A new framework for host-pathogen interaction research.

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.

Emerging Pattern of Post-COVID-19 Parosmia and Its Effect on Food Perception.

Olfactory dysfunction is amongst the many symptoms of Long COVID. Whilst most people that experience smell loss post COVID-19 recover their sense of smell and taste within a few weeks, about 10% of cases experience long-term problems, and their smell recovery journey often begins a few months later when everyday items start to smell distorted. This is known as parosmia. The aim of this study was to identify the key food triggers of parosmic distortions and investigate the relationship between distortion and disgust in order to establish the impact of parosmia on diet and quality of life. In this cross-sectional study (n = 727), respondents experiencing smell distortions completed a questionnaire covering aspects of smell loss, parosmia and the associated change in valence of everyday items. There was a significant correlation between strength and disgust (p < 0.0001), and when the selected items were reported as distorted, they were described as either unpleasant or gag-inducing 84% of the time. This change in valence associated with loss of expected pleasure and the presence of strange tastes and burning sensations must certainly lead to changes in eating behaviours and serious longer-term consequences for mental health and quality of life.

Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.

OBJECTIVE: We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. METHODS: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination and prior infection. RESULTS: Among 3,793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio (aHR) 1.12; 95% confidence interval (CI) 0.93; 1.34). Both Omicron waves had lower risk of severe outcomes than previous waves. Prior infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least 3 doses vs. no vaccine) were protective. CONCLUSION: Disease severity was similar amongst diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to prior infection and vaccination, both of which were strongly protective.

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

BACKGROUND: 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 (CIDO) in early 2020. RESULTS: 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. CONCLUSION: 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.

Young People’s Perspectives on the Value and Meaning of Art during the Pandemic

This contribution draws on the voices and reflections from young people as co-researchers in the Growing-Up Under Covid-19 project – a longitudinal ethnographic action research project to document, share, and respond to impacts of the pandemic on different spheres of young people’s lives. The research was conducted entirely online over 18 months in seven countries and has involved youth-led approaches to research, including video diaries and the use of artefacts and visual material to convey their experiences and support reflection and dialogue across research groups and with external stakeholders. In this contribution, the young co-researchers reflect on their rationale for using different visual media and why this was important for them. They also reflect on the significance of the representations in the visual images and how these images communicate how young people’s understanding of COVID and its impact on young people has changed (or given new meaning to) and how this in turn has given rise to particular responses and opportunities for young people. The article draws on examples of different visual forms selected by young people in Singapore, Italy, Lebanon, and the UK nations, including video, drawing, photography, and crafts. These different media and links to videos were included in the accompanying document. The contribution explores the different narratives and meanings behind the visuals, using the words of young people themselves, interspersed with narration from the adult researchers.

Rethinking Visual Arts–Based Methods of Knowledge Generation and Exchange in and beyond the Pandemic

This inaugural special issue of ‘Beyond the Text’ brings together a collection of visual arts (animation, creative and fine art, film, photographs, and zines) produced by children, young people, families, artists, and academics as part of co-created research during the 2020–2021 coronavirus pandemic. Our aim, in making these pieces available in this new publication format, is to illustrate the potential of visual arts as a form of co-creation and knowledge exchange which can transcend the challenges of researching ‘at a distance’, enable participants and co-researchers to share their stories, and support different ways of knowing for academic, policy, and public audiences. This is not to suggest that such methods offer transparent windows into participants’ worlds. As the reflections from the contributing authors consider, visual arts outputs leave room for audience interpretations, making them vulnerable to alternative readings, generating challenges and opportunities about how much it is possible to know about another and what is ethical to share. It is to these issues of ethics, representation, and voice that this special issue attends, reflecting on the possibilities of arts-based approaches for knowledge generation and exchange in and beyond the coronavirus pandemic.

CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed.

The Effects of Olfactory Loss and Parosmia on Food and Cooking Habits, Sensory Awareness, and Quality of Life-A Possible Avenue for Regaining Enjoyment of Food.

Olfactory dysfunction often has severe consequences on patients' quality of life. The most common complaint in these patients is their reduced enjoyment of food in both patients with olfactory loss and parosmia. How the different types of olfactory dysfunction differ in relation to food and cooking habits, sensory awareness, and food-related quality of life has not yet received much attention. By applying questionnaires on cooking, food, olfactory function, weight changes, sensory awareness, and food-related quality of life, we investigated how various aspects of eating differ between participants with olfactory loss (n = 271), parosmia (n = 251), and normosmic controls (n = 166). Cooking habits in olfactory dysfunction revealed pronounced differences as compared with normosmic controls. Cooking with olfactory dysfunction was associated with, e.g., a lack of comfort and inspiration for cooking and an inability to make new foods successfully. Significant differences in cooking were also found between olfactory loss and parosmia. Food items were less familiar in participants with olfactory loss and parosmia, while the ratings of liking food items differed between olfactory loss and parosmia, indicating the importance of adapting ingredients in meals separately for olfactory loss and parosmia. Parosmia was associated with a higher incidence of weight loss, but we found no difference in food-related quality of life between participants with olfactory loss and parosmia. While olfactory loss and parosmia have wide-ranging consequences on patients' cooking and food habits, adapting meals to include 'safer food items' and integrating multisensory stimulation may be a possible avenue for improving the enjoyment of food.

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.

OBJECTIVES: The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained. METHODS: In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. RESULTS: We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58). CONCLUSIONS: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.

