitivity to both approved and experimental drugs, as well as the antigenic profile of viruses, important considerations for evaluating prepandemic vaccine and antiviral strategies.
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Gebreyes WA, Jackwood D, de Oliveira CJB, Lee CW, Hoet AE, Thakur S. Molecular Epidemiology of Infectious Zoonotic and Livestock Diseases. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0011-2019. [PMID: 32220263 PMCID: PMC10773240 DOI: 10.1128/microbiolspec.ame-0011-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 12/20/2022] Open
Abstract
Zoonotic and livestock diseases are very important globally both in terms of direct impact on human and animal health and in terms of their relationship to the livelihood of farming communities, as they affect income generation and food security and have other, indirect consequences on human lives. More than two-thirds of emerging infectious diseases in humans today are known to be of animal origin. Bacterial, viral, and parasitic infections that originate from animals, including hypervirulent and multidrug-resistant (MDR) bacterial pathogens, such as livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), invasive nontyphoidal Salmonella of animal origin, hyperviruent Clostridium difficile, and others, are of major significance to public health. Understanding the origin, risk factors, transmission, prevention, and control of such strains has been a challenge for various reasons, particularly due to the transdisciplinary partnership between and among human, environment, and animal health sectors. MDR bacteria greatly complicate the clinical management of human infections. Food animal farms, pets in communities, and veterinary hospital environments are major sources of such infections. However, attributing such infections and pinpointing sources requires highly discriminatory molecular methods as outlined in other parts of this curated series. Genotyping methods, such as multilocus sequence typing, pulsed-field gel electrophoresis, restriction fragment length polymorphism, and several others, have been used to decipher sources of foodborne and other zoonotic infectious diseases. In recent years, whole-genome-sequence-based approaches have been increasingly used for molecular epidemiology of diseases at the interface of humans, animals, and the environment. This part of the series highlights the major zoonotic and foodborne disease issues. *This article is part of a curated collection.
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Affiliation(s)
- Wondwossen A Gebreyes
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH 43210
- Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Daral Jackwood
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Wooster, OH 44691
- Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Celso Jose Bruno de Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH 43210
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Wooster, OH 44691
- Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Armando E Hoet
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH 43210
- Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Siddhartha Thakur
- Population Health and Pathobiology (PHP), College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606
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MacIntyre CR, Adam DC, Turner R, Chughtai AA, Engells T. Public awareness, acceptability and risk perception about infectious diseases dual-use research of concern: a cross-sectional survey. BMJ Open 2020; 10:e029134. [PMID: 31911509 PMCID: PMC6955500 DOI: 10.1136/bmjopen-2019-029134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 11/23/2022] Open
Abstract
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.
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Affiliation(s)
- Chandini Raina MacIntyre
- Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
- College of Public Service & Community Solutions, Arizona State University, Tempe, Arizona, USA
| | - Dillon Charles Adam
- Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Robin Turner
- Centre for Biostatistics, Division of Health Sciences, University of Otago Dunedin School of Medicine, Dunedin, New Zealand
| | - Abrar Ahmad Chughtai
- University of New South Wales School of Public Health and Community Medicine, Sydney, New South Wales, Australia
| | - Thomas Engells
- University of Texas Medical Branch, Galveston, Texas, USA
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Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S. Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations. Cells 2019; 8:E958. [PMID: 31443542 PMCID: PMC6770435 DOI: 10.3390/cells8090958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/03/2019] [Accepted: 08/20/2019] [Indexed: 11/17/2022] Open
Abstract
Animal studies aimed at understanding influenza virus mutations that change host specificity to adapt to replication in mammalian hosts are necessarily limited in sample numbers due to high cost and safety requirements. As a safe, higher-throughput alternative, we explore the possibility of using readily available passage bias data obtained mostly from seasonal H1 and H3 influenza strains that were differentially grown in mammalian (MDCK) and avian cells (eggs). Using a statistical approach over 80,000 influenza hemagglutinin sequences with passage information, we found that passage bias sites are most commonly found in three regions: (i) the globular head domain around the receptor binding site, (ii) the region that undergoes pH-dependent structural changes and (iii) the unstructured N-terminal region harbouring the signal peptide. Passage bias sites were consistent among different passage cell types as well as between influenza A subtypes. We also find epistatic interactions of site pairs supporting the notion of host-specific dependency of mutations on virus genomic background. The sites identified from our large-scale sequence analysis substantially overlap with known host adaptation sites in the WHO H5N1 genetic changes inventory suggesting information from passage bias can provide candidate sites for host specificity changes to aid in risk assessment for emerging strains.
