A central tenet of medical ethics holds that it is permissible to perform a medical intervention on a competent individual only if that individual has given informed consent to the intervention. However, in some circumstances it is tempting to say that the moral reason to obtain informed consent prior to administering a medical intervention is outweighed. For example, if an individual’s refusal to undergo a medical intervention would lead to the transmission of a dangerous infectious disease to (...) other members of the community, one might claim that it would be morally permissible to administer the intervention even in the absence of consent. Indeed, as we shall discuss below, there are a number of examples of public health authorities implementing compulsory or coercive measures for the purposes of infectious disease control (IDC). The plausibility of the thought that non-consensual medical interventions might be justified when performed for the purpose of IDC raises the question of whether such interventions might permissibly be used to realize other public goods. In this article we focus on one possibility: whether it could be permissible to non-consensually impose certain interventions that alter brain states or processes through chemical or physical means on serious criminal offenders. We shall suggest that some such interventions might be permissible if they safely and effectively serve to facilitate the offender’s rehabilitation and thereby prevent criminal recidivism. (shrink)

Antimicrobial resistance (AMR) is a global public health disaster driven largely by antibiotic use in human health care. Doctors considering whether to prescribe antibiotics face an ethical conflict between upholding individual patient health and advancing public health aims. Existing literature mainly examines whether patients awaiting consultations desire or expect to receive antibiotic prescriptions, but does not report views of the wider public regarding conditions under which doctors should prescribe antibiotics. It also does not explore the ethical significance of public views (...) or their sensitivity to awareness of AMR risks or the standpoint (self-interested or impartial) taken by participants. Methods: An online survey was conducted with a sample of the U.S. public (n = 158). Participants were asked to indicate what relative priority should be given to individual patients and society-at-large from various standpoints and in various contexts, including antibiotic prescription. Results: Of the participants, 50.3% thought that doctors should generally prioritize individual patients over society, whereas 32.0% prioritized society over individual patients. When asked in the context of AMR, 39.2% prioritized individuals whereas 45.5% prioritized society. Participants were significantly less willing to prioritize society over individuals when they themselves were the patient, both in general (p = .001) and in relation to AMR specifically (p = .006). Conclusions: Participants’ attitudes were more oriented to society and sensitive to collective responsibility when informed about the social costs of antibiotic use and when considered from a third-person rather than first-person perspective. That is, as participants came closer to taking the perspective of an informed and impartial “ideal observer,” their support for prioritizing society increased. Our findings suggest that, insofar as antibiotic policies and practices should be informed by attitudes that are impartial and well-informed, there is significant support for prioritizing society. (shrink)

The study investigated ethical considerations and science diplomacy on coronavirus disease (Covid-19) pandemic in Nigeria. The outbreak of the coronavirus disease (Covid-19) in Nigeria has spread quickly to about 34 states out of the 36 states and over 5000 persons have tested positive as at the time of this research after the first index case of an Italian and there is a projection that in coming days and weeks the number of infected persons and states will increase. The (...) study was guided by two objectives and also adopted the normative ethical theory. The study employed the methods of exposition and critical analysis to explain better the ethical issues and science diplomacy of Covid-19 pandemic in Nigeria. Data was sourced from secondary sources such as journal articles, newspaper, books and internet sources. The findings of the study showed that the citizens have some obligations that will aid the containment of the virus and as well as the government. The study also found out that science diplomacy was used, which has led to Nigeria collaborating with China to get medical aids to effectively fight the pandemic. Consequently, the study recommended amongst others that the Ministry of Health and the Nigeria Center for Disease Control (NCDC) should adopt and enforce the World Health Organization (WHO) Guidance for Managing Ethical Issues in Infectious Disease Outbreak as a working document in crisis like the Covid-19 pandemic that has ravaged Nigeria and the government should involve more in science diplomacy with other countries so that it will help in the fight against Covid-19 and other diseases that may occur in the future. (shrink)

