Infectious Disease Threats: A Rebound To Resilience

Association between characteristics of employing healthcare facilities and healthcare worker infection rates and psychosocial experiences during the COVID-19 pandemic

BACKGROUND

Healthcare facility characteristics, such as ownership, size, and location, have been associated with patient outcomes. However, it is not known whether the outcomes of healthcare workers are associated with the characteristics of their employing healthcare facilities, particularly during the COVID-19 pandemic.

METHODS

This was an analysis of a nationwide registry of healthcare workers (the Healthcare Worker Exposure Response and Outcomes (HERO) registry). Participants were surveyed on their personal, employment, and medical characteristics, as well as our primary study outcomes of COVID-19 infection, access to personal protective equipment, and burnout. Participants from healthcare sites with at least ten respondents were included, and these sites were linked to American Hospital Association data to extract information about sites, including number of beds, teaching status, urban/rural location, and for-profit status. Generalized estimating equations were used to estimate linear regression models for the unadjusted and adjusted associations between healthcare facility characteristics and outcomes.

RESULTS

A total of 8,941 healthcare workers from 97 clinical sites were included in the study. After adjustment for participant demographics, healthcare role, and medical comorbidities, facility for-profit status was associated with greater odds of COVID-19 diagnosis (aOR 1.76, 95% CI 1.02-3.03, p = .042). Micropolitan location was associated with decreased odds of COVID-19 infection after adjustment (aOR = 0.42, 95% CI 0.24, 0.71, p = .002. For-profit facility status was associated with decreased odds of burnout after adjustment (aOR = 0.53, 95% CI 0.29-0.98), p = .044).

CONCLUSIONS

For-profit status of employing healthcare facilities was associated with greater odds of COVID-19 diagnosis but decreased odds of burnout after adjustment for demographics, healthcare role, and medical comorbidities. Future research to understand the relationship between facility ownership status and healthcare outcomes is needed to promote wellbeing in the healthcare workforce.

TRIAL REGISTRATION

The registry was prospectively registered: ClinicalTrials.gov Identifier (trial registration number) NCT04342806, submitted April 8, 2020.

An Integrated ddPCR Lab-on-a-Disc Device for Rapid Screening of Infectious Diseases

Digital droplet PCR (ddPCR) is a powerful amplification technique for absolute quantification of viral nucleic acids. Although commercial ddPCR devices are effective in the lab bench tests, they cannot meet current urgent requirements for on-site and rapid screening for patients. Here, we have developed a portable and fully integrated lab-on-a-disc (LOAD) device for quantitively screening infectious disease agents. Our designed LOAD device has integrated (i) microfluidics chips, (ii) a transparent circulating oil-based heat exchanger, and (iii) an on-disc transmitted-light fluorescent imaging system into one compact and portable box. Thus, droplet generation, PCR thermocycling, and analysis can be achieved in a single LOAD device. This feature is a significant attribute for the current clinical application of disease screening. For this custom-built ddPCR setup, we have first demonstrated the loading and ddPCR amplification ability by using influenza A virus-specific DNA fragments with different concentrations (diluted from the original concentration to 107 times), followed by analyzing the droplets with an external fluorescence microscope as a standard calibration test. The measured DNA concentration is linearly related to the gradient-dilution factor, which validated the precise quantification for the samples. In addition to the calibration tests using DNA fragments, we also employed this ddPCR-LOAD device for clinical samples with different viruses. Infectious samples containing five different viruses, including influenza A virus (IAV), respiratory syncytial virus (RSV), varicella zoster virus (VZV), Zika virus (ZIKV), and adenovirus (ADV), were injected into the device, followed by analyzing the droplets with an external fluorescence microscope with the lowest detected concentration of 20.24 copies/µL. Finally, we demonstrated the proof-of-concept detection of clinical samples of IAV using the on-disc fluorescence imaging system in our fully integrated device, which proves the capability of this device in clinical sample detection. We anticipate that this integrated ddPCR-LOAD device will become a flexible tool for on-site disease detection.