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Affiliation(s)
- Raphael T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671, Singapore
| | - Hsiao-Han Chang
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Colin A Russell
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Marc Lipsitch
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
- National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore.
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Sample M, Boulicault M, Allen C, Bashir R, Hyun I, Levis M, Lowenthal C, Mertz D, Montserrat N, Palmer MJ, Saha K, Zartman J. Multi-cellular engineered living systems: building a community around responsible research on emergence. Biofabrication 2019; 11:043001. [PMID: 31158828 PMCID: PMC7551891 DOI: 10.1088/1758-5090/ab268c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ranging from miniaturized biological robots to organoids, multi-cellular engineered living systems (M-CELS) pose complex ethical and societal challenges. Some of these challenges, such as how to best distribute risks and benefits, are likely to arise in the development of any new technology. Other challenges arise specifically because of the particular characteristics of M-CELS. For example, as an engineered living system becomes increasingly complex, it may provoke societal debate about its moral considerability, perhaps necessitating protection from harm or recognition of positive moral and legal rights, particularly if derived from cells of human origin. The use of emergence-based principles in M-CELS development may also create unique challenges, making the technology difficult to fully control or predict in the laboratory as well as in applied medical or environmental settings. In response to these challenges, we argue that the M-CELS community has an obligation to systematically address the ethical and societal aspects of research and to seek input from and accountability to a broad range of stakeholders and publics. As a newly developing field, M-CELS has a significant opportunity to integrate ethically responsible norms and standards into its research and development practices from the start. With the aim of seizing this opportunity, we identify two general kinds of salient ethical issues arising from M-CELS research, and then present a set of commitments to and strategies for addressing these issues. If adopted, these commitments and strategies would help define M-CELS as not only an innovative field, but also as a model for responsible research and engineering.
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Affiliation(s)
- Matthew Sample
- Pragmatic Health Ethics Research Unit, Institut de recherches cliniques de Montreal and Department of Neurology and Neurosurgery, McGill University, Canada
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Abstract
The recent de novo assembly of horsepox is an instructive example of an information hazard: published methods enabling poxvirus synthesis led to media coverage spelling out the implications, efficiently disseminating true information that might be used to cause harm. Whether or not the benefits justified the risks, the horsepox saga provides ample reason to upgrade the current system for screening synthesized DNA for hazardous sequences, which does not cover the majority of firms and cannot reliably prevent the assembly of potentially pandemic pathogens. An upgraded system might leverage one-way encryption to confidentially scrutinize virtually all commercial production by a cooperative international network of servers whose integrity can be verified by third parties. Funders could support participating institutions to ease the transition or outright subsidize the market to make clean DNA cheaper, while boycotts by journals, institutions, and funders could ensure compliance and require hardware-level locks on future DNA synthesizers. However, the underlying problem is that security and safety discussions among experts typically follow potentially hazardous events rather than anticipating them. Changing norms and incentives to favor preregistration and advisory peer review of planned experiments could test alternatives to the current closeted research model in select areas of science. Because the fields of synthetic mammalian virology and especially gene drive research involve technologies that could be unilaterally deployed and may self-replicate in the wild, they are compelling candidates for initial trials of early-stage peer review.