The Covid-19 pandemic raises the need for an ethical framework addressing unique questions of airborne infectious disease. In particular, are you ethically obliged to wear a face mask? If so, why and when? The Respiratory Ethics Framework (REF) herein derives answers from ethical norms. Always covering coughs and sneezes just in case you might be infectious is an ethical norm. But if you are infectious with an airborne illness, you are probably spreading germs even with (...) every breath and vocalization. Therefore, given that respiratory covering should be done to prevent spreading germs, you should wear a mask if you believe you are infectious because it also provides covering while breathing and vocalizing. REF is grounded in the non-harm principle. Why should we avoid spreading infections to others? Because they can cause bodily physical harm and we should act to prevent causing such harm to others without justifiable reason. Under REF, the magnitude of your obligation to mask is proportional to the magnitude of risk you pose to others by way of airborne germs. This functional relationship is logically modeled and visually mapped with a decision matrix in this essay. (shrink)

The genetic modification of pigs as a source of transplantable organs is one of several possible solutions to the chronic organ shortage. This paper describes existing ethical tensions in xenotransplantation (XTx) that argue against pursuing it. Recommendations for lifelong infectious disease surveillance and notification of close contacts of recipients are in tension with the rights of human research subjects. Parental/guardian consent for pediatric xenograft recipients is in tension with a child’s right to an open future. Individual consent to (...) transplant is in tension with public health threats that include zoonotic diseases. XTx amplifies concerns about justice in organ transplantation and could exacerbate existing inequities. The prevention of infectious disease in source animals is in tension with the best practices of animal care and animal welfare, requiring isolation, ethologically inappropriate housing, and invasive reproductive procedures that would severely impact the well-being of intelligent social creatures like pigs. (shrink)

The potential for vaccines to prevent the spread of infectious diseases is crucial for vaccination policy and ethics. In this paper, I discuss recent evidence that the current COVID-19 vaccines have only a modest and short-lived effect on reducing SARS-CoV-2 transmission and argue that this has at least four important ethical implications. First, getting vaccinated against COVID-19 should be seen primarily as a self-protective choice for individuals. Second, moral condemnation of unvaccinated people for causing direct harm to others (...) is unjustified. Third, the case for a harm-based moral obligation to get vaccinated against COVID-19 is weak. Finally, and perhaps most significantly, coercive COVID-19 vaccination policies (e.g., measures that exclude unvaccinated people from society) cannot be directly justified by the harm principle. (shrink)

This dissertation explores the idea and ethics of vaccination for the sake of others. It conceptually distinguishes four different kinds of vaccination—self-protective, paternalistic, altruistic, and indirect—based on who receives the primary benefits of vaccination and who ultimately makes the vaccination decision. It describes the results of focus group studies that were conducted to investigate what people who might get vaccinated altruistically think of this idea. It also applies the different kinds of vaccination to ethical issues surrounding COVID-19, such as (...) lockdown measures, routine or mandatory vaccination of healthy children, and the ethical justification of restrictive measures for unvaccinated people. A more general philosophical account of vaccination ethics is ultimately developed, which is based not on moral duties, but on the moral reasons that people may have to get vaccinated for the sake of others. It is argued that such reasons may be stronger or weaker, depending on various factors related to the vaccines in question and the specific epidemiological circumstances. (shrink)

Over 60% of all epidemics have a zoonotic origin, that is, they result from the transmission of infectious diseases from animals to humans. The spill-over of diseases often happens because humans exploit and use animals. In this article, I outline the four most common interfaces that favour the emergence and spread of zoonotic infectious diseases: wildlife hunting, small-scale farming, industrialised farming practices and live animal markets. I analyse which practices serve human food security – and thus have a (...) non-trivial purpose – and which predominantly have an economic purpose or serve as a symbol of wealth. I conclude that many practices that increase the risk for zoonotic infectious disease outbreaks actually do not contribute to the survival and food security of humans. I make two arguments in turn. First, I argue that in cases where the consumption and use of animal products does not contribute to the food security of a population, then this population has a duty to abstain from them, since they impose a grave and avoidable risk to themselves as well as to innocent third-parties. However, some communities must sometimes rely on practices that increase the risk of emergence and transmission of zoonotic infectious diseases, because they have no healthy alternatives. That is, the food security of the local population depends on the consumption and use of risky animal products. The second argument I advance is that, in such scenarios, the international community has a duty to provide the communities concerned with alternative food options, as well as economic and educational opportunities and technologies, in order to reduce the spill-over risk of infectious diseases. Given that abstention from such practices contributes signifcantly to the public good and benefits the international community, the latter has a corresponding duty to provide local communities which abandon such practices with alternatives. (shrink)