Enhanced EPIRISK tool for rapid epidemic risk analysis

OBJECTIVES

This study aims to create an enhanced EPIRISK tool in order to correctly predict COVID-19 severity in various countries. The original EPIRISK tool was developed in 2018 to predict the epidemic risk and prioritise response. The tool was validated against nine historical outbreaks prior to 2020. However, it rated many high-income countries that had poor performance during the COVID-19 pandemic as having lower epidemic risk.

STUDY DESIGN

This study was designed to modify EPIRISK by reparameterizing risk factors and validate the enhanced tool against different outbreaks, including COVID-19.

METHODS

We identified three factors that could be indicators of poor performance witnessed in some high-income countries: leadership, culture and universal health coverage. By adding these parameters to EPIRISK, we created a series of models for the calibration and validation. These were tested against non-COVID outbreaks in nine countries and COVID-19 outbreaks in seven countries to identify the best-fit model. The COVID-19 severity was determined by the global incidence and mortality, which were equally divided into four levels.

RESULTS

The enhanced EPIRISK tool has 17 parameters, including seven disease-related and 10 country-related factors, with an algorithm developed for risk level classification. It correctly predicted the risk levels of COVID-19 for all seven countries and all nine historical outbreaks.

CONCLUSIONS

The enhanced EPIRSIK is a multifactorial tool that can be widely used in global infectious disease outbreaks for rapid epidemic risk analysis, assisting first responders, government and public health professionals with early epidemic preparedness and prioritising response to infectious disease outbreaks.

Authoritarianism, perceptions of security threats, and the COVID-19 pandemic: A new perspective

This article offers a new perspective on when and why individual-level authoritarian perceptions of security threats change. We reexamine claims that authoritarian members of the public responded to the COVID-19 pandemic in a counterintuitive fashion. The response was counterintuitive in that, rather than a desire for a stronger government with the ability to impose measures to address the pandemic and its consequences, authoritarian individuals rejected a stronger government response and embraced individual autonomy. The article draws on perceptions of security threats-issues that directly or indirectly harm personal or collective safety and welfare-from surveys in two different contexts in England: 2012, when perceptions of the threat from infectious disease was low relative to most other security threats, and 2020, when perceptions of the personal and collective threat of COVID-19 superseded all other security threats. We argue that the authoritarian response was not counterintuitive once we account for the type of threat it represented.

Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence

Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.

Local implementation of public health policies revealed by the COVID-19 crisis: the French case

BACKGROUND

Improving health system performance depends on the quality of health policy implementation at the local level. However, in general, the attention of researchers is mainly directed towards issues of health policy design and evaluation rather than implementation at the local level. The management of the COVID-19 crisis, especially in Europe, has particularly highlighted the complexity of implementing health policies, decided at the national or supranational level, at the local level.

METHODS

We conducted 23 semi-structured interviews with the main stakeholders in the management of the COVID-19 crisis in the second largest French region in order to identify the different actors and modes of coordination of the local implementation of health policies that this crisis management illustrates in a very visible way. Our methodology is complemented by a content analysis of the main guidelines and decisions related to this implementation.

RESULTS

The analysis of these data allows us to identify three levels of implementation of health policies at the local level (administrative, organizational and operational). Interviews also reveal the existence of different types of coordination specific to each of these levels of local implementation of health policies. These results then make it possible to identify important managerial avenues for promoting global coordination of these three levels of implementation.

CONCLUSIONS

Although research on health services emphasizes the existence of several levels of local implementation of health policies, it offers little in the way of definition or characterization of these levels. The identification in this study of the three levels of local implementation of health policies and their specific forms of coordination contribute to a more precise characterization of this implementation in order to promote, in practice, its global coordination.