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Affiliation(s)
- Kevin M. Esvelt
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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15
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Abstract
This chapter makes the case against performing exceptionally dangerous gain-of-function experiments that are designed to create potentially pandemic and novel strains of influenza, for example, by enhancing the airborne transmissibility in mammals of highly virulent avian influenza strains. This is a question of intense debate over the last 5 years, though the history of such experiments goes back at least to the synthesis of viable influenza A H1N1 (1918) based on material preserved from the 1918 pandemic. This chapter makes the case that experiments to create potential pandemic pathogens (PPPs) are nearly unique in that they present biosafety risks that extend well beyond the experimenter or laboratory performing them; an accidental release could, as the name suggests, lead to global spread of a virulent virus, a biosafety incident on a scale never before seen. In such cases, biosafety considerations should be uppermost in the consideration of alternative approaches to experimental objectives and design, rather than being settled after the fact, as is appropriately done for most research involving pathogens. The extensive recent discussion of the magnitude of risks from such experiments is briefly reviewed. The chapter argues that, while there are indisputably certain questions that can be answered only by gain-of-function experiments in highly pathogenic strains, these questions are narrow and unlikely to meaningfully advance public health goals such as vaccine production and pandemic prediction. Alternative approaches to experimental influenza virology and characterization of existing strains are in general completely safe, higher throughput, more generalizable, and less costly than creation of PPP in the laboratory and can thereby better inform public health. Indeed, virtually every finding of recent PPP experiments that has been cited for its public health value was predated by similar findings using safe methodologies. The chapter concludes that the unique scientific and public health value of PPP experiments is inadequate to justify the unique risks they entail and that researchers would be well-advised to turn their talents to other methodologies that will be safe and more rewarding scientifically.
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Affiliation(s)
- Marc Lipsitch
- Departments of Epidemiology and Immunology and Infectious Diseases, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA, USA.
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16
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Frazar SL, Hund GE, Bonheyo GT, Diggans J, Bartholomew RA, Gehrig L, Greaves M. Defining the Synthetic Biology Supply Chain. Health Secur 2017; 15:392-400. [PMID: 28767286 DOI: 10.1089/hs.2016.0083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several recent articles have described risks posed by synthetic biology and spurred vigorous discussion in the scientific, commercial, and government communities about how to best detect, prevent, regulate, and respond to these risks. The Pacific Northwest National Laboratory's (PNNL) deep experience working with dual-use technologies for the nuclear industry has shown that analysis of supply chains can reveal security vulnerabilities and ways to mitigate security risk without hindering beneficial research and commerce. In this article, a team of experts in synthetic biology, data analytics, and national security describe the overall supply chain surrounding synthetic biology to illustrate new insights about the effectiveness of current regulations, the possible need for different screening approaches, and new technical solutions that could help identify or mitigate risks in the synthetic biology supply chain.
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17
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Farquhar S, Cotton-Barratt O, Snyder-Beattie A. Pricing Externalities to Balance Public Risks and Benefits of Research. Health Secur 2017; 15:401-408. [PMID: 28767274 PMCID: PMC5576218 DOI: 10.1089/hs.2016.0118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
How should scientific funders evaluate research with public health risks? Some risky work is valuable, but accepting too much risk may be ethically neglectful. Recent controversy over H5N1 influenza experiments has highlighted the difficulty of this problem. Advocates of the research claim the work is needed to understand pandemics, while opponents claim that accidents or misuse could release the very pandemic the work is meant to prevent. In an attempt to resolve the debate, the US government sponsored an independent evaluation that successfully produced a quantitative estimate of the risks involved, but only a qualitative estimate of the benefits. Given the difficulties of this “apples-to-oranges” risk-benefit analysis, what is the best way forward? Here we outline a general approach for balancing risks and benefits of research with public risks. Instead of directly comparing risks and benefits, our approach requires only an estimate of risk, which is then translated into a financial price. This estimate can be obtained either through a centrally commissioned risk assessment or by mandating liability insurance, which allows private markets to estimate the financial burden of risky research. The resulting price can then be included in the cost of the research, enabling funders to evaluate grants as usual—comparing the scientific merits of a project against its full cost to society. This approach has the advantage of aligning incentives by assigning costs to those responsible for risks. It also keeps scientific funding decisions in the hands of scientists, while involving the public on questions of values and risk experts on risk evaluation. How should scientific funders evaluate research with public health risks? Some risky work is valuable, but accepting too much risk may be ethically neglectful. Recent controversy over H5N1 influenza experiments has highlighted the difficulty of this problem. The authors outline a general approach for balancing risks and benefits of research with public risks.