The COVID-19 pandemic has coincided with the proliferation of ethical guidance documents to assist public health authorities, health care providers, practitioners and staff with responding to ethical challenges posed by the pandemic. Like ethical guidelines relating to infectious disease that have preceded them, what unites many COVID-19 guidance documents is their dependency on an under-developed approach to bioethical principlism, a normative framework that attempts to guide actions based on a list of prima facie, unranked ethical principles. By situating (...) them in relation to the key philosophical debates concerning bioethical principlism, we aim to explore the limits and limitations of pandemic ethical guidance documents as, specifically, ethics documents – documents that fulfil the functions of ethics as a fundamentally normative discipline. This means not only determining whether such ethical guidance documents can, in principle, provide adequate action guidance and action justification, but also, more importantly where pandemics are concerned, determining whether they support consistent decision making and transparent processes of justification. Having highlighted the problems with merely furnishing ethical guidelines with substantive ethical content in terms of principles and values, we argue that organizations that develop these documents should, instead, focus on the procedural dimensions of action guidance and action justification, which extend to questions regarding the make-up of the committees, panels and groups that develop such guidelines, the public transparency of justifications for specific pandemic-related advice or interventions and the development of explicit procedures for transparent and consistent decision making. (shrink)

The Covid-19 pandemic raises the need for an ethical framework that addresses the unique ethical challenges and questions arising from airborne infectious diseases. For example, are we ever ethically obliged to wear a face mask? If so, why and when? The Respiratory Ethics Framework (REF) herein proposes pathways to answers grounded in ethical norms and the moral principles of non-harm, beneficence and respect for personal autonomy. REF is a personal ethics wherein your ethical duty to increase your (...) respiratory hygiene efforts—such as by donning a mask—is proportional to your estimation of an increase in the likelihood that your respiratory effluent poses a risk of harmful infection to others. REF includes illustrated decision models that instantiate a framework of proportionality between levels of risk, ethical duty and mitigation that shapes risk mitigation across domains. (shrink)

Concerns about emerging and re-emerging infectious diseases have given a new lease of life to quarantinist measures: a series of time-honoured techniques for controlling the spread of infectious diseases through breaking the chain of human contagion. Since such measures typically infringe individual rights or privacy their use is subject to legal regulations and gives rise to ethical and political worries and suspicions. Yet in some circumstances they can be very effective. After considering some case studies that show how (...) epidemics are unique, fluid and affected by a multitude of contingent factors, it is argued that the legal and ethical guidelines may not always be the best approach to discipline the use of quarantinist measures. An alternative model based on ex-post political accountability for reasonableness is proposed. This model restores the centrality of political decision and expert judgement in situations characterized by high risk, uncertainty and contingency. It is argued that such alternative model affords quicker and more flexible responses to serious outbreaks of infections, while providing adequate protection against abuses. (shrink)

The principles which can justify significantly risky nontherapeutic research on children are a combination of: (1) direct or indirect benefits to the child participants now and/or in the future (and these benefits need not necessarily be medical, they can also be socioeconomic or otherwise non-medical); (2) a high standard of informed consent that fundamentally focuses on the child participant's understanding (and capacity for understanding) of relevant features of informed consent. Researchers, parents and guardians, as well as child participants themselves, have (...) different roles and obligations towards one another. This is not an issue of seeking to find excuses to expose children to risk, but rather an issue of seeking the least risky and most ethical way to do so if and when required by public health emergencies or to achieve directly beneficial scientific breakthroughs. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases (...) and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

Ebola is a deadly disease with no cure; there is no vaccine developed yet. Many died during the 2014 outbreak in West Africa, and many healthcare professionals went to the virus infected area to treat the patients while placing their lives in danger. Not every medical professional placed in the field is a fully trained specialist, and sometimes one or two under-trained doctors are in charge of the entire clinic with some nurses and operating technicians. When unexpected outbreaks of (...) the virus occur in the places, the doctor(s) would encounter medical and ethical dilemmas. Should they leave or stay? In fact, this dilemma is not confined to the Ebola pandemic but relevant to all similar cases. In this paper, three authors, a medical resident, a clinical bioethicist, and a theoretical bioethicist respond to the dilemma. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

