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)

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)

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)

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)

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)

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.

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 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)

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)

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)

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)

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)

In this article, I will reconstruct the monocausal model and argue that modern 'multifactorial diseases' are not monocausal by definition. 'Multifactorial diseases' are instead defined according to a constitutive disease model. On closer analysis, infectious diseases are also defined using the constitutive model rather than the monocausal model. As a result, our classification models alone cannot explain why infectious diseases have a universal etiology while chronic and noncommunicable diseases lack one. The explanation is instead provided by the (...) nineteenth-century germ theorists. (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)

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)

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)

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)

Non-communicable diseases (NCDs) such as cardiovascular diseases and diabetes are reported to have caused significant deaths for more than a decade. Consequently, NCDs have posed as a threat to the socio-economic well-being of individuals and families, contributed to a rise in healthcare costs and largely undermined the attainment of the Sustainable Development Goals (SDGs) especially in developing countries. According to the World Health Organization (WHO), the prevalence of NCDs have compounded the problem of already ill equipped healthcare systems in these (...) countries as they are faced with constraints to deal with the burden of both infectious and non-communicable diseases. Informed largely by the rapid increase in NCDs and their subsequent threat to public health, we aimed to ascertain the various healthcare interventions that Ghana has fashioned out in her bid to prevent and control the incidence of NCDs, how these interventions were rolled out and examined past and present barriers to their implementation since 1990. We culled the data gathered for this paper from both primary and secondary sources to construct a coherent synthesis and to facilitate discussions on Ghana’s NCDs interventions from 1990 to 2018. A systematic analysis of the data gathered, revealed that Ghana’s healthcare system has by far tackled the NCDs burden in two folds; the clinical care aspect and the health promotion aspect. While certain healthcare interventions were purposively directed toward addressing NCDs, others were directed at promoting healthy lifestyles but had a bearing on the prevention and control of NCDs. Present challenges concerning shortfalls in interventions are a reflection of unresolved challenges in the past. We argue that despite the significant strides made for more than two decades, the interventions have addressed the burden of NCDs with limited success given the trends in NCDs mortality and morbidity. (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 devastating impact of the COVID‐19 (coronavirus disease 2019) pandemic is prompting renewed scrutiny of practices that heighten the risk of infectious disease. One such practice is refusing available vaccines known to be effective at preventing dangerous communicable diseases. For reasons of preventing individual harm, avoiding complicity in collective harm, and fairness, there is a growing consensus among ethicists that individuals have a duty to get vaccinated. I argue that these same grounds establish an analogous duty to (...) avoid buying and eating most meat sold today, based solely on a concern for human welfare. Meat consumption is a leading driver of infectious disease. Wildlife sales at wet markets, bushmeat hunting, and concentrated animal feeding operations (CAFOs) are all exceptionally risky activities that facilitate disease spread and impose immense harms on human populations. If there is a moral duty to vaccinate, we also should recognize a moral duty to avoid most meat. The paper concludes by considering the implications of this duty for policy. (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)

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 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)

Monkeypox, an infectious disease caused by the Orthopoxvirus, was identified in humans in 1970. It has recently emerged as a global health concern due to outbreaks beyond its endemic regions in Central and West Africa. This review examines the current state of medical treatments for monkeypox as of 2024, focusing on antiviral agents, immunotherapies, and supportive care measures. Monkeypox manifests with symptoms including fever, rash, and lymphadenopathy, with severe cases more common in immunocompromised individuals. Antiviral therapies such as (...) tecovirimat and brincidofovir are central to treatment strategies, with tecovirimat demonstrating efficacy in alleviating symptoms and reducing viral shedding. Emerging treatment strategies involve novel lipid-based formulations and combination therapies that integrate antivirals with immune-modulating agents. Supportive care remains essential, involving analgesics and antibiotics for secondary infections, while the MVA-BN vaccine plays a critical role in prevention. Research emphasizes the need for a deeper understanding of viral pathogenesis and host immune responses to improve therapeutic and preventive measures. Despite significant advancements, challenges remain, including potential antiviral resistance, disparities in healthcare access, and the necessity for enhanced diagnostic and surveillance capabilities. This review highlights the imperative for ongoing research, international collaboration, and investment in healthcare infrastructure to advance the management and prevention of monkeypox and to prepare for future outbreaks. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (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)

