Potential Pandemic Pathogens Research Articles

Balancing Innovation and Safety: Frameworks and Considerations for the Governance of Dual-Use Research of Concern and Potential Pandemic Pathogens

Balancing Innovation and Safety: Frameworks and Considerations for the Governance of Dual-Use Research of Concern and Potential Pandemic Pathogens

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

This study provides empirical data on the knowledge and practices of biosafety and biosecurity professionals and researchers involved in research on enhanced Potential Pandemic Pathogens (ePPPs) and Dual Use Research of Concern (DURC) within various U.S. sectors. The goal is to improve public health interventions and oversight for DURC and ePPP, contributing valuable insights for policy development. A notable finding was the association between larger biosafety/biosecurity teams and a higher likelihood of conducting high-risk biological research. A survey of 541 biosafety and biosecurity professionals was conducted between March 8 and 10 April 2024, with results analyzed using SAS at a significance level of 0.05. The study received approval from the Institutional Review Boards (IRBs) at Arizona State University and the University of Nevada, Reno. Government organizations were more likely to conduct DURC compared to other sectors (e.g., Academic, Commercial, Consulting). Public institutions reviewed more experiments outside the scope of the U.S. DURC Policy than private for-profit institutions. Institutions with larger biosafety/biosecurity teams reported greater research activity and more effective non-compliance reporting mechanisms (e.g., anonymous hotlines, reporting forms). Additionally, financial support and the challenges of policy implementation varied significantly across sectors. The findings emphasize the need for appropriate staffing and resource allocation for high-risk biosafety and biosecurity research. A differentiated regulatory approach and equitable distribution of resources are essential for effective oversight. Moreover, robust non-compliance reporting systems are critical to mitigating the risks associated with DURC and ePPP research.

Call for Volume 30 (2025) Special Issue Papers: Biosafety and Biosecurity for Potential Pandemic Pathogens and Dual-Use Research of Concern: Deadline for Manuscript Submission: October 31, 2024.

Call for Volume 30 (2025) Special Issue Papers: Biosafety and Biosecurity for Potential Pandemic Pathogens and Dual-Use Research of Concern: Deadline for Manuscript Submission: October 31, 2024.

Reply to Ebright et al., "Implementing governmental oversight of enhanced potential pandemic pathogen research".

Reply to Ebright et al., "Implementing governmental oversight of enhanced potential pandemic pathogen research".

Future pandemics and the urge to ‘do something’

Research with enhanced potential pandemic pathogens (ePPP) makes pathogens substantially more lethal, communicable, immunosuppressive or otherwise capable of triggering a pandemic. We briefly relay an existing argument that the benefits...

Enterovirus D68 3C protease antagonizes type I interferon signaling by cleaving signal transducer and activator of transcription 1.

Following the successful control of poliovirus, the re-emergence of respiratory enterovirus D68 (EV-D68), a prominent non-polio enterovirus, has become a serious public health concern worldwide. Host innate immune responses are the primary defense against EV-D68 invasion; however, the mechanism underlying viral evasion of the antiviral activity of interferons (IFN) remains unclear. In this study, we found that EV-D68 inhibited type I IFN signaling by cleaving signal transducer and activator of transcription 1 (STAT1), a crucial factor in cellular responses to interferons and other cytokines. We observed that the prototype and circulating EV-D68 strains conserved their ability to induce STAT1 cleavage and attenuate IFN signal transduction. Further investigation revealed that EV-D68 3C protease cleaves STAT1 at the 131Q residue. Interestingly, not all enterovirus-encoded 3C proteases exhibited this ability. EV-D68 and poliovirus 3C proteases efficiently induced STAT1 cleavage; whereas, 3C proteases from EV-A71, coxsackievirus A16, and echoviruses did not. STAT1 cleavage also abolished the nuclear translocation capacity of STAT1 in response to IFN stimulation to activate downstream signaling elements. Overall, these results suggest that STAT1, targeted by viral protease 3C, is utilized by EV-D68 to subvert the host's innate immune response.IMPORTANCEEnterovirus D68 (EV-D68) has significantly transformed over the past decade, evolving from a rare pathogen to a potential pandemic pathogen. The interferon (IFN) signaling pathway is an important defense mechanism and therapeutic target for the host to resist viral invasion. Previous studies have reported that the EV-D68 virus blocks or weakens immune recognition and IFN production in host cells through diverse strategies; however, the mechanisms of EV-D68 resistance to IFN signaling have not been fully elucidated. Our study revealed that EV-D68 relies on its own encoded protease, 3C, to directly cleave signal transducer and activator of transcription 1 (STAT1), a pivotal transduction component in the IFN signaling pathway, disrupting the IFN-mediated antiviral response. Previous studies on human enteroviruses have not documented direct cleavage of the STAT1 protein to evade cellular immune defenses. However, not all enteroviral 3C proteins can cleave STAT1. These findings highlight the diverse evolutionary strategies different human enteroviruses employ to evade host immunity.

