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Background: Since the COVID-19 pandemic has occurred, nations showed their unpreparedness to deal with a mass casualty incident of this proportion and severity, which resulted in a tremendous number of deaths even among healthcare workers. The World Society of Emergency Surgery conceived this position paper with the purpose of providing evidence-based recommendations for the management of emergency surgical patients under COVID-19 pandemic for the safety of the patient and healthcare workers. Method: A systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) through the MEDLINE (PubMed), Embase and SCOPUS databases. Synthesis of evidence, statements and recommendations were developed in accordance with the GRADE methodology. Results: Given the limitation of the evidence, the current document represents an effort to join selected high-quality articles and experts' opinion. Conclusions: The aim of this position paper is to provide an exhaustive guidelines to perform emergency surgery in a safe and protected environment for surgical patients and for healthcare workers under COVID-19 and to offer the best management of COVID-19 patients needing for an emergency surgical treatment. We recommend screening for COVID-19 infection at the emergency department all acute surgical patients who are waiting for hospital admission and urgent surgery. The screening work-up provides a RT-PCR nasopharyngeal swab test and a baseline (non-contrast) chest CT or a chest X-ray or a lungs US, depending on skills and availability. If the COVID-19 screening is not completed we recommend keeping the patient in isolation until RT-PCR swab test result is not available, and to manage him/she such as an overt COVID patient. The management of COVID-19 surgical patients is multidisciplinary. If an immediate surgical procedure is mandatory, whether laparoscopic or via open approach, we recommend doing every effort to protect the operating room staff for the safety of the patient. [ABSTRACT FROM AUTHOR]

Background: COVID-19 vaccine coverage in low- and middle-income countries continues to be challenging. As supplies increase, coverage is increasingly becoming determined by rollout capacity. Methods: We developed a deterministic compartmental model of COVID-19 transmission to explore how age-, risk-, and dose-specific vaccine prioritisation strategies can minimise severe outcomes of COVID-19 in Sierra Leone. Results: Prioritising booster doses to older adults and adults with comorbidities could reduce the incidence of severe disease by 23% and deaths by 34% compared to the use of these doses as primary doses for all adults. Providing a booster dose to pregnant women who present to antenatal care could prevent 38% of neonatal deaths associated with COVID-19 infection during pregnancy. The vaccination of children is not justified unless there is sufficient supply to not affect doses delivered to adults. Conclusions: Our paper supports current WHO SAGE vaccine prioritisation guidelines (released January 2022). Individuals who are at the highest risk of developing severe outcomes should be prioritised, and opportunistic vaccination strategies considered in settings with limited rollout capacity. [ABSTRACT FROM AUTHOR]

Background: Non-pharmaceutical interventions (NPIs) were adopted in Belgium in order to decrease social interactions between people and as such decrease viral transmission of SARS-CoV-2. With the aim to better evaluate the impact of NPIs on the evolution of the pandemic, an estimation of social contact patterns during the pandemic is needed when social contact patterns are not available yet in real time. Methods: In this paper we use a model-based approach allowing for time varying effects to evaluate whether mobility and pre-pandemic social contact patterns can be used to predict the social contact patterns observed during the COVID-19 pandemic between November 11, 2020 and July 4, 2022. Results: We found that location-specific pre-pandemic social contact patterns are good indicators for estimating social contact patterns during the pandemic. However, the relationship between both changes with time. Considering a proxy for mobility, namely the change in the number of visitors to transit stations, in interaction with pre-pandemic contacts does not explain the time-varying nature of this relationship well. Conclusion: In a situation where data from social contact surveys conducted during the pandemic are not yet available, the use of a linear combination of pre-pandemic social contact patterns could prove valuable. However, translating the NPIs at a given time into appropriate coefficients remains the main challenge of such an approach. In this respect, the assumption that the time variation of the coefficients can somehow be related to aggregated mobility data seems unacceptable during our study period for estimating the number of contacts at a given time. [ABSTRACT FROM AUTHOR]

Background: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. Results: In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. Conclusions: The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs. [ABSTRACT FROM AUTHOR]