Impact of simplicial complexes on epidemic spreading in partially mapping activity-driven multiplex networks

Over the past decade, the coupled spread of information and epidemic on multiplex networks has become an active and interesting topic. Recently, it has been shown that stationary and pairwise interactions have limitations in describing inter-individual interactions , and thus, the introduction of higher-order representation is significant. To this end, we present a new two-layer activity-driven network epidemic model, which considers the partial mapping relationship among nodes across two layers and simultaneously introduces simplicial complexes into one layer, to investigate the effect of 2-simplex and inter-layer mapping rate on epidemic transmission. In this model, the top network, called the virtual information layer, characterizes information dissemination in online social networks, where information can be diffused through simplicial complexes and/or pairwise interactions. The bottom network, named as the physical contact layer, denotes the spread of infectious diseases in real-world social networks. It is noteworthy that the correspondence among nodes between two networks is not one-to-one but partial mapping. Then, a theoretical analysis using the microscopic Markov chain (MMC) method is performed to obtain the outbreak threshold of epidemics, and extensive Monte Carlo (MC) simulations are also carried out to validate the theoretical predictions. It is obviously shown that MMC method can be used to estimate the epidemic threshold; meanwhile, the inclusion of simplicial complexes in the virtual layer or introductory partial mapping relationship between layers can inhibit the spread of epidemics. Current results are conducive to understanding the coupling behaviors between epidemics and disease-related information.

Use of interviewer-administered telephone surveys during infectious disease outbreaks, epidemics and pandemics: a scoping review

INTRODUCTION

During the COVID-19 crisis, researchers had to collect data remotely. Telephone surveys and interviews can quickly gather data from a distance without heavy expense. Although interviewer-administered telephone surveys (IATS) can accommodate the needs of international public health research, the literature on their use during infectious disease outbreaks is scarce. This scoping review aimed to map the characteristics of IATS during infectious disease outbreaks.

METHODS

IATS conducted principally during infectious disease outbreaks and answered by informants at least 18 years old were searched from PubMed and EBSCO. There was a manual addition of relevant documents identified during an initial search. Overall trends were reported using different groupings, including WHO regions, and study details were compared before and during the COVID-19 pandemic.

RESULTS

70 IATS published between 2003 and 2022 were identified. 57.1% were conducted during the COVID-19 pandemic. Among 30 IATS conducted before the COVID-19 pandemic in the world, only 3.3% were carried out in low-income and middle-income countries (LMICs). This percentage of studies in LMICs out of all the IATS rose to 32.5% during the pandemic. The share of qualitative studies grew from 6.7% before the COVID-19 outbreak to 32.5% during the outbreak. IATS performed during the COVID-19 pandemic focused on more diverse, specific population groups, such as patients and healthcare professionals. Mobile phones are increasingly used for IATS over time.

CONCLUSION

IATS are used globally with high frequency in the Western Pacific Region and high-income countries. Technical and financial challenges continue to exist, and assessments of inclusiveness and representativeness should be carefully conducted. A lack of details related to methods was observed, and this scoping review urges researchers using this data collection method in the future to specify how they executed IATS for better use and more efficient deployment.

Transformative dimensions of resilience and brittleness during health systems' collapse: a case study in Brazil using the Functional Resonance Analysis Method

BACKGROUND

As health systems struggle to tackle the spread of Covid-19, resilience becomes an especially relevant attribute and research topic. More than strength or preparedness, to perform resiliently to emerging shocks, health systems must develop specific abilities that aim to increase their potential to adapt to extraordinary situations while maintaining their regular functioning. Brazil has been one of the most affected countries during the pandemic. In January 2021, the Amazonas state's health system collapsed, especially in the city of Manaus, where acute Covid-19 patients died due to scarcity of medical supplies for respiratory therapy.

METHODS

This paper explores the case of the health system's collapse in Manaus to uncover the elements that prevented the system from performing resiliently to the pandemic, by carrying out a grounded-based systems analysis of the performance of health authorities in Brazil using the Functional Resonance Analysis Method. The major source of information for this study was the reports from the congressional investigation carried out to unveil the Brazilian response to the pandemic.

RESULTS

Poor cohesion between the different levels of government disrupted essential functions for managing the pandemic. Moreover, the political agenda interfered in the abilities of the system to monitor, respond, anticipate, and learn, essential aspects of resilient performance.

CONCLUSIONS

Through a systems analysis approach, this study describes the implicit strategy of "living with Covid-19", and an in-depth view of the measures that hampered the resilience of the Brazilian health system to the spread of Covid-19.