Emerging Pattern of Post-COVID-19 Parosmia and Its Effect on Food Perception

Olfactory dysfunction is amongst the many symptoms of Long COVID. Whilst most people that experience smell loss post COVID-19 recover their sense of smell and taste within a few weeks, about 10% of cases experience long-term problems, and their smell recovery journey often begins a few months later when everyday items start to smell distorted. This is known as parosmia. The aim of this study was to identify the key food triggers of parosmic distortions and investigate the relationship between distortion and disgust in order to establish the impact of parosmia on diet and quality of life. In this cross-sectional study (n = 727), respondents experiencing smell distortions completed a questionnaire covering aspects of smell loss, parosmia and the associated change in valence of everyday items. There was a significant correlation between strength and disgust (p < 0.0001), and when the selected items were reported as distorted, they were described as either unpleasant or gag-inducing 84% of the time. This change in valence associated with loss of expected pleasure and the presence of strange tastes and burning sensations must certainly lead to changes in eating behaviours and serious longer-term consequences for mental health and quality of life.

Patients' Perspectives on Qualitative Olfactory Dysfunction: Thematic Analysis of Social Media Posts.

BACKGROUND: The impact of qualitative olfactory disorders is underestimated. Parosmia, the distorted perception of familiar odors, and phantosmia, the experience of odors in the absence of a stimulus, can arise following postinfectious anosmia, and the incidences of both have increased substantially since the outbreak of COVID-19. OBJECTIVE: The aims of this study are to explore the symptoms and sequalae of postinfectious olfactory dysfunction syndrome using unstructured and unsolicited threads from social media, and to articulate the perspectives and concerns of patients affected by these debilitating olfactory disorders. METHODS: A thematic analysis and content analysis of posts in the AbScent Parosmia and Phantosmia Support group on Facebook was conducted between June and December 2020. RESULTS: In this paper, we identify a novel symptom, olfactory perseveration, which is a triggered, identifiable, and usually unpleasant olfactory percept that persists in the absence of an ongoing stimulus. We also observe fluctuations in the intensity and duration of symptoms of parosmia, phantosmia, and olfactory perseveration. In addition, we identify a group of the most common items (coffee, meat, onion, and toothpaste) that trigger distortions; however, people have difficulty describing these distortions, using words associated with disgust and revulsion. The emotional aspect of living with qualitative olfactory dysfunction was evident and highlighted the detrimental impact on mental health. CONCLUSIONS: Qualitative and unsolicited data acquired from social media has provided useful insights into the patient experience of parosmia and phantosmia, which can inform rehabilitation strategies and ongoing research into understanding the molecular triggers associated with parosmic distortions and research into patient benefit.

Growing Up Under COVID-19: Young People's Agency in Family Dynamics.

The COVID-19 pandemic transformed the nature of family life in countries across the world. School, and workplace closures meant that families spent more time at home and had to confront new economic, social, and psychological challenges as a result of lockdowns and the greater proximity of family members. Policy, research and media coverage of the pandemic's impact on family life has focused primarily on the economic costs borne by households. This article draws on the findings from an empirical research project funded by the UK Nuffield Foundation on "Politics, Participation and Pandemics: Growing up under COVID-19", which worked with young people as co-researchers, to present an innovative perspective on the impact of lockdown on family relationships. The research team adopted a longitudinal ethnographic action research approach to document and make sense of the experiences of young people (aged 14-18) in four countries: Italy, Lebanon Singapore and the United Kingdom. The project used digital ethnography and participatory methods to track the responses of 70 young people to the challenges created by the pandemic. The study used the family as a prism for understanding how the lives of children and young people in different family circumstances and relationships were affected by the crisis. This article analyses, firstly, the complex shifting dynamics within households to identify the transformative effects of the pandemic on family life in various socio-cultural contexts. Secondly, it examines how young people's agency shaped family dynamics. In conclusion, the authors recommend how the findings from the study can be used to inform government interventions designed to minimise the impacts of the pandemic on the social well-being and rights of children and young people, and to recognise them as active participants in family and civic life both during and after the pandemic.

The Infectious Disease Ontology in the age of COVID-19.

BACKGROUND: Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules. RESULTS: To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term acellular structure to cover viruses and other acellular entities studied by virologists. We now distinguish between infectious agents - organisms with an infectious disposition - and infectious structures - acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core's content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices. CONCLUSIONS: IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises.

Altered smell and taste: Anosmia, parosmia and the impact of long Covid-19.

BACKGROUND: Qualitative olfactory (smell) dysfunctions are a common side effect of post-viral illness and known to impact quality of life and health status. Evidence is emerging that taste and smell loss are common symptoms of Covid-19 that may emerge and persist long after initial infection. The aim of the present study was to document the impact of post Covid-19 alterations to taste and smell. METHODS: We conducted exploratory thematic analysis of user-generated text from 9000 users of the AbScent Covid-19 Smell and Taste Loss moderated Facebook support group from March 24 to 30th September 2020. RESULTS: Participants reported difficulty explaining and managing an altered sense of taste and smell; a lack of interpersonal and professional explanation or support; altered eating; appetite loss, weight change; loss of pleasure in food, eating and social engagement; altered intimacy and an altered relationship to self and others. CONCLUSIONS: Our findings suggest altered taste and smell with Covid-19 may lead to severe disruption to daily living that impacts on psychological well-being, physical health, relationships and sense of self. More specifically, participants reported impacts that related to reduced desire and ability to eat and prepare food; weight gain, weight loss and nutritional insufficiency; emotional wellbeing; professional practice; intimacy and social bonding; and the disruption of people's sense of reality and themselves. Our findings should inform further research and suggest areas for the training, assessment and treatment practices of health care professionals working with long Covid.