Background: Two years into the COVID-19 pandemic and with more than five million deaths worldwide, the healthcare establishment continues to struggle with every new wave of the pandemic resulting from a new coronavirus variant. Research has demonstrated that there are variations in the symptoms, and even in the order of symptom presentations, in COVID-19 patients infected by different SARS-CoV-2 variants (e.g., Alpha and Omicron). Textual data in the form of admission notes and physician notes in the Electronic Health Records (EHRs) is rich in information regarding the symptoms and their orders of presentation. Unstructured EHR data is often underutilized in research due to the lack of annotations that enable automatic extraction of useful information from the available extensive volumes of textual data. Methods: We present the design of a COVID Interface Terminology (CIT), not just a generic COVID-19 terminology, but one serving a specific purpose of enabling automatic annotation of EHRs of COVID-19 patients. CIT was constructed by integrating existing COVID-related ontologies and mining additional fine granularity concepts from clinical notes. The iterative mining approach utilized the techniques of 'anchoring' and 'concatenation' to identify potential fine granularity concepts to be added to the CIT. We also tested the generalizability of our approach on a hold-out dataset and compared the annotation coverage to the coverage obtained for the dataset used to build the CIT. Results: Our experiments demonstrate that this approach results in higher annotation coverage compared to existing ontologies such as SNOMED CT and Coronavirus Infectious Disease Ontology (CIDO). The final version of CIT achieved about 20% more coverage than SNOMED CT and 50% more coverage than CIDO. In the future, the concepts mined and added into CIT could be used as training data for machine learning models for mining even more concepts into CIT and further increasing the annotation coverage. Conclusion: In this paper, we demonstrated the construction of a COVID interface terminology that can be utilized for automatically annotating EHRs of COVID-19 patients. The techniques presented can identify frequently documented fine granularity concepts that are missing in other ontologies thereby increasing the annotation coverage. [ABSTRACT FROM AUTHOR]

Around the world, the 2019 Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised serious public health problems and major medical challenges. The Italian Society of Pediatric Gastroenterology, Hepatology and Nutrition (SIGENP) published several papers on the impact of COVID-19 on the current management, diagnosis, and treatment of acute and chronic gastrointestinal, hepatic, immune-mediated, and functional disorders. The present article summarizes the most relevant SIGENP reports and consensus during and after the peak of the COVID-19 outbreak, including the diagnosis and treatment of inflammatory bowel disease (IBD), indications and timing of digestive endoscopy, and insights into the novel hepatitis. [ABSTRACT FROM AUTHOR]

Introduction: The COVID-19 epidemic and various control and mitigation measures to combat the widespread outbreak of the disease may affect other parts of health care systems. There is a concern that the COVID-19 pandemic could disrupt HIV services. Therefore, this study aimed to systematically evaluate the effect of the COVID-19 pandemic on service delivery and treatment outcomes in people with HIV. Methods: In this study, a systematic search was conducted using the keywords in the online databases including Scopus, PubMed, Web of Science, and Cochrane databases. The retrieved articles underwent a two-step title/abstract and full-text review process, and the eligible papers were selected and included in the qualitative synthesis. Result: We selected 16 studies out of 529 retrieved records that met the inclusion criteria for this review. Study populations of the selected studies were either HIV-positive patients or HIV clinics and healthcare providers. Most studies were focused on adhering to and obtaining medication and attending clinical appointments and their decrement during the pandemic. Other aspects of HIV care (alternative healthcare settings, viral suppression, psychological care, etc.) were discussed to a lesser extent by the included studies. Conclusion: Interruption in in-person visits and medical follow-up services, loss of adherence to treatment, and subsequent increase in mortality due to the COVID-19 pandemic complications in PLHIV have led to growing concerns. Other challenges were psychological disorders such as anxiety and depression, an increase in substance abuse, and a rise in experienced stigma and discrimination. However, the use of telemedicine in some countries helps to alleviate the situation to some extent and is recommended in similar settings in the future. [ABSTRACT FROM AUTHOR]