The moderating role of Covid-19-related support on urban livelihood capitals: Evidence from suburban Accra

In the Global South, the COVID-19 crisis has compelled varied efforts to quickly address the pandemic's impact on urban livelihoods. Families, friends as well as public, private, and civil society organizations have mobilized various resources to avert the pandemic's onslaught on the survival of the urban vulnerable. Indeed, there is a burgeoning ‘pandemic urban scholarship’ that shed insights on COVID-19 risks, local responses, and impacts on everyday urban life. Yet, it is unclear how many of these responses are affecting urban livelihoods. This paper thus investigates the impact of COVID-19 on urban livelihood capitals (financial, human, social, and physical) and analyses the moderating role of COVID-19-related support (from families, friends, government agencies, faith-based and non-governmental organizations) to address the pandemic's impact on these capitals. Drawing on a quantitative study in Adenta Municipality of the Greater Accra Region, Ghana, the study finds a negative association between COVID-19 impacts and all urban livelihood capitals. Crucially, COVID-19-related support only reduced the negative impact of the pandemic on financial capital, and not on the other forms of capital. The study suggests that building post-pandemic community resilience warrants the need to transition from the usual reactive, fragmented support to integrated, holistic, and contextually embedded long-term strategies that consider the multi-dimensionality of everyday urban life.

Rapid evidence review: Policy actions for the integration of public health and health care in the United States

Objective

To identify policy actions that may improve the interface of public health and health care in the United States.

Methods

A rapid review of publicly-available documents informing the integration of public health and health care, and case examples reporting objective measures of success, with abstraction of policy actions, related considerations, and outcomes.

Results

Across 109 documents, there were a number of recurrent themes related to policy actions and considerations to facilitate integration during peace time and during public health emergencies. The themes could be grouped into the need for adequate and dedicated funding; mandates and shared governance for integration; joint leadership that has the authority/ability to mobilize shared assets; adequately staffed and skilled workforces in both sectors with mutual awareness of shared functions; shared health information systems with modernized data and IT capabilities for both data collection and dissemination of information; engagement with multiple stakeholders in the community to be maximally inclusive; and robust communication strategies and training across partners and with the public.

Conclusion

While the evidence does not support a hierarchy of policies on strengthening the interface of public health and health care, recurrent policy themes can inform where to focus efforts.

Public Health Implications of Invasive Plants: A Scientometric Study

Movements of organisms through distinct places can change the dynamics of ecological interactions and make the habitat conducive to the spread of diseases. Faced with a cyclical scenario of invasions and threats in a One Health context, we conducted a scientometric study to understand how disturbances in environments with invaded vegetation affect the incidence of parasites and disease prevalence rates. The search was carried out in Web of Science and Scopus databases, with keywords delimited by Boolean operators and based on the PRISMA protocol. Thirty-sixarticles were full-read to clarify the interaction between diseases and invaded areas. The analysis covered publications from 2005 to 2022, with a considerable increase in the last ten years and a significant participation of the USA on the world stage. Trends were found in scientific activities, and we explored how invasive species can indirectly damage health, as higher concentrations of pathogens, vectors, and hosts were related to structurally altered communities. This paper reveals invaded plants threats that enhance disease transmission risks. It is likely that, with frequent growth in the number of introduced species worldwide due to environmental disturbances and human interventions, the negative implications will be intensified in the coming years.

Politically-polarized perceptions of governmental autonomy-support impact internal motivations to comply with COVID-19 safety guidelines

Compliance with health safety guidelines is essential during pandemics. However, political polarization in the U.S. is reducing compliance. We investigated how polarized perceptions of government leaders' autonomy-support and enforcement policies impacted security and internally-motivated compliance with national (Study 1a) and state (Study 1b) safety guidelines. We surveyed 773 Republicans and Democrats from four states (California, Florida, New York, Texas) during the first wave of the 2020 COVID-19 pandemic. Overall, participants perceived that the decision processes of opposing political administrations did not support their autonomy. Lack of autonomy-support was associated with reduced security and internal motivations to comply (R ² = 50.83%). When political administrations enforced health safety mandates (Democrat state leaders in this study) and were perceived as autonomy-supportive, participants reported the highest security and internally-motivated compliance (R ² = 49.57%). This effect was especially pronounced for Republicans, who reacted negatively to enforcement without autonomy-support. Political leaders who use fair and supportive decision-making processes may legitimize enforcement of health safety guidelines, improving compliance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11031-022-09974-x.