In bioethics vaccine refusal is often discussed as an instance of free riding on the herd immunity of an infectious disease. However, the social science of vaccine refusal suggests that the reasoning behind refusal to vaccinate more often stems from previous negative experiences in healthcare practice as well as deeply felt distrust of healthcare institutions. Moreover, vaccine refusal often acts like an exit mechanism. Whilst free riding is often met with sanctions, exit, according to Albert Hirschman’s theory of (...) exit and voice is most efficiently met by addressing concerns and increasing the quality and number of feedback channels. If the legitimate grievances responsible for vaccine refusal are not heard or addressed by healthcare policy, further polarization of attitudes to vaccines is likely to ensue. Thus, there is a need in the bioethics of vaccine refusal to understand the diverse ethical questions of this inflammable issue in addition to those of individual responsibility to vaccinate. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions (...) is given along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction (...) of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Vaccine refusal forces us to confront tensions between many values, including scientific expertise, parental rights, children’s best interests, social responsibility, public trust, and community health. Recent outbreaks of vaccine-preventable and emerging infectious diseases have amplified these issues. The prospect of a coronavirus disease 2019 vaccine signals even more friction on the horizon. In this contentious sociopolitical landscape, it is therefore more important than ever for clinicians to identify ethically justified responses to vaccine refusal.

Background: Earlier study without actual trial indicated that caregivers needed delivery of information about outbreak situations independently of their job status. This report describes, for about two months in winter, actual delivery outbreak information to families with preschool children. The study objective was to confirm the usefulness of this information delivery. Method: Participants receiving outbreak information were recruited from the Child Care Support Service in a ward in Tokyo, Japan. Outbreak information was obtained from the Nursery School Absenteeism Surveillance System (...) (NSASSy) covering approximately 40% of all nursery schools in Japan, prescription surveillance and other resources. Delivery of outbreak information started in December 2017 and ceased at the end of February in 2018. After the delivery period, a questionnaire survey was administered to participants. Results: For this area, NSASSy showed the most dominant disease was influenza, with 707 patients, followed by group A streptococcal pharyngitis with 98 patients. The outbreak peak was inferred to be as Monday, 22 January, and it was announced by e-mail on 23 January. Of the 202 persons joined this trial, 60 participants responded to the questionnaire survey after the delivery period. Of those respondents, 98% wanted delivery of that information to continue. Conclusion: We found that almost all respondents confirmed usefulness of the information about infectious diseases which was delivered. (shrink)

The global pandemic of COVID 19 has changed consumer behaviour to reduce the risk. This is common for all interpersonal interactions of individuals especially in maintaining the recommended interpersonal distance based on the recommendations from the health experts. Sri Lanka as a developing country affected by COVID 19, observed changes in individuals' day today’ consumption decision making due to pandemic. Importantly the retailing sector is highly influenced by the conditions since the frequency of interpersonal interactions and degree of interaction is (...) higher in the retailing sector. Interestingly the retailing sector with its largest contributor, the SMEs need to identify the unique changes that happen to the consumer behaviour in responding to them. Accordingly, the objective of the study is to examine the impact of infectious disease risk on the perceived retail crowding in two perspectives of human density and the spatial density. The study has used a quantitative survey in collecting data with the online self-administrated questionnaire with a sample of 100 consumers. Data analysis has been done by using a PLS-SEM with the support of SmartPLS version 3. The key findings of the study emphasize the significant positive influence of infectious disease risk on human density as well as on the spatial density. Based on the findings the study attempts to provide the implications for the retailing industry to cope with situational changes in the environment. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious (...) class='Hi'>Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Among the many potential benefits arising from the rapidly advancing field of nanomedicine is the possibility of a whole new range of nanovaccines in which novel delivery mechanisms utilizing nanoparticles could make obsolete the use of needles for administering any vaccine. However, as the massive resources of the worldwide pharmaceutical industry are deployed to develop nanovaccines, urgent questions arise as to which diseases should be targeted and which populations will benefit most. -/- This paper explores how such targeting of nanovaccines (...) might be decided in an ethically optimal way and considers some of the practical considerations and potential problems of implementing such a global nanovaccine policy. There seems little doubt that nanomedical research could develop vaccines against most major global infectious diseases. Throughout the history of medicine, however, it is well recognized that insufficient attention and resources have been given to public health and preventive medicine and the environmental causes of ill-health remain under-researched. We urge that national governments and regional authorities of wealthier countries incentivise their powerful pharmaceutical corporations to develop nanovaccines within a global and long term perspective and not just to focus on the diseases of the developed world. (shrink)