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18
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Adam DC, Magee D, Bui CM, Scotch M, MacIntyre CR. Does influenza pandemic preparedness and mitigation require gain-of-function research? Influenza Other Respir Viruses 2017; 11:306-310. [PMID: 28502086 PMCID: PMC5485867 DOI: 10.1111/irv.12458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 11/30/2022] Open
Abstract
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.
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Affiliation(s)
- Dillon C Adam
- School of Public Health and Community Medicine, UNSW, Sydney, NSW, Australia
| | - Daniel Magee
- Biodesign Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Department of Biomedical Informatics, College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Chau M Bui
- School of Public Health and Community Medicine, UNSW, Sydney, NSW, Australia
| | - Matthew Scotch
- School of Public Health and Community Medicine, UNSW, Sydney, NSW, Australia.,Biodesign Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Department of Biomedical Informatics, College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - C Raina MacIntyre
- School of Public Health and Community Medicine, UNSW, Sydney, NSW, Australia.,College of Public Service & Community Solutions, Arizona State University, Tempe, AZ, USA
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Abstract
Working in an area such as influenza is a free ticket into science communication, a pathway aided amply by the amazing evolutionary powers of the virus; regular outbreaks keep the media engaged and the audience keen. Everyone has heard of flu, and they probably already have an opinion: 'I don't take the vaccine, it gives me the flu anyway.' 'Didn't the government waste loads of money on that Tamiflu drug that doesn't work?' 'I've never had flu because I eat a banana every day and sleep with a boiled onion when I've sat next to someone on the train who was coughing.' Such muddled messages and folklore fallacies could be very damaging unless we as scientists stand up and correct them. In addition, there are wider ethical debates around sharing data from clinical trials and the acceptable limits of scientific research to which we must all contribute.
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Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response. J Virol 2017; 91:JVI.02215-16. [PMID: 28100622 PMCID: PMC5355609 DOI: 10.1128/jvi.02215-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/10/2017] [Indexed: 11/20/2022] Open
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 viruses continue to circulate in nature and threaten public health. Although several viral determinants and host factors that influence the virulence of HPAI H5N1 viruses in mammals have been identified, the detailed molecular mechanism remains poorly defined and requires further clarification. In our previous studies, we characterized two naturally isolated HPAI H5N1 viruses that had similar viral genomes but differed substantially in their lethality in mice. In this study, we explored the molecular determinants and potential mechanism for this difference in virulence. By using reverse genetics, we found that a single amino acid at position 158 of the hemagglutinin (HA) protein substantially affected the systemic replication and pathogenicity of these H5N1 influenza viruses in mice. We further found that the G158N mutation introduced an N-linked glycosylation at positions 158 to 160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and induced stronger host immune and inflammatory responses to viral infection. These findings further our understanding of the determinants of pathogenicity of H5N1 viruses in mammals. IMPORTANCE Highly pathogenic avian influenza (HPAI) H5N1 viruses continue to evolve in nature and threaten human health. Key mutations in the virus hemagglutinin (HA) protein or reassortment with other pandemic viruses endow HPAI H5N1 viruses with the potential for aerosol transmissibility in mammals. A thorough understanding of the pathogenic mechanisms of these viruses will help us to develop more effective control strategies; however, such mechanisms and virulent determinants for H5N1 influenza viruses have not been fully elucidated. In this study, we identified glycosylation at positions 158 to 160 of the HA protein of two naturally occurring H5N1 viruses as an important virulence determinant. This glycosylation event enhanced viral productivity, exacerbated the host response, and thereby contributed to the high pathogenicity of H5N1 virus in mice.