Re-evaluating Our Knowledge of Health System Resilience During COVID-19: Lessons From the First Two Years of the Pandemic

BACKGROUND

Health challenges like coronavirus disease 2019 (COVID-19) are becoming increasingly complex, transnational, and unpredictable. Studying health system responses to the COVID-19 pandemic is an opportunity to enhance our understanding of health system resilience and establish a clearer link between theoretical concepts and practical ideas on how to build resilience.

METHODS

This narrative literature review aims to address four questions using a health system resilience framework: (i) What do we understand about the dimensions of resilience? (ii) What aspects of the resilience dimensions remain uncertain? (iii) What aspects of the resilience dimensions are missing from the COVID-19 discussions? and (iv) What has COVID-19 taught us about resilience that is missing from the framework? A scientific literature database search was conducted in December 2020 and in April 2022 to identify publications that discussed health system resilience in relation to COVID-19, excluding articles on psychological and other types of resilience. A total of 63 publications were included.

RESULTS

There is good understanding around information sharing, flexibility and good leadership, learning, maintaining essential services, and the need for legitimate, interdependent systems. Decision-making, localized trust, influences on interdependence, and transformation remain uncertain. Vertical interdependence, monitoring risks beyond the health system, and consequences of changes on the system were not discussed. Teamwork, actor legitimacy, values, inclusivity, trans-sectoral resilience, and the role of the private sector are identified as lessons from COVID-19 that should be further explored for health system resilience.

CONCLUSION

Knowledge of health system resilience has continued to cohere following the pandemic. The eventual consequences of system changes and the resilience of subsystems are underexplored. Through governance, the concept of health system resilience can be linked to wider issues raised by the pandemic, like inclusivity. Our findings show the utility of resilience theory for strengthening health systems for crises and the benefit of continuing to refine existing resilience theory.

Spatial governance for COVID-19 prevention and control in China's development zones

Mandatory policy networks are an important collaborative governance model for crisis response. To reveal the operation and effectiveness of public sector-led crisis governance at the development zone level, this study draws on collaborative governance theory to develop a theoretical framework that reveals the external constraints, collaborative dynamics, collaborative actions, and collaborative outcomes of crisis governance in development zones. Based on qualitative research methods, this study analyzes pandemic prevention policy documents issued during the pandemic by China's national economic and technological development zones and their localities to reflect the complete process of governance. The findings indicate that a mandatory policy network, guided by a local governance framework, facilitated the rapid achievement of collaboration in development zones in responding to the crisis. Top-down leadership developed over time in the public sector, and the responsiveness and innovation of enterprises and social organizations played an important role in collaborative governance. Wins at each stage of the governance process are necessary for the continuation of collaborative actions and can drive the adaptation of a collaborative approach in development zones.

Unveiling conflicting strategies in the Brazilian response to COVID-19: A cross-sectional study using the Functional Resonance Analysis Method

By the time the present study was completed, Brazil had been the second epicenter of COVID-19. In addition, the actions taken to respond to the pandemic in Brazil were the subject of extensive debate, since some diverged from recommendations from health authorities and scientists. Since then, the resulting political and social turmoil showed conflicting strategies to tackle the pandemic in Brazil, with visible consequences in the numbers of casualties, but also with effects on the resilience of the overall health system. Thus, this article explores the actions taken in Brazil to cope with the pandemic from a systems analysis perspective. The structure of the domain was analyzed using Work Domain Analysis, and the activated functions were analyzed using the Functional Resonance Analysis Method, identifying the variability resulting from the conflicting strategies carried out and the consequences to the capacity of the Brazilian health system to respond resiliently to the pandemic. Results of the study show that functions that overlapped the operation of the overall system were introduced, causing the health system to operate under conflicting objectives, in which functions were created to restrict the outcomes of each other during the entire COVID-19 crisis.

Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses

COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine how to reduce the risk of future events. We review major RNA virus outbreaks since 1967 to identify common features and opportunities to prevent emergence, including ancestral viral origins in birds, bats, and other mammals; animal reservoirs and intermediate hosts; and pathways for zoonotic spillover and community spread, leading to local, regional, or international outbreaks. The increasing scientific evidence concerning the origins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is most consistent with a zoonotic origin and a spillover pathway from wildlife to people via wildlife farming and the wildlife trade. We apply what we know about these outbreaks to identify relevant, feasible, and implementable interventions. We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife–livestock–human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential. We discuss new models to address the challenges of creating an inclusive and effective governance structure, with the necessary stable funding for cross-disciplinary collaborative research. Finally, we offer recommendations for feasible actions to close the knowledge gaps across the One Health continuum and improve preparedness and response in the future.

A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

Emerging diseases caused by coronaviruses of likely bat origin (e.g., SARS, MERS, SADS, COVID-19) have disrupted global health and economies for two decades. Evidence suggests that some bat SARS-related coronaviruses (SARSr-CoVs) could infect people directly, and that their spillover is more frequent than previously recognized. Each zoonotic spillover of a novel virus represents an opportunity for evolutionary adaptation and further spread; therefore, quantifying the extent of this spillover may help target prevention programs. We derive current range distributions for known bat SARSr-CoV hosts and quantify their overlap with human populations. We then use probabilistic risk assessment and data on human-bat contact, human viral seroprevalence, and antibody duration to estimate that a median of 66,280 people (95% CI: 65,351–67,131) are infected with SARSr-CoVs annually in Southeast Asia. These data on the geography and scale of spillover can be used to target surveillance and prevention programs for potential future bat-CoV emergence.

Coronaviruses may spill over from bats to humans. This study uses epidemiological data, species distribution models, and probabilistic risk assessment to map overlap among people and SARSr-CoV bat hosts and estimate how many people are infected with bat-origin SARSr-CoVs in Southeast Asia annually.

Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology

Background

Knowledges graphs (KGs) serve as a convenient framework for structuring knowledge. A number of computational methods have been developed to generate KGs from biomedical literature and use them for downstream tasks such as link prediction and question answering. However, there is a lack of computational tools or web frameworks to support the exploration and visualization of the KG themselves, which would facilitate interactive knowledge discovery and formulation of novel biological hypotheses.

Method

We developed a web framework for Knowledge Graph Exploration and Visualization (KGEV), to construct and visualize KGs in five stages: triple extraction, triple filtration, metadata preparation, knowledge integration, and graph database preparation. The application has convenient user interface tools, such as node and edge search and filtering, data source filtering, neighborhood retrieval, and shortest path calculation, that work by querying a backend graph database. Unlike other KGs, our framework allows fast retrieval of relevant texts supporting the relationships in the KG, thus allowing human reviewers to judge the reliability of the knowledge extracted.

Results

We demonstrated a case study of using the KGEV framework to perform research on COVID-19. The COVID-19 pandemic resulted in an explosion of relevant literature, making it challenging to make full use of the vast and heterogenous sources of information. We generated a COVID-19 KG with heterogenous information, including literature information from the CORD-19 dataset, as well as other existing knowledge from eight data sources. We showed the utility of KGEV in three intuitive case studies to explore and query knowledge on COVID-19. A demo of this web application can be accessed at http://covid19nlp.wglab.org. Finally, we also demonstrated a turn-key adaption of the KGEV framework to study clinical phenotypic presentation of human diseases by Human Phenotype Ontology (HPO), illustrating the versatility of the framework.

Conclusion

In an era of literature explosion, the KGEV framework can be applied to many emerging diseases to support structured navigation of the vast amount of newly published biomedical literature and other existing biological knowledge in various databases. It can be also used as a general-purpose tool to explore and query gene-phenotype-disease-drug relationships interactively.

Trust in the U.S. Government and Its Health Agencies in the Time of COVID-19

This article examines the factors affecting Americans' trust in their federal government and its health agencies during the COVID-19 public health crisis. More specifically, we examine the evolution of Americans' trust in their government and health system and how, in the context of the COVID-19 pandemic response, it has been affected by multiple factors. Several academic journals, government policy recommendations and public health polls were evaluated to understand the public's trust in the federal government and its health institutions. Public trust in institutions during a global pandemic is essential in influencing adherence to a pandemic response (both non-pharmaceutical and medical interventions). Americans' trust in institutions is built and maintained by a variety of factors. We focus on: political polarization and involvement, media influence and health communications, history of systemic racism and socioeconomic inequalities, and pandemic fatigue. Based on the interplay of these factors, we conclude with recommendations for future pandemic response strategies.