Due to the high transmission rate and mortality index of the current coronavirus pandemic, many settings in Africa instituted lockdowns to reduce its rate of spread and avert exponential growth rate. At the early stage, this measure seemed to heighten awareness of the virus and subsequently minimized exponential growth of cases. However, these lockdowns have had great consequences on the weak health systems and frail economy in place in many African countries. In this paper, we examine the impact of lockdown measures in these countries and provides key recommendations in dealing with present and future pandemics. [ABSTRACT FROM AUTHOR]

Background: To our knowledge, the treatment, outcome, clinical presentation, risk stratification of patients with venous thromboembolism and COVID-19 have not been well characterized. Methods: We searched for systematic reviews, cohorts, case series, case reports, editor letters, and venous thromboembolism COVID-19 patients' abstracts following PRISMA and PROSPERO statements. We analyzed therapeutic approaches and clinical outcomes of venous thromboembolism COVID-19 patients. Inclusion: COVID-19 patients with venous thromboembolism confirmed by an imaging method (venous doppler ultrasound, ventilation-perfusion lung scan, computed tomography pulmonary angiogram, pulmonary angiography). We assessed and reported the original Pulmonary Embolism Severity Index for each pulmonary embolism patient. In addition, we defined major bleedings according to the International Society of Thrombosis and Haemostasis criteria. Results: We performed a systematic review from August 9 to August 30, 2020. We collected 1,535 papers from PubMed, Scopus, Web of Science, Wiley, and Opengrey. We extracted data from 89 studies that describe 143 patients. Unfractionated and low-molecular-weight heparin was used as parenteral anticoagulation in 85/143 (59%) cases. The Food and Drug Administration-approved alteplase regimen guided the advanced treatment in 39/143 (27%) patients. The mortality was high (21.6%, CI 95% 15.2-29.3). The incidence of major bleeding complications was 1 (0.9%) in the survival group and 1 (3.2%) in the death group. Pulmonary Embolism Severity Index was class I in 11.6% and II in 22.3% in survivors compared to 0% and 6.5% in non-survivors, respectively. Patients who experienced venous thromboembolism events at home were more likely to live than in-hospital events. Conclusions: We determined a high mortality incidence of pulmonary embolism and a low rate of bleeding. Unfractionated and low-molecular-weight heparin drove parenteral anticoagulation and alteplase the advanced treatment in both groups. The original Pulmonary Embolism Severity Index could be helpful in the risk stratification. [ABSTRACT FROM AUTHOR]

Background: The COVID-19 pandemic has affected the world extraordinarily. This disease has a potential to cause a significantly severe course of disease leading to respiratory complications, multiple organ failure and possibly death. In the fight against this pandemic-causing disease, medical professionals around the world are searching for pharmacological agents that could treat and prevent disease progression and mortality. To speed the search of promising treatment options, already existing pharmacological agents are repurposed for the potential treatment of COVID-19 and tested in clinical trials. The aim of this literature review is to investigate the efficacy and safety of repurposed pharmacological agents for the treatment of COVID-19 at different pathophysiologic stages of the disease. For this literature review, online-databases PubMed and Google Scholar were utilised. Keywords "COVID-19", "SARS-CoV-2", "pathogenesis", "drug targets", "pharmacological treatment", "cytokine storm", "coagulopathy" and individual drug names were used. Scientific articles, including reviews, clinical trials, and observational cohorts, were collected and analysed. Furthermore, these articles were examined for references to find more clinical trials testing for the potential treatment of COVID-19. In total, 97 references were used to conduct this research paper.Results: The most beneficial pharmacological agent for the treatment of COVID-19 are corticosteroids, especially dexamethasone, for the treatment of mechanically ventilated COVID-19 patients. Other promising agents are remdesivir for the treatment of patients with COVID-19 pneumonia requiring minimal supplemental oxygen therapy, and IL-6 receptor antagonist monoclonal antibodies in severe COVID-19. Lopinavir/ritonavir, as well as chloroquine or hydroxychloroquine with or without azithromycin demonstrate the least efficacy in the treatment of COVID-19. The clinical benefits of the treatment of a COVID-19-specific coagulopathy with increased dosing of anticoagulation need further research and confirmation of randomised controlled trials.Conclusion: The search for pharmacological treatment of COVID-19 has elicited great controversy. Whereas drugs like chloroquine, hydroxychloroquine, and lopinavir/ritonavir have not shown proven benefit, the agents remdesivir and dexamethasone are recommended for clinical use for the treatment of COVID-19. Further randomised trials for other pharmacological treatment strategies are awaited. [ABSTRACT FROM AUTHOR]