The paper begins with a retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is a more evolved form on the evolutionary scale of life. In addition, the study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. The subject of pandemics is approached starting from the existentialism of Albert Camus and Sartre, the replacement (...) of the exclusion ritual with the disciplinary mechanism of Michel Foucault, and about the Gaia hypothesis, developed by James Lovelock and supported in the current pandemic by Bruno Latour. The social dimensions of pandemics, their connection to global warming, which has led to an increase in infectious diseases, and the deforestation of large areas, which have caused viruses to migrate from their native area (their "reservoir") are highlighted below. The ethics of pandemics is approached from several philosophical points of view, of which the most important in a crisis of such global dimensions is utilitarianism which involves maximizing benefits for society in direct conflict with the usual (Kantian) view of respect for people as individuals. After a retrospective of the COVID-19 virus that caused the current pandemic, its life cycle and its history, with an emphasis on the philosophy of death, the concept of biopower initially developed by Foucault is discussed, with reference to the practice of modern states of control of the populations and the debate generated by Giorgio Agamben who states that what is manifested in this pandemic is the growing tendency to use the state of emergency as a normal paradigm of government. An interesting and much debated approach is the one generated by the works of Slavoj Žižek, who states that the current pandemic has led to the bankruptcy of the current "barbaric" capitalism, wondering if the path that humanity will take is a neo-communism. Another important negative effect is desocialization, with the conclusion of some philosophers that we cannot exist independently of our relationships with others, that a person's humanity depends on the humanity of those around him. The last section is dedicated to forecasting what the world will look like after the pandemic, and there are already signs of a paradigm shift, including the sudden disappearance of the "wall" ideology: a cough was enough to make it suddenly impossible to avoid the responsibility that every individual has it towards all living beings for the simple fact that he is part of this world, and of the desire to be part of it. The whole is always involved in part, because everything is, in a sense, in everything and in nature there are no autonomous regions that are an exception. The COVID-19 pandemic seems to restore the supremacy that once belonged to politics. One of the virtues of the virus is its ability to generate a more sober idea of ​​freedom: to be free means to do what needs to be done in a specific situation. -/- CONTENTS: -/- Abstract Introduction 1 Viruses 1.1 Ontology 2 Pandemics 2.1 Social dimensions 2.2 Ethics 3 COVID-19 3.1 Biopolitics 3.2 Neocommunism 3.3 Desocialising 4 Forecasting Bibliography -/- DOI: 10.13140/RG.2.2.31039.74405/1. (shrink)

The background paper provides an introduction to the concept of pandemics and to the ethical and political issues related with pandemic preparedness.

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant (...) new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated (...) the development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

This paper has two objectives 1) to study the influence of digital and new technology on COVID-19 diagnosis and healthcare 2) To propose the integral guideline solutions of the infectious disease for the future. COVID-19 stands for corona (CO), virus (VI), disease (D), or SARS-CoV-2, is a respiratory virus first identified in December 2019 in Wuhan, China(WHO, 2019). It is an epidemiological crisis that caused the deaths and sudden destruction of wealth and health of people around the (...) world. Many countries responded to the crisis with what could only be called urgent prevention and treatment. In the 21st century, our society is based on digital and new technology that can control and prevent the COVID-19 pandemics. However, these ways for solving the problem of COVID-19 pandemics are rising an epistemological crisis too. There are some problems with the COVID-19 diagnosis. From Buddhist philosophy perspective, COVID-19 teaches us the coronavirus is causing us to experience some heightened forms of the three marks of our existence which are the impermanence (aniccā), the suffering (duḥkha), and the non-self (anatta). The establishment of scientific expertise and innovation has shown its value and educating the public about testing, diagnosis, communication, treatment, and vaccine development technology for prevention the of infectious diseases in the future. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the (...) Virus Infectious Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

On May 16, 2020, the Center for Academic Research and Training in Anthropogeny organized the symposium “Impact of Infectious Disease on Humans and Our Origins”. The symposium aimed to gather experts on infectious diseases in one place and discuss the interrelationship between different pathogens and humans in an evolutionary context. The talks discussed topics including SARS-CoV-2, dengue and Zika, the notion of human-specific diseases, streptococci, microbiome in the human reproductive tract, Salmonella enterica, malaria, and human immunological memory.