Investigating public support for biosecurity measures to mitigate pathogen transmission through the herpetological trade

The expanding global trade in herpetofauna has contributed to new infectious disease dynamics and pathways that allow for the rapid spread of pathogens geographically. Improved biosecurity is needed to mitigate adverse biodiversity, economic and human health impacts associated with pathogen transmission through the herpetological trade. However, general lack of knowledge of the pathogen transmission risks associated with the global trade in herpetofauna and public opposition to biosecurity measures are critical obstacles to successfully preventing pathogen transmission. In 2019 we administered a survey to 2,007 members of the public in the United States of America to ascertain their support for interventions to prevent the spread of Batrachochytrium dendrobatidis (Bd), Batrachochytrium salamandrivorans (Bsal), ranaviruses, and Salmonella through the herpetological trade. We presented survey respondents with different potential hazards associated with pathogen transmission through this trade, namely ecological, economic, and human health impacts. We used structural equation models to determine how these different hazards and respondents’ characteristics influenced respondents’ support for quarantine and veterinary observation of herpetofauna imported into the United States, mandatory tests for diseases of concern, and best practices to reduce stress and improve the care of live herpetofauna during transport to the United States. Respondents’ values and their perceived susceptibility and sensitivity to different hazards associated with pathogen transmission were key determinants of their support for biosecurity. Respondents with strong biospheric and altruistic values demonstrated sensitivity to ecological and human health impacts associated with pathogen transmission, whereas respondents with strong egoistic values demonstrated sensitivity to economic impacts. Respondents had limited knowledge of Bd, Bsal or ranaviruses, the size of the herpetological trade, or how this trade may contribute to pathogen transmission. Improved outreach and education on pathogen transmission through the herpetological trade is required, but it is important that messages are tailored to people with different values to elicit their support for biosecurity.

How an outbreak became a pandemic: a chronological analysis of crucial junctures and international obligations in the early months of the COVID-19 pandemic

Understanding the spread of SARS-CoV-2, how and when evidence emerged, and the timing of local, national, regional, and global responses is essential to establish how an outbreak became a pandemic and to prepare for future health threats. With that aim, the Independent Panel for Pandemic Preparedness and Response has developed a chronology of events, actions, and recommendations, from December, 2019, when the first cases of COVID-19 were identified in China, to the end of March, 2020, by which time the outbreak had spread extensively worldwide and had been characterised as a pandemic. Datapoints are based on two literature reviews, WHO documents and correspondence, submissions to the Panel, and an expert verification process. The retrospective analysis of the chronology shows a dedicated initial response by WHO and some national governments, but also aspects of the response that could have been quicker, including outbreak notifications under the International Health Regulations (IHR), presumption and confirmation of human-to-human transmission of SARS-CoV-2, declaration of a Public Health Emergency of International Concern, and, most importantly, the public health response of many national governments. The chronology also shows that some countries, largely those with previous experience with similar outbreaks, reacted quickly, even ahead of WHO alerts, and were more successful in initially containing the virus. Mapping actions against IHR obligations, the chronology shows where efficiency and accountability could be improved at local, national, and international levels to more quickly alert and contain health threats in the future. In particular, these improvements include necessary reforms to international law and governance for pandemic preparedness and response, including the IHR and a potential framework convention on pandemic preparedness and response.

High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples

In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using established visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable “how-to” reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and long-read nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.

The U.S. Needs a National Human Health Observing System

The COVID-19 pandemic and increasing frequency and severity of environmental disasters reveal an urgent need for a robust health observing/surveillance system. With the possible exception of Brazil, we know of no such comprehensive health observing capacity. The US should create a national system of linked regionally-based health monitoring systems similar to those for weather, ocean conditions, and climate. Like those for weather, the health observing system should operate continuously, collecting mental, physical, and community health data before, during, and after events. The system should include existing cross-sectional health data surveys, along with significant new investment in regional longitudinal cohort studies. The recently described framework for a Gulf of Mexico Community Health Observing System is suggested as a potential model for development of a nation-wide system.