Background: 2019-nCoV has been spreading around the world and becoming a global concern. To prevent further widespread of 2019-nCoV, confirmed and suspected cases of COVID-19 infection are suggested to be kept in quarantine. However, the diagnose of COVID-19 infection is quite time-consuming and labor-intensive. To alleviate the burden on the medical staff, we have done some research on the intelligent diagnosis of COVID-19.Methods: In this paper, we constructed a COVID-19 Diagnosis Ontology (CDO) by utilizing Protégé, which includes the basic knowledge graph of COVID-19 as well as diagnostic rules translated from Chinese government documents. Besides, SWRL rules were added into the ontology to infer intimate relationships between people, thus facilitating the efficient diagnosis of the suspected cases of COVID-19 infection. We downloaded real-case data and extracted patients' syndromes from the descriptive text, so as to verify the accuracy of this experiment.Results: After importing those real instances into Protégé, we demonstrated that the COVID-19 Diagnosis Ontology showed good performances to diagnose cases of COVID-19 infection automatically.Conclusions: In conclusion, the COVID-19 Diagnosis Ontology will not only significantly reduce the manual input in the diagnosis process of COVID-19, but also uncover hidden cases and help prevent the widespread of this epidemic. [ABSTRACT FROM AUTHOR]

Background: The global spread of the novel coronavirus pneumonia is still continuing, and a new round of more serious outbreaks has even begun in some countries. In this context, this paper studies the dynamics of a type of delayed reaction-diffusion novel coronavirus pneumonia model with relapse and self-limiting treatment in a temporal-spatial heterogeneous environment.Methods: First, focus on the self-limiting characteristics of COVID-19, incorporate the relapse and self-limiting treatment factors into the diffusion model, and study the influence of self-limiting treatment on the diffusion of the epidemic. Second, because the traditional Lyapunov stability method is difficult to determine the spread of the epidemic with relapse and self-limiting treatment, we introduce a completely different method, relying on the existence conditions of the exponential attractor of our newly established in the infinite-dimensional dynamic system to determine the diffusion of novel coronavirus pneumonia. Third, relapse and self-limiting treatment have led to a change in the structure of the delayed diffusion COVID-19 model, and the traditional basic reproduction number [Formula: see text] no longer has threshold characteristics. With the help of the Krein-Rutman theorem and the eigenvalue method, we studied the threshold characteristics of the principal eigenvalue and found that it can be used as a new threshold to describe the diffusion of the epidemic.Results: Our results prove that the principal eigenvalue [Formula: see text] of the delayed reaction-diffusion COVID-19 system with relapse and self-limiting treatment can replace the basic reproduction number [Formula: see text] to describe the threshold effect of disease transmission. Combine with the latest official data and the prevention and control strategies, some numerical simulations on the stability and global exponential attractiveness of the diffusion of the COVID-19 epidemic in China and the USA are given.Conclusions: Through the comparison of numerical simulations, we find that self-limiting treatment can significantly promote the prevention and control of the epidemic. And if the free activities of asymptomatic infected persons are not restricted, it will seriously hinder the progress of epidemic prevention and control. [ABSTRACT FROM AUTHOR]