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21
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Chan WT, Espinosa M. The Streptococcus pneumoniae pezAT Toxin-Antitoxin System Reduces β-Lactam Resistance and Genetic Competence. Front Microbiol 2016; 7:1322. [PMID: 27610103 PMCID: PMC4997998 DOI: 10.3389/fmicb.2016.01322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
Chromosomally encoded Type II Toxin–Antitoxin operons are ubiquitous in bacteria and archaea. Antitoxins neutralize the toxic effect of cognate Toxins by protein–protein interactions and sequestering the active residues of the Toxin. Toxins target essential bacterial processes, mostly translation and replication. However, one class apart is constituted by the PezAT pair because the PezT toxin target cell wall biosynthesis. Here, we have examined the role of the pezAT toxin–antitoxin genes in its natural host, the pathogenic bacterium Streptococcus pneumoniae. The pezAT operon on Pneumococcal Pathogenicity Island 1 was deleted from strain R6 and its phenotypic traits were compared with those of the wild type. The mutant cells formed shorter chains during exponential phase, leading to increased colony-forming units. At stationary phase, the mutant was more resilient to lysis. Importantly, the mutant exhibited higher resistance to antibiotics targeting cell walls (β-lactams), but not to antibiotics acting at other levels. In addition, the mutants also showed enhanced genetic competence. We suggest that PezAT participates in a subtle equilibrium between loss of functions (resistance to β-lactams and genetic competence) and gain of other traits (virulence).
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Affiliation(s)
- Wai T Chan
- Bacterial Gene Expression and Gene Transfer, Molecular Microbiology and Infectious Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Manuel Espinosa
- Bacterial Gene Expression and Gene Transfer, Molecular Microbiology and Infectious Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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22
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Selgelid MJ. Gain-of-Function Research: Ethical Analysis. SCIENCE AND ENGINEERING ETHICS 2016; 22:923-964. [PMID: 27502512 PMCID: PMC4996883 DOI: 10.1007/s11948-016-9810-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/12/2016] [Indexed: 06/01/2023]
Abstract
Gain-of-function (GOF) research involves experimentation that aims or is expected to (and/or, perhaps, actually does) increase the transmissibility and/or virulence of pathogens. Such research, when conducted by responsible scientists, usually aims to improve understanding of disease causing agents, their interaction with human hosts, and/or their potential to cause pandemics. The ultimate objective of such research is to better inform public health and preparedness efforts and/or development of medical countermeasures. Despite these important potential benefits, GOF research (GOFR) can pose risks regarding biosecurity and biosafety. In 2014 the administration of US President Barack Obama called for a "pause" on funding (and relevant research with existing US Government funding) of GOF experiments involving influenza, SARS, and MERS viruses in particular. With announcement of this pause, the US Government launched a "deliberative process" regarding risks and benefits of GOFR to inform future funding decisions-and the US National Science Advisory Board for Biosecurity (NSABB) was tasked with making recommendations to the US Government on this matter. As part of this deliberative process the National Institutes of Health commissioned this Ethical Analysis White Paper, requesting that it provide (1) review and summary of ethical literature on GOFR, (2) identification and analysis of existing ethical and decision-making frameworks relevant to (i) the evaluation of risks and benefits of GOFR, (ii) decision-making about the conduct of GOF studies, and (iii) the development of US policy regarding GOFR (especially with respect to funding of GOFR), and (3) development of an ethical and decision-making framework that may be considered by NSABB when analyzing information provided by GOFR risk-benefit assessment, and when crafting its final recommendations (especially regarding policy decisions about funding of GOFR in particular). The ethical and decision-making framework ultimately developed is based on the idea that there are numerous ethically relevant dimensions upon which any given case of GOFR can fare better or worse (as opposed to there being necessary conditions that are either satisfied or not satisfied, where all must be satisfied in order for a given case of GOFR to be considered ethically acceptable): research imperative, proportionality, minimization of risks, manageability of risks, justice, good governance (i.e., democracy), evidence, and international outlook and engagement. Rather than drawing a sharp bright line between GOFR studies that are ethically acceptable and those that are ethically unacceptable, this framework is designed to indicate where any given study would fall on an ethical spectrum-where imaginable cases of GOFR might range from those that are most ethically acceptable (perhaps even ethically praiseworthy or ethically obligatory), at one end of the spectrum, to those that are most ethically problematic or unacceptable (and thus should not be funded, or conducted), at the other. The aim should be that any GOFR pursued (and/or funded) should be as far as possible towards the former end of the spectrum.