Recommendations to Strengthen the US Government's Enhanced Potential Pandemic Pathogen Framework and Dual Use Research of Concern Policies

Recommendations to Strengthen the US Government's Enhanced Potential Pandemic Pathogen Framework and Dual Use Research of Concern Policies

The Arenaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens.

Lassa virus (LASV), Junin virus (JUNV), and several other members of the Arenaviridae family are capable of zoonotic transfer to humans and induction of severe viral hemorrhagic fevers. Despite the importance of arenaviruses as potential pandemic pathogens, numerous gaps exist in scientific knowledge pertaining to this diverse family, including gaps in understanding replication, immunosuppression, receptor usage, and elicitation of neutralizing antibody responses, that in turn complicates development of medical countermeasures. A further challenge to the development of medical countermeasures for arenaviruses is the requirement for use of animal models at high levels of biocontainment, where each model has distinct advantages and limitations depending on, availability of space, animals species-specific reagents, and most importantly the ability of the model to faithfully recapitulate human disease. Designation of LASV and JUNV as prototype pathogens can facilitate progress in addressing the public health challenges posed by members of this important virus family.

Recombination between coronaviruses and synthetic RNAs and biorisk implications motivated by a SARS-CoV-2 FCS origin controversy.

The urgent need for improved policy, regulation, and oversight of research with potential pandemic pathogens (PPPs) has been widely acknowledged. A 2022 article in Frontiers in Virology raises questions, reporting on a 100% sequence homology between the SARS-CoV-2 furin cleavage site (FCS) and the negative strand of a 2017 patented sequence. Even though Ambati and collaborators suspect a possible inadvertent or intentional cause leading to the FCS insert, the related underpinnings have not been studied from the perspective of potential biorisk policy gaps. A commentary on their article contests the low coincidence likelihood that was calculated by Ambati et al., arguing that the sequence match could have been a chance occurrence alone. Additionally, it has been suggested that the odds of the recombination event may be low. These considerations seem to have put many speculations related to any implied viral beginnings, notably from a research setting likely outside the Wuhan Institute of Virology, to rest. However, potential implications for future disasters in terms of biosafety and biosecurity have not been addressed. To demonstrate the feasibility of the Ambati et al. postulate, a theoretical framework is developed that substantially extends the research orientations implicated by these authors and the related patent. It is argued that specific experimental conditions, in combination, could significantly increase the implied recombination profile between coronaviruses and synthetic RNAs. Consequently, this article scrutinizes these largely unrecognized vulnerabilities to discuss implications across the spectrum of the biological risk landscape, with special attention to a potential "crime harvest." Focusing on insufficiently understood features of interaction between the natural and man-made world, vulnerabilities related to contaminants, camouflaging, and various misuse potentials fostered by the digitization and computerization of synthetic biology, it highlights novel biorisk gaps not covered by existing PPP policy. Even though this work does not aim to provide proof of the viral origin, it will make the point that, in theory, a convergence of under-appreciated lab experiments and technologies could have led to the SARS-CoV-2 FCS insert, which analogously could be exploited by various threat actors for the clandestine genesis of similar or even worse pathogens.

Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens.

The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last 20 years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare the dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) that bundles nucleotide identity, recombination, and phylogenetic analysis into a single pipeline. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from undersampled or unsampled lineages, including in typically highly conserved regions of the genome. In several cases, no parental origin of recombinant regions could be found in genetic databases, demonstrating our shallow characterization of coronavirus diversity and expanding the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.