COVID-19 affected to the people all around the world. As its first and second wave has been passed and we are facing currently to third wave, but all around the world no one can overcome to this viral infectious disease. Likewise it is affecting to people like a viral disease physically but along with its effect, its huge effect on mental health worldwide. The significant academic research has shown that there is a correlation of mental issues and (...) covid-19 pandemic. Among all people it has seen that mostly students are affected. Recent studies have suggest that psychiatric problems, includes nervousness, depressive symptom, disappointment in students due to exposure of covid-19. However the mental health strategies of lockdown are unknown. In addition, illness perceptions and relevant consequences facing the pandemic have played role due to restrictions. Survey type studies are conducted for the investigation of anxiety and depression during pandemic lockdown. All people like adults, men, women, students are invited for survey through social media. (shrink)

Clinical microbiology serves as a partner to clinicians in the diagnosis and treatment of infectious diseases. Antibiotics are prescribed empirically before the availability of antimicrobial susceptibility testing data, especially when the patient's medical status could deteriorate by suspending the treatment. To investigate the impact of antimicrobial susceptibility testing on the management of outpatients with suspected bacterial infection in Libyan patients, a cross-sectional prospective study concluded on microbial microdroplet culture by including outpatients with suspected bacterial infection, who have done antimicrobial (...) susceptibility testing. Thus, 53 Libyan patients with urinary tract infections and 14 Libyan patients with skin infections were included in this study. Before the availability of antimicrobial susceptibility testing data, 25 patients were appropriately treated while 42 patients were inappropriately treated. After the availability of antimicrobial susceptibility testing data, the number of appropriately treated patients increased to 57 patients. Thus, antimicrobial susceptibility testing improved the management of 41 patients by discontinuing an unnecessary antibiotic in four patients, starting necessary antibiotic therapy in 18 patients, and changing to more appropriate antibiotic in 19 patients. However, the antimicrobial susceptibility testing has no impact on the management of 24 patients and has led to the worsening of the management of two patients. The effect of antimicrobial susceptibility testing of antibiotic de-escalation was assessed in 35 patients; however, antibiotic de-escalation occurred in six patients. Thus, data of antimicrobial susceptibility testing has improved the management of Libyan outpatients with bacterial infection but their role in antibiotic de-escalation was slight. (shrink)

In this paper, I offer one example of conceptual change. Specifically, I contend that the discovery that viruses could cause cancer represents an excellent example of branch jumping, one of Thagard’s nine forms of conceptual change. Prior to about 1960, cancer was generally regarded as a degenerative, chronic, non-infectious disease. Cancer causation was therefore usually held to be a gradual process of accumulating cellular damage, caused by relatively non-specific component causes, acting over long periods of time. Viral infections, (...) on the other hand, were generally understood to be acute processes, whereby single, specific and necessary causal agents acted alone to produce disease. However, during the 1960s and 1970s, a number of cancers were discovered to have an infectious aetiology. Of particular note were two—Burkitt’s lymphoma and cervical cancer—which I will discuss in detail later in this piece. Together, these discoveries led, in the short term, to a tentative aetiological reclassification of some types of cancer as infectious diseases and, in the longer term, to a full-blown reclassification of cancer as an aetiological disease branch in its own right. This process of reclassification forms the empirical basis for my concluding remarks on the influence of classification upon causation in medicine. Through this, I aim to demonstrate that conceptual change, far from being a purely abstract concern of the philosopher of science, is of substantial import to scientific practitioners. (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)

In some jurisdictions, the institutions of criminal justice may subject individuals who have committed crimes to preventive detention. By this, I mean detention of criminal offenders (i) who have already been punished to (or beyond) the point that no further punishment can be justified on general deterrent, retributive, restitutory, communicative or other backwardlooking grounds, (ii) for preventive purposes—that is, for the purposes of preventing the detained individual from engaging in further criminal or otherwise socially costly conduct. Preventive detention, thus understood, (...) shares many features with the quarantine measures sometimes employed in the context of infectious disease control. Both interventions involve imposing (usually severe) constraints on freedom of movement and association. Both interventions are standardly undeserved: in quarantine, the detained individual deserves no detention (or so I will, for the moment, assume), and in preventive detention, the individual has already endured any detention that can be justified by reference to desert. Both interventions are, in contrast to civil commitment under mental health legislation, normally imposed on more-or-less fully autonomous individuals. And both interventions are intended to reduce the risk that the constrained individual poses to the public. Yet despite these similarities, preventive detention and quarantine have received rather different moral report cards. (shrink)