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Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenza. PLoS Pathog 2016; 12:e1005576. [PMID: 27124727 PMCID: PMC4849778 DOI: 10.1371/journal.ppat.1005576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/23/2016] [Indexed: 12/12/2022] Open
Abstract
Many bacterial species actively take up and recombine homologous DNA into their genomes, called natural competence, a trait that offers a means to identify the genetic basis of naturally occurring phenotypic variation. Here, we describe “transformed recombinant enrichment profiling” (TREP), in which natural transformation is used to generate complex pools of recombinants, phenotypic selection is used to enrich for specific recombinants, and deep sequencing is used to survey for the genetic variation responsible. We applied TREP to investigate the genetic architecture of intracellular invasion by the human pathogen Haemophilus influenzae, a trait implicated in persistence during chronic infection. TREP identified the HMW1 adhesin as a crucial factor. Natural transformation of the hmw1 operon from a clinical isolate (86-028NP) into a laboratory isolate that lacks it (Rd KW20) resulted in ~1,000-fold increased invasion into airway epithelial cells. When a distinct recipient (Hi375, already possessing hmw1 and its paralog hmw2) was transformed by the same donor, allelic replacement of hmw2AHi375 by hmw1A86-028NP resulted in a ~100-fold increased intracellular invasion rate. The specific role of hmw1A86-028NP was confirmed by mutant and western blot analyses. Bacterial self-aggregation and adherence to airway cells were also increased in recombinants, suggesting that the high invasiveness induced by hmw1A86-028NP might be a consequence of these phenotypes. However, immunofluorescence results found that intracellular hmw1A86-028NP bacteria likely invaded as groups, instead of as individual bacterial cells, indicating an emergent invasion-specific consequence of hmw1A-mediated self-aggregation. Many bacteria are naturally competent, actively taking up DNA from their surroundings and incorporating it into their genomes by homologous recombination. This cellular process has had a large impact on the evolution of these species, for example by enabling pathogens to acquire virulence factors and antibiotic resistances from their relatives. But natural competence can also be exploited by researchers to identify the underlying genetic variation responsible for naturally varying phenotypic traits, similar to how eukaryotic geneticists use meiotic recombination during sexual reproduction to create genetically admixed populations. Here we exploited natural competence, phenotypic selection, and deep sequencing to rapidly identify the hmw1 locus as a major contributor to intracellular invasion of airway epithelial cells by the human pathogen Haemophilus influenzae, a trait that likely allows bacterial cells to evade the immune system and therapeutic interventions during chronic infections. Genetic variation in this locus can strongly modulate bacterial intracellular invasion rates, and possession of a certain allele favors adhesion and self-aggregation, which appear to prompt bacteria to invade airway cells as groups, rather than as individuals. Overall, our findings indicate that targeting HMW1 could block the ability of H. influenzae to invade airway cells, which would make antibiotic therapy to treat chronic lung infections more effective. Furthermore, our new approach to identifying the genetic basis of natural phenotypic variation is applicable to a wide-range of phenotypically selectable traits within the widely distributed naturally competent bacterial species, including pathogenesis traits in many human pathogens.