In the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major (...) gene and polygenic predispositions), they attempt to unify infectious diseases from a genetic point of view. In this article, I analyze this explicit example of a genetic theory, which relies on mechanisms and is applied only to a specific category of diseases, what we call “a regional genetic theory.” I have three aims: to prove that a genetic theory of disease can be devoid of genocentrism, to consider the possibility of a genetic theory applied to every disease, and to introduce two hypotheses about the form that such a genetic theory could take by distinguishing between a genetic theory of diseases and a genetic theory of Disease. Finally, I suggest that network medicine could be an interesting framework for a genetic theory of Disease. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The (...) latest treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious (...) class='Hi'>Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

We are witnesses to a major reshaping of our world: the World and our lives as we used to know are ending and they are reshaping constantly and drastically under pressure. Everything we knew about this world, our old habits, values, human rights, ethical patterns et all. These days, since the pandemic outburst, I saw the perceptions we have/had on religious impositions and requirements changing for an unprecedented behavior and inconsiderably reshaping religious phenomenon could have ever think of. With the (...) title taken from the topic of this volume, Inspired by the conference titled, we have tried to envision the actual human environment through the ongoing pandemic that revolutions the entire human society in a way we had never considered as possible and so that we will not recognize in a year or so. Following the Philosophy of Dialectics and seeing a larger number of possibilities beyond those that were revealed to us in most obvious ways, we wonder thus, what makes us, in fact, do these changes – is the pandemic itself and its requirements or is it just US, humans, that were long longing for a change, a motif to do it all new again? It is though a human-divine desire to anew all from time to time and seek a reboot to all wrongness that grows in the world. (shrink)

Biomarker-based predictive tests for subjectively asymptomatic Alzheimer’s disease (AD) are utilized in research today. Novel applications of artificial intelligence (AI) promise to predict the onset of AD several years in advance without determining biomarker thresholds. Until now, little attention has been paid to the new ethical challenges that AI brings to the early diagnosis in asymptomatic individuals, beyond contributing to research purposes, when we still lack adequate treatment. The aim of this paper is to explore the ethical arguments put (...) forward for AI aided AD prediction in subjectively asymptomatic individuals and their ethical implications. The ethical assessment is based on a systematic literature search. Thematic analysis was conducted inductively of 18 included publications. The ethical framework includes the principles of autonomy, beneficence, non-maleficence, and justice. Reasons for offering predictive tests to asymptomatic individuals are the right to know, a positive balance of the risk-benefit assessment, and the opportunity for future planning. Reasons against are the lack of disease modifying treatment, the accuracy and explicability of AI aided prediction, the right not to know, and threats to social rights. We conclude that there are serious ethical concerns in offering early diagnosis to asymptomatic individuals and the issues raised by the application of AI add to the already known issues. Nevertheless, pre-symptomatic testing should only be offered on request to avoid inflicted harm. We recommend developing training for physicians in communicating AI aided prediction. (shrink)

As the Zika virus pandemic continues to bring worry and fear to health officials and medical scientists, Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) have recommended that residents of the Zika-infected countries, e.g., Brazil, and those who have traveled to the area should delay having babies which may involve artificial contraceptive, particularly condom. This preventive policy, however, is seemingly at odds with the Roman Catholic Church’s position on the contraceptive. As least since the promulgation (...) of Paul VI’s 1968 encyclical, Humanae Vitae, the Church has explicitly condemned artificial birth control as intrinsic evil. However, the current pontiff, Pope Francis, during his recent visit to Latin America, remarked that the use of artificial contraception may not be in contradiction to the teaching of Humanae Vitae while drawing a parallel between the current Zika Crisis and the 1960’s Belgian Congo Nun Controversy. The pope mentioned that the traditional ethical principle of the lesser of two evils may be the doctrine that justified the exceptions. The authors of this paper attempt to expand the theological rationale of the pope’s suggestion. In so doing, the authors rely on casuistical reasoning as an analytic tool that compares the Belgian Congo Nun case and the given Zika case, and suggest that the former is highly similar to, if not the same as, the latter in terms of normative moral feature. That is, in both cases the use of artificial contraception is theologically justified in reference to the criteria that the doctrine of the lesser of two evils requires. The authors wish that the paper would provide a solid theological-ethical ground based on which condom-use as the most immediate and effective preventive measure can be recommended in numerous Catholic hospitals as well as among Catholic communities in the world, particularly the most Zika-affected and largest Catholic community in the world, Brazil – 123 million present Brazilian citizens are reported to be Roman Catholic. (shrink)