Conceptual metaphors have received much attention in research on discourse about infectious diseases in recent years. Most studies found that conceptual metaphors of war dominate media discourse about disease. Similarly, a great deal of research has been undertaken on the new coronavirus, i.e., COVID-19, especially in the English news discourse as opposed to other languages. The present study, in contrast, analyses the conceptual metaphors used in COVID-19 discourse in French-language newspapers. The study explored the linguistic metaphors used in (...) COVID-19 discourse in these newspapers and conceptual metaphors that underlie and motivate them, using a conceptual metaphor theory framework (CMT). Therefore, two North African French-language newspapers, namely Libération, published in Morocco, and La Presse de Tunisie, published in Tunisia, formed the corpus of the current study. The results showed that the most frequent framing of COVID-19 was in terms of WAR, followed by DISASTER and KILLER, respectively. (shrink)

We ask whether it is reasonable to delay or refuse to take COVID-19 vaccines that have been shown in clinical trials to be safe and effective against infectious diseases. We consider two kinds of vaccine hesitancy. The first is geared to scientifically informed open questions about vaccines. We argue that in cases where the data is not representative of relevant groups, such as pregnant women and ethnic minorities, hesitancy can be reasonable on epistemic grounds. However, we argue that hesitancy (...) is not reasonable if a vaccine has passed well-conducted clinical trials. The second kind of hesitancy is to do with beliefs about the institutions offering a successfully trialled vaccine and the justifiability of cooperating with those institutions. For example, in the UK, distrust of the UK Government or the National Health Service is identified as a factor in the vaccine hesitancy of minority ethnic populations. We ask whether this sort of hesitation is reasonable given normative requirements of fair co-operation, both with those institutions and the wider population. We suggest that the answer is not straightforward. Sometimes the hesitation is unreasonable but understandable. -/- . (shrink)

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, (...) interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota. -/- . (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 was written to study the order of medical advances throughout history. It investigates changing human beliefs concerning the causes of diseases, how modern surgery developed and improved methods of diagnosis and the use of medical statistics. Human beliefs about the causes of disease followed a logical progression from supernatural causes, such as the wrath of the Gods, to natural causes, involving imbalances within the human body. The invention of the microscope led to the discovery of microorganisms which (...) were eventually identified as the cause of infectious diseases. Identification of the particular microorganism causing a disease led to immunization against the disease. Modern surgery only developed after the ending of the taboo against human dissection and the discovery of modern anesthesia and the discovery of the need for anti-septic practices. Modern diagnostic practices began with the discovery of x-rays and the invention of medical scanners. Improved mathematics, especially in probability theory, led to statistical studies which led to a much greater ability, to identify the causes of disease, and to evaluate the effectiveness of treatments. These discoveries all occurred in a necessary and inevitable order with the easiest discoveries being made first and the harder discoveries being made later. The order of discovery determined the course of the history of medicine and is an example of how social and cultural history has to follow a particular course determined by the structure of the world around us. (shrink)

COVID-19 affected to the people all around the world. As its first and second wave has been passed and we are facing currently to third wave, but all around the world no one can overcome to this viral infectious disease. Likewise it is affecting to people like a viral disease physically but along with its effect, its huge effect on mental health worldwide. The significant academic research has shown that there is a correlation of mental issues and (...) covid-19 pandemic. Among all people it has seen that mostly students are affected. Recent studies have suggest that psychiatric problems, includes nervousness, depressive symptom, disappointment in students due to exposure of covid-19. However the mental health strategies of lockdown are unknown. In addition, illness perceptions and relevant consequences facing the pandemic have played role due to restrictions. Survey type studies are conducted for the investigation of anxiety and depression during pandemic lockdown. All people like adults, men, women, students are invited for survey through social media. (shrink)