Reconsidering the need for gain-of-function research on enhanced potential pandemic pathogens in the post-COVID-19 era.

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.

Dual-use research on modified pathogens in the laboratory: What framework for what issue?

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.

Viral Environmental Warfare: Technology Bill of Rights Critically Needed

The ongoing “hidden in plain sight” geoengineering operations including the pervasive, near global spraying of ultrafine particles into the troposphere pose an existential risk to the biosphere and humanity. Likewise, bioengineering and genetic manipulation of potential pandemic pathogens with associated accidental or deliberate release represents a dire risk to the modern world. Compelling evidence to date indicates that the chimeric structure and added furin cleavage site of SARS-CoV-2 was the result of human manipulation in the laboratory. Coronavirus and vaccine patents indicate a foreknowledge of the COVID-19 pandemic, which conveniently serves the interests of the global elites. The new COVID-19 vaccines, hailed as the answer to the pandemic, have potential toxicity, fail to prevent transmission, drive the development of new variants, and over time may predispose recipients to antibody-dependent enhancement (ADE) of infection. Other important technological threats include Internet-based censorship, nano-particulate pollution, electro-pollution and the massive amounts of electromagnetic energy inflicted on humans and Earth’s natural environment. A Technology Bill of Rights is critically needed to protect humanity and salvage what remains of earth’s life support systems.

System-oriented optimization of multi-target 2,6-diaminopurine derivatives: Easily accessible broad-spectrum antivirals active against flaviviruses, influenza virus and SARS-CoV-2.

The worldwide circulation of different viruses coupled with the increased frequency and diversity of new outbreaks, strongly highlight the need for new antiviral drugs to quickly react against potential pandemic pathogens. Broad-spectrum antiviral agents (BSAAs) represent the ideal option for a prompt response against multiple viruses, new and re-emerging. Starting from previously identified anti-flavivirus hits, we report herein the identification of promising BSAAs by submitting the multi-target 2,6-diaminopurine chemotype to a system-oriented optimization based on phenotypic screening on cell cultures infected with different viruses. Among the synthesized compounds, 6i showed low micromolar potency against Dengue, Zika, West Nile and Influenza A viruses (IC50 = 0.5–5.3 μM) with high selectivity index. Interestingly, 6i also inhibited SARS-CoV-2 replication in different cell lines, with higher potency on Calu-3 cells that better mimic the SARS-CoV-2 infection in vivo (IC50 = 0.5 μM, SI = 240). The multi-target effect of 6i on flavivirus replication was also analyzed in whole cell studies (in vitro selection and immunofluorescence) and against isolated host/viral targets.

Structure of the multiple functional domains from coronavirus nonstructural protein 3

ABSTRACT Coronaviruses (CoVs) are potential pandemic pathogens that can infect a variety of hosts and cause respiratory, enteric, hepatic and neurological diseases. Nonstructural protein 3 (nsp3), an essential component of the replication/transcription complex, is one of the most important antiviral targets. Here, we report the first crystal structure of multiple functional domains from porcine delta-coronavirus (PDCoV) nsp3, including the macro domain (Macro), ubiquitin-like domain 2 (Ubl2) and papain-like protease (PLpro) catalytic domain. In the asymmetric unit, two of the subunits form the head-to-tail homodimer with an interaction interface between Macro and PLpro. However, PDCoV Macro-Ubl2-PLpro mainly exists as a monomer in solution. Then, we conducted fluorescent resonance energy transfer-based protease assays and found that PDCoV PLpro can cleave a peptide by mimicking the cognate nsp2/nsp3 cleavage site in peptide substrates and exhibits deubiquitinating and de-interferon stimulated gene(deISGylating) activities by hydrolysing ubiquitin-7-amino-4-methylcoumarin (Ub-AMC) and ISG15-AMC substrates. Moreover, the deletion of Macro or Macro-Ubl2 decreased the enzyme activity of PLpro, indicating that Macro and Ubl2 play important roles in maintaining the stability of the PLpro domain. Two active sites of PLpro, Cys260 and His398, were determined; unexpectedly, the conserved site Asp412 was not the third active site. Furthermore, the motif “NGYDT” (amino acids 409–413) was important for stabilizing the enzyme activity of PLpro, and the N409A mutant significantly decreased the enzyme activity of PLpro. These results provide novel insights into the replication mechanism of CoV and new clues for future drug design.