Whipple disease is a rare, infectious, disease first described from a single case by Whipple in 1907. As well as characterising the clinical and pathological features of the condition, Whipple made two suggestions regarding its aetiology. These were either than the disease was caused by an infectious agent, or that it was of metabolic origin. As the disease is now thought to be caused by infection with the bacterium Tropheryma whipplei, historical reviews of the (...) history of the disease typically mention only the first of these suggestions. In this paper, we therefore revisit Whipple’s other theory. We argue that a diverse and often successful research programme was developed around this mechanism of disease causation which gave rise to many useful findings on the condition. In the later parts of this article, we then turn to discuss the surprising neglect of this period of Whipple disease research in the current literature, and conclude by offering a brief reconstruction of this early history suitable for use in a technical context. (shrink)

Many countries in Africa, and more generally those in the Global South with tropical areas, are plagued by illnesses that the wealthier parts of the world (mainly ‘the West’) neither suffer from nor put systematic effort into preventing, treating or curing. What does an ethic with a recognizably African pedigree entail for the ways various agents ought to respond to such diseases? As many readers will know, a characteristically African ethic prescribes weighty duties to aid on the part of those (...) in a position to do so, and it therefore entails that there should have been much more contribution from the Western, ‘developed’ world. However, what else does it prescribe, say, on the part of sub-Saharan governments and the African Union, and are they in fact doing it? I particularly seek to answer these questions here, by using the 2013-16 Ebola crisis in West Africa to illustrate what should have happened but what by and large did not. (shrink)

This article, based on a case study, examines issues of confidentiality and family impact in a diagnosis of Huntington's disease. Genetic-based illness transcends individualistic models of patient autonomy because it also involves other family members, requiring a new approach to patient confidentiality.

Eyal et al have recently argued that researchers should consider conducting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human challenge studies to hasten vaccine development. We have conducted (J. L.) and overseen (L. D.) human challenge studies and agree that they can be useful in developing anti-infective agents. We also agree that adults can autonomously choose to undergo risks with no prospect of direct benefit to themselves. However, we disagree that SARS-CoV-2 challenge studies are ethically appropriate at this time, for (...) 3 reasons: (1) current scientific knowledge of SARS-CoV-2 infection is insufficient to manage risks; (2) autonomous decision making, while necessary, does not override concerns about risk; and (3) undertaking challenge studies now would imperil confidence in the research enterprise, potentially undermining the global response to the coronavirus disease 2019 (COVID-19) pandemic. (shrink)

Venomous snakebite is a neglected tropical disease and disease of poverty, affecting hundreds of thousands of people annually. The only effective medical intervention for snakebite is antivenom, produced primarily using captive venomous snakes as a source of venom. This paper analyzes snakes’ welfare at venom labs within this global health context. I recommend significant changes to improve the welfare of captive snakes, particularly in light of recent ethological research and attention on snakes. These recommendations are broadly consequentialist, aiming (...) to improve the lives of the snakes and ensure that people have increased access to affordable antivenom. (shrink)

Rare diseases pose a particular priority setting problem. The UK gives rare diseases special priority in healthcare priority setting. Effectively, the National Health Service is willing to pay much more to gain a quality-adjusted life-year related to a very rare disease than one related to a more common condition. But should rare diseases receive priority in the allocation of scarce healthcare resources? This article develops and evaluates four arguments in favour of such a priority. These pertain to public values, (...) luck egalitarian distributive justice the epistemic difficulties of obtaining knowledge about rare diseases and the incentives created by a higher willingness to pay. The first is at odds with our knowledge regarding popular opinion. The three other arguments may provide a reason to fund rare diseases generously. However, they are either overinclusive because they would also justify funding for many non-rare diseases or underinclusive in the sense of justifying priority for only some rare diseases. The arguments thus fail to provide a justification that tracks rareness as such. There are no data in this work. (shrink)