A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

Emerging diseases caused by coronaviruses of likely bat origin (e.g. SARS, MERS, SADS and COVID-19) have disrupted global health and economies for two decades. Evidence suggests that some bat SARS-related coronaviruses (SARSr-CoVs) could infect people directly, and that their spillover is more frequent than previously recognized. Each zoonotic spillover of a novel virus represents an opportunity for evolutionary adaptation and further spread; therefore, quantifying the extent of this "hidden" spillover may help target prevention programs. We derive biologically realistic range distributions for known bat SARSr-CoV hosts and quantify their overlap with human populations. We then use probabilistic risk assessment and data on human-bat contact, human SARSr-CoV seroprevalence, and antibody duration to estimate that ∼400,000 people (median: ∼50,000) are infected with SARSr-CoVs annually in South and Southeast Asia. These data on the geography and scale of spillover can be used to target surveillance and prevention programs for potential future bat-CoV emergence.

Impact of information diffusion on epidemic spreading in partially mapping two-layered time-varying networks

We propose a new epidemic model considering the partial mapping relationship in a two-layered time-varying network, which aims to study the influence of information diffusion on epidemic spreading. In the model, one layer represents the epidemic-related information diffusion in the social networks, while the other layer denotes the epidemic spreading in physical networks. In addition, there just exist mapping relationships between partial pairs of nodes in the two-layered network, which characterizes the interaction between information diffusion and epidemic spreading. Meanwhile, the information and epidemics can only spread in their own layers. Afterwards, starting from the microscopic Markov chain (MMC) method, we can establish the dynamic equation of epidemic spreading and then analytically deduce its epidemic threshold, which demonstrates that the ratio of correspondence between two layers has a significant effect on the epidemic threshold of the proposed model. Finally, it is found that MMC method can well match with Monte Carlo (MC) simulations, and the relevant results can be helpful to understand the epidemic spreading properties in depth.

Basics for Improved Use of Phages for Therapy

Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted removal from blood. Pathogenic bacteria are targets during classical phage therapy. Metastatic tumors are potential future targets, during use of drug delivery vehicles (DDVs) that are phage derived. Phage therapy has, to date, only sometimes been successful. One cause of failure is low phage persistence. A three-step strategy for increasing persistence is to increase (1) the speed of lytic phage isolation, (2) the diversity of phages isolated, and (3) the effectiveness and speed of screening phages for high persistence. The importance of high persistence-screening is illustrated by our finding here of persistence dramatically higher for coliphage T3 than for its relative, coliphage T7, in murine blood. Coliphage T4 is more persistent, long-term than T3. Pseudomonas chlororaphis phage 201phi2-1 has relatively low persistence. These data are obtained with phages co-inoculated and separately assayed. In addition, highly persistent phage T3 undergoes dispersal to several murine organs and displays tumor tropism in epithelial tissue (xenografted human oral squamous cell carcinoma). Dispersal is an asset for phage therapy, but a liability for phage-based DDVs. We propose increased focus on phage persistence—and dispersal—screening.

Vital Directions For Health And Health Care: Priorities For 2021

In 2016, in anticipation of the US presidential election and forthcoming new administration, the National Academy of Medicine launched a strategic initiative to marshal expert guidance on pressing health and health care priorities. Published as Vital Directions for Health and Health Care, the products of the initiative provide trusted, nonpartisan, evidence-based analysis of critical issues in health, health care, and biomedical science. The current collection of articles published in Health Affairs builds on the initial Vital Directions series by addressing a set of issues that have a particularly compelling need for attention from the next administration: health costs and financing, early childhood and maternal health, mental health and addiction, better health and health care for older adults, and infectious disease threats. The articles also reflect the current experience with both the coronavirus disease 2019 (COVID-19) pandemic and the health inequities that have been drawn out sharply by COVID-19, as well as the implications going forward for action.