The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19.

Type I interferons (IFN-I) were first discovered over 60 years ago in a classical experiment by Isaacs and Lindenman, who showed that IFN-Is possess antiviral activity. Later, it became one of the first approved protein drugs using heterologous protein expression systems, which allowed its large-scale production. It has been approved, and widely used in a pleiotropy of diseases, including multiple-sclerosis, hepatitis B and C, and some forms of cancer. Preliminary clinical data has supported its effectiveness against potential pandemic pathogens such as Ebola and SARS. Still, more efficient and specific drugs have taken its place in treating such diseases. The COVID-19 global pandemic has again lifted the status of IFN-Is to become one of the more promising drug candidates, with initial clinical trials showing promising results in reducing the severity and duration of the disease. Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I–receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Furthermore, I discuss how these may guide the optimized use IFN-Is in combatting COVID-19.

Brave New World: Omens and Opportunities in the Age of COVID-19

In this inaugural issue of IJVTPR, the authors have focused on a variety of themes that are intended to highlight some of the ongoing controversies in the vaccine literature, controversies that have been made all the more acute by the emergence of COVID-19. With this pandemic have come societal disruptions that have caused governments around the globe to move rapidly to “state of exception” measures. It is at times such as this, that independent scholarly research is most urgently needed. The current issue is our opening salvo that attempts to bring rigorous independent and unbiased research to the subject of vaccine safety and analysis. The article by Shaw looks at how the process that has governed scientific review for centuries — peer review — has been corrupted in an attempt to sanitize the literature in order to remove studies that do not conform to a corporate line. It seems certain that in the new age of COVID-19, such measures will only increasingly harm and obscure honest science. The paper by Oller et al. follows up on the 2017 article about the apparent distribution of a World Health Organization anti-fertility vaccine represented as a prophylactic for maternal and neonatal tetanus. The article by David Lewis takes an important alternative look at potential etiological factors that might contribute to the rising prevalence of autism, factors that are not per se the direct result of vaccination but that involve some of the pathogens and components from that industry. Next, Sin Hang Lee takes an intensive critical look at the components in Gardasil9. It is a vaccine deploying gene-edited recombinant capsid L1 proteins converted to virus like particles to stimulate immunity against human papilloma viruses of types 6, 11, 16, 18, 31, 33, 45, 52, and 58. In theory it also requires one or more strong adjuvants to jump start the generation of antibodies against the various viruses. Because Lee’s paper addresses an application of gene editing research in vaccine development, it adumbrates our next issue in which we intend to address so-called “dual use” and “gain of function” research with potential pandemic pathogens preceding the present COVID-19 pandemic.

Proposed Changes to U.S. Policy on Potential Pandemic Pathogen Oversight and Implementation.

We propose here changes to the U.S. government policy on potential pandemic pathogen (PPP) oversight and implementation, emphasizing transparency of the review process and the content of the review, publication of the review in advance, responsible publication of enhanced PPP research, high-level signoff on approvals of enhanced PPP experiments, and the need for a significant effort to establish a common international approach to enhanced PPP work. We advocate that the U.S. government recommend, and non-U.S. government funders and journals adopt, a set of best practices that would extend important considerations of biosafety and biosecurity to all work on enhanced potential pandemic pathogens regardless of funding source.

Is regulation preventing the development of therapeutics that may prevent future coronavirus pandemics?

Is regulation preventing the development of therapeutics that may prevent future coronavirus pandemics?

Ethical and Philosophical Considerations for Gain-of-Function Policy: The Importance of Alternate Experiments.

The Department of Health and Human Services Framework for Guiding Funding Decisions about Proposed Research Involving Enhanced Potential Pandemic Pathogens (PPPs) contains a series of principles for governing the funding and conduct of gain-of-function (GOF) research resulting in the creation of PPPs. In this article, I address one of these principles, governing the replacement of GOF research with alternate experiments. I argue that the principle fails to address the way that different experiments can promote the same values as those promoted by GOF research resulting in PPPs. I then address some objections to this claim, and provide policy recommendations moving forward.