Background: During the first wave of the COVID-19 pandemic various ambulatory health care models (SARS-CoV-2 contact points: Subspecialised Primary Care Practices, Fever Clinics, and Special Places for Corona-Testing) were organised in a short period in Baden-Wuerttemberg, a region in Southern Germany. The aim of these SARS-CoV-2 contact points was to ensure medical treatment for patients with (suspected) and without SARS-CoV-2 infection. The present study aimed to assess the beliefs and practices of primary care physicians who either led a Subspecialised Primary Care Practice or a Primary Care Practice providing care as usual in Baden-Wuerttemberg during the first wave of the COVID-19 pandemic. Methods: This cross-sectional study was based on a paper-based questionnaire in primary care physicians during the first wave of the pandemic. Participants were identified via the web page of the Association of Statutory Health Insurance Physicians Baden-Wuerttemberg. The questionnaire was distributed in June and July 2020. It measured knowledge, practices, self-efficacy and fears towards SARS-CoV-2, using newly developed questions. Data was descriptively analysed. Results: One hundred fifty-five participants (92 leads of SARS-CoV-2 contact points/ 63 leads of primary care practices) completed the questionnaire. Out of 92 leads of SARS-CoV-2 contact points 74 stated to lead n Subspecialised Primary Care Practices. About half participants of both groups did not fear an own infection with the novel virus (between 50.8% and 62.2%), however about 75% feared financial loss. Knowledge was gained using various sources; main sources were the Association of Statutory Health Insurance Physicians (between 82.5% and 83.8%) and the German Society for Hygiene and Microbiology (RKI) (between 88.9% and 95.9%). Leads of Subspecialised Primary Care Practice felt more confident to perform anamnestic/diagnostic procedures (p < 0.001). The same was found for the confidence level regarding decision-making concerning the further treatment (p < 0.001). Several prevention measures to contain the spread of SARS-CoV-2 were adopted. Subspecialised Primary Care Practice had treated on average more patients with (suspected) COVID-19 (mean 408.12) than primary care practices (mean 83.8) (p < 0.001). Conclusion: The results of this study suggest that the Subspecialised Primary Care Practice that were implemented during the first wave of the SARS-CoV-2 pandemic contributed containment of the pandemic. Leads of Subspecialised Primary Care Practice indicated that physical separation of patients with potential SARS-CoV-2 infection was easier compared to those who continued working in their own practice. Additionally, leads of Subspecialised Primary Care Practice felt more confident in dealing with patients with SARS-CoV-2 infection. Trial registration: The study has been prospectively registered at the German Clinical Trial Register (DRKS00022224). [ABSTRACT FROM AUTHOR]

Background: With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and comprehensive picture of host-coronavirus interaction (HCI) mechanisms. As of early April 2021, the ImmPort database has stored 7 studies (with 6 having details) that cover topics including molecular immune signatures, epitopes, and sex differences in terms of mortality in COVID-19 patients. The Coronavirus Infectious Disease Ontology (CIDO) represents basic HCI information. We hypothesize that the CIDO can be used as the platform to represent newly recorded information from ImmPort leading the reinforcement of CIDO. Methods: The CIDO was used as the semantic platform for logically modeling and representing newly identified knowledge reported in the 6 ImmPort studies. A recursive eXtensible Ontology Development (XOD) strategy was established to support the CIDO representation and enhancement. Secondary data analysis was also performed to analyze different aspects of the HCI from these ImmPort studies and other related literature reports. Results: The topics covered by the 6 ImmPort papers were identified to overlap with existing CIDO representation. SARS-CoV-2 viral S protein related HCI knowledge was emphasized for CIDO modeling, including its binding with ACE2, mutations causing different variants, and epitope homology by comparison with other coronavirus S proteins. Different types of cytokine signatures were also identified and added to CIDO. Our secondary analysis of two cohort COVID-19 studies with cytokine panel detection found that a total of 11 cytokines were up-regulated in female patients after infection and 8 cytokines in male patients. These sex-specific gene responses were newly modeled and represented in CIDO. A new DL query was generated to demonstrate the benefits of such integrative ontology representation. Furthermore, IL-10 signaling pathway was found to be statistically significant for both male patients and female patients. Conclusion: Using the recursive XOD strategy, six new ImmPort COVID-19 studies were systematically reviewed, the results were modeled and represented in CIDO, leading to the enhancement of CIDO. The enhanced ontology and further seconary analysis supported more comprehensive understanding of the molecular mechanism of host responses to COVID-19 infection. [ABSTRACT FROM AUTHOR]