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Buller RM, Connell ND, Morse SS, Campbell M, Tait RC. Strengthening the role of the IBC in the 21st century. ENSURING NATIONAL BIOSECURITY 2016. [PMCID: PMC7149545 DOI: 10.1016/b978-0-12-801885-9.00013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The US government (USG) has not fully implemented a robust system to evaluate dual-use research (DUR). In particular, the USG has failed to effectively fund, support, and expand the role of the local Institutional Biosafety Committee in the oversight of DUR and in the changing scientific landscape; a comprehensive education program for all in life sciences research with regard to the dual-use dilemma has not been forthcoming; and finally, there has been no systematic evaluation of the impact of USG policy, regulations, and guidance on an institution’s cost structure and on scientific discovery. We detail our judgments on current USG DUR policy and provide recommendations for future oversight of DUR from our perspective as senior administrators and laboratory scientists charged with the responsibility of conducting life-sciences research in an era of increasing regulatory requirements and decreasing federal support.
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What Lies Ahead? VIRAL PATHOGENESIS 2016. [PMCID: PMC7149599 DOI: 10.1016/b978-0-12-800964-2.00022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Viral pathogenesis is a field in rapid evolution, reflecting the dynamic development of systems biology and the continuing introduction of new or improved methodologies. Therefore, this final chapter is dedicated to “futurism,” a look at what lies ahead for this field. We have recruited a number of scientists to write short pieces where they are free to speculate on future developments in their respective areas of expertise.
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Inglesby TV, Relman DA. How likely is it that biological agents will be used deliberately to cause widespread harm? Policymakers and scientists need to take seriously the possibility that potential pandemic pathogens will be misused. EMBO Rep 2015; 17:127-30. [PMID: 26682799 DOI: 10.15252/embr.201541674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Thomas V Inglesby
- Center for Health Security, University of Pittsburgh Medical Center, Baltimore, MD, USA University of Pittsburgh Schools of Medicine and Public Health, Pittsburgh, PA, USA
| | - David A Relman
- Departments of Microbiology and Immunology, and Medicine, and Center for International Security and Cooperation, Stanford University, Stanford, CA, USA
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27
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Dermody TS, Pfeiffer JK. Genetics in Virology Research. Annu Rev Virol 2015; 2:vii-x. [PMID: 29084487 DOI: 10.1146/annurev-vi-2-102915-100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Terence S Dermody
- Department of Pediatrics, 2Department of Pathology, Microbiology, and Immunology, and 3Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, Tennessee 37232;
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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28
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Kilianski A, Murch RS. When gain-of-function research is not "gain-of-function" research. EMBO Rep 2015; 16:1586-7. [PMID: 26538418 DOI: 10.15252/embr.201541617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Andy Kilianski
- Biodefense Branch, BioSciences Division, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Randall S Murch
- Office of the Vice President National Capital Region, Arlington, VA, USA School of Public and International Affairs, Arlington, VA, USA Department of Plant Pathology, Physiology and Weed Science, Virginia Tech University, Arlington, VA, USA
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29
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Kilianski A, Nuzzo JB, Modjarrad K. Gain-of-Function Research and the Relevance to Clinical Practice. J Infect Dis 2015; 213:1364-9. [PMID: 26416657 PMCID: PMC7107371 DOI: 10.1093/infdis/jiv473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/02/2015] [Indexed: 11/13/2022] Open
Abstract
The ongoing moratorium on gain-of-function (GOF) research with highly pathogenic avian influenza virus, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus has drawn attention to the current debate on these research practices and the potential benefits and risks they present. While much of the discussion has been steered by members of the microbiology and policy communities, additional input from medical practitioners will be highly valuable toward developing a broadly inclusive policy that considers the relative value and harm of GOF research. This review attempts to serve as a primer on the topic for the clinical community by providing a historical context for GOF research, summarizing concerns about its risks, and surveying the medical products that it has yielded.