The modern concept of ideology was established by the liberal politician and philosopher Destutt de Tracy, with the objective of creating an all-embracing and general science of ideas, which followed the sensualist and empiricist trend initiated by Locke that culminated in the positivism of Comte. Natural selection and immunity are two key concepts in the history of biology that were strongly based on the Malthusian concept of struggle for existence. This concept wrongly assumed that population grew faster than the means (...) of existence. This “natural” law contained implicitly the idea that the poor and least gifted would not survive. This idea led to the progressive development of the concept of natural selection, whose definitive version was given by Darwin. Mechnikov took the concepts of struggle for existence and natural selection and conceived infectious diseases as a struggle between a host and its invader, the so-called phagocytosis theory. This theory created the necessity to possess mechanisms to discriminate between the own and the foreign, and led to the conception of the immune self. These concepts were not developed from ideas coming from perceptions or sensations, but from ideas coming from their values: individual interest, inevitable inequality, property, utility and profit. Values are ideals that constitute an ideological matrix which exerts a numinous activity and influence the development of our future actions. In consequence, science and its practice cannot avoid and ignore the values that drive them and impulse them towards certain directions. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary (...) dispositions involved in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Clinical microbiology serves as a partner to clinicians in the diagnosis and treatment of infectious diseases. Antibiotics are prescribed empirically before the availability of antimicrobial susceptibility testing data, especially when the patient's medical status could deteriorate by suspending the treatment. To investigate the impact of antimicrobial susceptibility testing on the management of outpatients with suspected bacterial infection in Libyan patients, a cross-sectional prospective study concluded on microbial microdroplet culture by including outpatients with suspected bacterial infection, who have done antimicrobial (...) susceptibility testing. Thus, 53 Libyan patients with urinary tract infections and 14 Libyan patients with skin infections were included in this study. Before the availability of antimicrobial susceptibility testing data, 25 patients were appropriately treated while 42 patients were inappropriately treated. After the availability of antimicrobial susceptibility testing data, the number of appropriately treated patients increased to 57 patients. Thus, antimicrobial susceptibility testing improved the management of 41 patients by discontinuing an unnecessary antibiotic in four patients, starting necessary antibiotic therapy in 18 patients, and changing to more appropriate antibiotic in 19 patients. However, the antimicrobial susceptibility testing has no impact on the management of 24 patients and has led to the worsening of the management of two patients. The effect of antimicrobial susceptibility testing of antibiotic de-escalation was assessed in 35 patients; however, antibiotic de-escalation occurred in six patients. Thus, data of antimicrobial susceptibility testing has improved the management of Libyan outpatients with bacterial infection but their role in antibiotic de-escalation was slight. (shrink)

Background: Critically ill patients often require complex clinical care by highly trained staff within a specialized intensive care unit (ICU) with advanced equipment. There are currently limited data on the costs of critical care in low-and middle-income countries (LMICs). This study aims to investigate the direct-medical costs of key infectious disease (tetanus, sepsis, and dengue) patients admitted to ICU in a hospital in Ho Chi Minh City (HCMC), Vietnam, and explores how the costs and cost drivers can vary (...) between the different diseases. -/- Methods: We calculated the direct medical costs for patients requiring critical care for tetanus, dengue and sepsis. Costing data (stratified into different cost categories) were extracted from the bills of patients hospitalized to the adult ICU with a dengue, sepsis and tetanus diagnosis that were enrolled in three studies conducted at the Hospital for Tropical Diseases in HCMC from January 2017 to December 2019. The costs were considered from the health sector perspective. The total sample size in this study was 342 patients. -/- Results: ICU care was associated with significant direct medical costs. For patients that did not require mechanical ventilation, the median total ICU cost per patient varied between US$64.40 and US$675 for the different diseases. The costs were higher for patients that required mechanical ventilation, with the median total ICU cost per patient for the different diseases varying between US$2,590 and US$4,250. The main cost drivers varied according to disease and associated severity. -/- Conclusion: This study demonstrates the notable cost of ICU care in Vietnam and in similar LMIC settings. Future studies are needed to further evaluate the costs and economic burden incurred by ICU patients. The data also highlight the importance of evaluating novel critical care interventions that could reduce the costs of ICU care. (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)

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.