International air travel has been highlighted as a concern since the beginning of the COVID-19 pandemic with respect to importation of cases. We summarise the available evidence for in-flight transmission of wild type SARS-CoV-2 during 2020, and for imported COVID-19 clusters to cause outbreaks. This paper provides a data baseline prior to the emergence of new mutations causing SARS-CoV-2 variants of concern, whose characteristics may increase the potential risk of in-flight transmission and imported outbreaks. The evidence on in-flight transmission of wild-type SARS-CoV-2 is limited, and is described in a small number of published reports. Most of the available evidence pertains to the early phase of the COVID-19 pandemic, during a period without non-pharmaceutical interventions such as distancing and in-flight mask wearing. There is considerable potential for outbreaks of COVID-19 from imported cases or clusters when public health guidance around quarantine of travellers and self-isolation of cases is not adhered to. Risks can be mitigated by measures such as: avoiding non-essential travel, targeted testing and quarantine of travellers from high incidence regions or regions of concern, managed quarantine processes, and protocols for rapid investigation and control of transmission from a possible variant of concern. Measures should be dynamically assessed and proportionate to the level of risk. [ABSTRACT FROM AUTHOR]

Background: The ongoing COVID-19 pandemic has highlighted the vast differences in approaches to the control and containment of coronavirus across the world and has demonstrated the varied success of such approaches in minimizing the transmission of coronavirus. While previous studies have demonstrated high predictive power of incorporating air travel data and governmental policy responses in global disease transmission modelling, factors influencing the decision to implement travel and border restriction policies have attracted relatively less attention. This paper examines the role of globalization on the pace of adoption of international travel-related non-pharmaceutical interventions (NPIs) during the coronavirus pandemic. This study aims to offer advice on how to improve the global planning, preparation, and coordination of actions and policy responses during future infectious disease outbreaks with empirical evidence.Methods and Data: We analyzed data on international travel restrictions in response to COVID-19 of 185 countries from January to October 2020. We applied time-to-event analysis to examine the relationship between globalization and the timing of travel restrictions implementation.Results: The results of our survival analysis suggest that, in general, more globalized countries, accounting for the country-specific timing of the virus outbreak and other factors, are more likely to adopt international travel restrictions policies. However, countries with high government effectiveness and globalization were more cautious in implementing travel restrictions, particularly if through formal political and trade policy integration. This finding is supported by a placebo analysis of domestic NPIs, where such a relationship is absent. Additionally, we find that globalized countries with high state capacity are more likely to have higher numbers of confirmed cases by the time a first restriction policy measure was taken.Conclusions: The findings highlight the dynamic relationship between globalization and protectionism when governments respond to significant global events such as a public health crisis. We suggest that the observed caution of policy implementation by countries with high government efficiency and globalization is a by-product of commitment to existing trade agreements, a greater desire to 'learn from others' and also perhaps of 'confidence' in a government's ability to deal with a pandemic through its health system and state capacity. Our results suggest further research is warranted to explore whether global infectious disease forecasting could be improved by including the globalization index and in particular, the de jure economic and political, and de facto social dimensions of globalization, while accounting for the mediating role of government effectiveness. By acting as proxies for a countries' likelihood and speed of implementation for international travel restriction policies, such measures may predict the likely time delays in disease emergence and transmission across national borders. [ABSTRACT FROM AUTHOR]

The early identification of asymptomatic yet infectious cases is vital to curb the 2019 coronavirus (COVID-19) pandemic and to control the disease in the post-pandemic era. In this paper, we propose a fast, inexpensive and high-throughput approach using painless nasal-swab self-collection followed by direct RT-qPCR for the sensitive PCR detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This approach was validated in a large prospective cohort study of 1038 subjects, analysed simultaneously using (1) nasopharyngeal swabs obtained with the assistance of healthcare personnel and analysed by classic two-step RT-qPCR on RNA isolates and (2) nasal swabs obtained by self-collection and analysed with direct RT-qPCR. Of these subjects, 28.6% tested positive for SARS-CoV-2 using nasopharyngeal swab sampling. Our direct RT-qPCR approach for self-collected nasal swabs performed well with results similar to those of the two-step RT-qPCR on RNA isolates, achieving 0.99 positive and 0.98 negative predictive values (cycle threshold [Ct] < 37). Our research also reports on grey-zone viraemia, including samples with near-cut-off Ct values (Ct ≥ 37). In all investigated subjects (n = 20) with grey-zone viraemia, the ultra-small viral load disappeared within hours or days with no symptoms. Overall, this study underscores the importance of painless nasal-swab self-collection and direct RT-qPCR for mass testing during the SARS-CoV-2 pandemic and in the post-pandemic era. [ABSTRACT FROM AUTHOR]