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Affiliation(s)
- Andy Kilianski
- BioDefense Branch, Biosciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground
| | - Jennifer B Nuzzo
- University of Pittsburgh Medical Center-Center for Health Security, Baltimore
| | - Kayvon Modjarrad
- US Military HIV Research Program, Walter Reed Army Institute for Research, Silver Spring, Maryland
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30
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Frank GM, Adalja A, Barbour A, Casadevall A, Dormitzer PR, Duchin J, Hayden FG, Hirsch MS, Hynes NA, Lipsitch M, Pavia AT, Relman DA. Infectious Diseases Society of America and Gain-of-Function Experiments With Pathogens Having Pandemic Potential. J Infect Dis 2015; 213:1359-61. [PMID: 26416656 PMCID: PMC7313907 DOI: 10.1093/infdis/jiv474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 11/17/2022] Open
Affiliation(s)
| | - Amesh Adalja
- UPMC Center for Health Security, University of Pittsburgh Medical Center, Pennsylvania
| | - Alan Barbour
- Department of Medicine, University of California-Irvine Department of Microbiology and Molecular Genetics, University of California-Irvine
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Baltimore, Maryland
| | | | - Jeff Duchin
- Public Health-Seattle and King County, Seattle University of Washington, Seattle
| | | | - Martin S Hirsch
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School
| | - Noreen A Hynes
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Marc Lipsitch
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Andrew T Pavia
- Department of Pediatrics, Primary Children's Medical Center, University of Utah School of Medicine, Salt Lake City
| | - David A Relman
- Department of Medicine, Center for International Security and Cooperation at Stanford University, California Department of Microbiology and Immunology, Center for International Security and Cooperation at Stanford University, California
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Abstract
The 1977-1978 influenza epidemic was probably not a natural event, as the genetic sequence of the virus was nearly identical to the sequences of decades-old strains. While there are several hypotheses that could explain its origin, the possibility that the 1977 epidemic resulted from a laboratory accident has recently gained popularity in discussions about the biosafety risks of gain-of-function (GOF) influenza virus research, as an argument for why this research should not be performed. There is now a moratorium in the United States on funding GOF research while the benefits and risks, including the potential for accident, are analyzed. Given the importance of this historical epidemic to ongoing policy debates, we revisit the evidence that the 1977 epidemic was not natural and examine three potential origins: a laboratory accident, a live-vaccine trial escape, or deliberate release as a biological weapon. Based on available evidence, the 1977 strain was indeed too closely matched to decades-old strains to likely be a natural occurrence. While the origin of the outbreak cannot be conclusively determined without additional evidence, there are very plausible alternatives to the laboratory accident hypothesis, diminishing the relevance of the 1977 experience to the modern GOF debate.
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Coelho AC, García Díez J. Biological Risks and Laboratory-Acquired Infections: A Reality That Cannot be Ignored in Health Biotechnology. Front Bioeng Biotechnol 2015; 3:56. [PMID: 25973418 PMCID: PMC4412124 DOI: 10.3389/fbioe.2015.00056] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/10/2015] [Indexed: 12/16/2022] Open
Abstract
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.
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Affiliation(s)
- Ana Cláudia Coelho
- Department of Veterinary Sciences, Veterinary and Animal Science Center (CECAV), School of Agrarian and Veterinary Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Juan García Díez
- Department of Veterinary Sciences, Veterinary and Animal Science Center (CECAV), School of Agrarian and Veterinary Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
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Schoch-Spana M. Public engagement and the governance of gain-of-function research. Health Secur 2015; 13:69-73. [PMID: 25813979 DOI: 10.1089/hs.2015.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The White House recently called for a "robust and broad deliberative process" to assess the risks and benefits of select gain-of-function studies, pausing current experiments and further grants until new federal policy on research funding and oversight is developed. At issue is whether and under what conditions laboratory studies that enhance the transmissibility and/or virulence of potential pandemic pathogens such as the H5N1 avian influenza virus should go forward. To date, professionals from medicine, public health, and the life sciences have dominated the debate, and each side of the controversy has cited the public's well-being as the principal motivator for their position. A major stakeholder, the general public, has not yet actively and systematically weighed in on the matter. This commentary considers in what form and with what benefit public participation may materialize in the current debate regarding the governance of gain-of-function research.
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Is the debate and "pause" on experiments that alter pathogens with pandemic potential influencing future plans of graduate students and postdoctoral fellows? mBio 2015; 6:mBio.02525-14. [PMID: 25604793 PMCID: PMC4313916 DOI: 10.1128/mbio.02525-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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