Response to commentary. We are grateful to Crockett and Craigie for their interesting remarks on our paper. We accept Crockett’s claim that there is a need for caution in drawing inferences about patient groups from work on healthy volunteers in the laboratory. However, we believe that the evidence we cited established a strong presumption that many of the patients who are routinely taking a medication, including many people properly prescribed the medication for a medical condition, have morally significant aspects of (...) their cognition and behavior modified in a way that is unintended and may sometimes be unwelcome. Crockett notes that in some cases the effects of long-term drug use may differ, sometimes markedly, from the effects of short-term use. However, if acute use of a drug affects a neural system involved in mediating moral cognition or behavior, this nevertheless provides some evidence that chronic use of the drug may affect that same system and thus have morally significant effects. It is also plausible, in some cases, that an acute moral effect would give rise to a chronic moral effect via cognitive mechanisms. ... (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, (...) pathogenesis, diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance (...) purposes. (shrink)

Similarly to other accounts of disease, Christopher Boorse’s Biostatistical Theory (BST) is generally presented and considered as conceptual analysis, that is, as making claims about the meaning of currently used concepts. But conceptual analysis has been convincingly critiqued as relying on problematic assumptions about the existence, meaning, and use of concepts. Because of these problems, accounts of disease and health should be evaluated not as claims about current meaning, I argue, but instead as proposals about how to define (...) and use these terms in the future, a methodology suggested by Quine and Carnap. I begin this article by describing problems with conceptual analysis and advantages of “philosophical explication,” my favored approach. I then describe two attacks on the BST that also question the entire project of defining “disease.” Finally, I defend the BST as a philosophical explication by showing how it could define useful terms for medical science and ethics. (shrink)

The U.S. FDA has issued emergency use authorizations for monoclonal antibodies for non-hospitalized patients with mild or moderate COVID-19 disease and for individuals exposed to COVID-19 as post-exposure prophylaxis. One EUA for an oral antiviral drug, molnupiravir, has also been recommended by FDA’s Antimicrobial Drugs Advisory Committee, and others appear likely in the near future. Due to increased demand because of the Delta variant, the federal government resumed control over the supply and asked states to ration doses. As future (...) variants with increased infectivity and/or severity emerge, further rationing may be required. We identify relevant ethical principles and priority groups for access to therapies based on an integrated approach to population health and medical factors. Using priority categories to allocate scarce therapies effectively operationalizes important ethical values. This strategy is preferable to the current approach of categorical rules based on vaccination, immunocompromise status, or older age, or the ad hoc consideration of clinical risk factors. (shrink)

Abstract: In recent years, the outbreak of various poultry diseases has posed a significant threat to the global poultry industry. Therefore, the accurate and timely detection of chicken diseases is critical to reduce economic losses and prevent the spread of diseases. In this study, we propose a method for classifying chicken diseases using a convolutional neural network (CNN). The proposed method involves preprocessing the chicken images, building and training a CNN model, and evaluating the performance of the model. The dataset (...) used in this study comprises chicken images of three different diseases: Newcastle disease, avian influenza, and infectious bursal disease. The proposed method achieved an overall F1-score of 99.04% in classifying the chicken diseases. The results demonstrate the effectiveness of using CNN in classifying chicken diseases and provide a promising approach for early detection and diagnosis of poultry diseases. (shrink)

Claims about whether or not infertility is a disease are sometimes invoked to defend or criticize the provision of state-funded treatment for infertility. In this paper, I suggest that this strategy is problematic. By exploring infertility through key approaches to disease in the philosophy of medicine, I show that there are deep theoretical disagreements regarding what subtypes of infertility qualify as diseases. Given that infertility's disease status remains unclear, one cannot uncontroversially justify or undermine its claim to (...) medical treatment by claiming that it is or is not a disease. Instead of focusing on disease status, a preferable strategy to approach the debate about state-funded treatment is to explicitly address the specific ethical considerations raised by infertility. I show how this alternative strategy can be supported by a recent theoretical framework in the philosophy of medicine, which avoids the problems associated with the concepts of health and disease. (shrink)