Background: During the first wave of the COVID-19 pandemic various ambulatory health care models (SARS-CoV-2 contact points: Subspecialised Primary Care Practices, Fever Clinics, and Special Places for Corona-Testing) were organised in a short period in Baden-Wuerttemberg, a region in Southern Germany. The aim of these SARS-CoV-2 contact points was to ensure medical treatment for patients with (suspected) and without SARS-CoV-2 infection. The present study aimed to assess the beliefs and practices of primary care physicians who either led a Subspecialised Primary Care Practice or a Primary Care Practice providing care as usual in Baden-Wuerttemberg during the first wave of the COVID-19 pandemic. Methods: This cross-sectional study was based on a paper-based questionnaire in primary care physicians during the first wave of the pandemic. Participants were identified via the web page of the Association of Statutory Health Insurance Physicians Baden-Wuerttemberg. The questionnaire was distributed in June and July 2020. It measured knowledge, practices, self-efficacy and fears towards SARS-CoV-2, using newly developed questions. Data was descriptively analysed. Results: One hundred fifty-five participants (92 leads of SARS-CoV-2 contact points/ 63 leads of primary care practices) completed the questionnaire. Out of 92 leads of SARS-CoV-2 contact points 74 stated to lead n Subspecialised Primary Care Practices. About half participants of both groups did not fear an own infection with the novel virus (between 50.8% and 62.2%), however about 75% feared financial loss. Knowledge was gained using various sources; main sources were the Association of Statutory Health Insurance Physicians (between 82.5% and 83.8%) and the German Society for Hygiene and Microbiology (RKI) (between 88.9% and 95.9%). Leads of Subspecialised Primary Care Practice felt more confident to perform anamnestic/diagnostic procedures (p < 0.001). The same was found for the confidence level regarding decision-making concerning the further treatment (p < 0.001). Several prevention measures to contain the spread of SARS-CoV-2 were adopted. Subspecialised Primary Care Practice had treated on average more patients with (suspected) COVID-19 (mean 408.12) than primary care practices (mean 83.8) (p < 0.001). Conclusion: The results of this study suggest that the Subspecialised Primary Care Practice that were implemented during the first wave of the SARS-CoV-2 pandemic contributed containment of the pandemic. Leads of Subspecialised Primary Care Practice indicated that physical separation of patients with potential SARS-CoV-2 infection was easier compared to those who continued working in their own practice. Additionally, leads of Subspecialised Primary Care Practice felt more confident in dealing with patients with SARS-CoV-2 infection. Trial registration: The study has been prospectively registered at the German Clinical Trial Register (DRKS00022224). [ABSTRACT FROM AUTHOR]

Could asymptomatic carriers spread the SARS-CoV-2 infection? We read with great interest the recent paper by Shiyi Cao et al. [[1]] entitled "Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China" regarding the mass screening program of SARS-CoV-2 infection conducted in the metropolitan city of Wuhan, China. We used the Allplex™ SARS-CoV-2 multiplex real-time PCR assay (Seegene Inc.) to detect 4 target genes: RdRP, S and N genes specific for SARS-CoV-2, and E gene expressed in all Sarbecovirus' including SARS-CoV-2. [Extracted from the article]

Background: Antimicrobial resistance (AMR) is a growing global problem to which the ongoing COVID-19 pandemic may further contribute. With resources deployed away from antimicrobial stewardship, evidence of substantial pre-emptive antibiotic use in COVID-19 patients and indirectly, with deteriorating economic conditions fuelling poverty potentially impacting on levels of resistance, AMR threat remains significant. Main body: In this paper, main AMR countermeasures are revisited and priorities to tackle the issue are re-iterated. The need for collaboration is stressed, acknowledging the relationship between human health, animal health and environment ("One Health" approach). Among the stated priorities, the initiative by the European Medicines Regulatory Network to further strengthen the measures in combatting AMR is highlighted. Likewise, it is asserted that other emerging health threats require global collaboration with the One Health approach offering a valuable blueprint for action. Conclusion: The authors stress the importance of an integrated preparedness strategy to tackle this public health peril. [ABSTRACT FROM AUTHOR]

Background: Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. Results: As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Conclusions: Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4). [ABSTRACT FROM AUTHOR]

Introduction: The Covid-19 pandemic affects maternal health both directly and indirectly, and direct and indirect effects are intertwined. To provide a comprehensive overview on this broad topic in a rapid format behooving an emergent pandemic we conducted a scoping review. Methods: A scoping review was conducted to compile evidence on direct and indirect impacts of the pandemic on maternal health and provide an overview of the most significant outcomes thus far. Working papers and news articles were considered appropriate evidence along with peer-reviewed publications in order to capture rapidly evolving updates. Literature in English published from January 1st to September 11 2020 was included if it pertained to the direct or indirect effects of the COVID-19 pandemic on the physical, mental, economic, or social health and wellbeing of pregnant people. Narrative descriptions were written about subject areas for which the authors found the most evidence. Results: The search yielded 396 publications, of which 95 were included. Pregnant individuals were found to be at a heightened risk of more severe symptoms than people who are not pregnant. Intrauterine, vertical, and breastmilk transmission were unlikely. Labor, delivery, and breastfeeding guidelines for COVID-19 positive patients varied. Severe increases in maternal mental health issues, such as clinically relevant anxiety and depression, were reported. Domestic violence appeared to spike. Prenatal care visits decreased, healthcare infrastructure was strained, and potentially harmful policies implemented with little evidence. Women were more likely to lose their income due to the pandemic than men, and working mothers struggled with increased childcare demands. Conclusion: Pregnant women and mothers were not found to be at higher risk for COVID-19 infection than people who are not pregnant, however pregnant people with symptomatic COVID-19 may experience more adverse outcomes compared to non-pregnant people and seem to face disproportionate adverse socio-economic consequences. High income and low- and middle-income countries alike faced significant struggles. Further resources should be directed towards quality epidemiological studies. Plain English summary: The Covid-19 pandemic impacts reproductive and perinatal health both directly through infection itself but also indirectly as a consequence of changes in health care, social policy, or social and economic circumstances. The direct and indirect consequences of COVID-19 on maternal health are intertwined. To provide a comprehensive overview on this broad topic we conducted a scoping review. Pregnant women who have symptomatic COVID-19 may experience more severe outcomes than people who are not pregnant. Intrauterine and breastmilk transmission, and the passage of the virus from mother to baby during delivery are unlikely. The guidelines for labor, delivery, and breastfeeding for COVID-19 positive patients vary, and this variability could create uncertainty and unnecessary harm. Prenatal care visits decreased, healthcare infrastructure was strained, and potentially harmful policies are implemented with little evidence in high and low/middle income countries. The social and economic impact of COVID-19 on maternal health is marked. A high frequency of maternal mental health problems, such as clinically relevant anxiety and depression, during the epidemic are reported in many countries. This likely reflects an increase in problems, but studies demonstrating a true change are lacking. Domestic violence appeared to spike. Women were more vulnerable to losing their income due to the pandemic than men, and working mothers struggled with increased childcare demands. We make several recommendations: more resources should be directed to epidemiological studies, health and social services for pregnant women and mothers should not be diminished, and more focus on maternal mental health during the epidemic is needed. [ABSTRACT FROM AUTHOR]

Background: Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypotheses by querying extensive single-cell datasets. Large single-cell datasets like Human Cell Atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics, and vaccine targets, as the world struggles to cope with the on-going spread of COVID-19 infections. Main body: In this manuscript we describe REVEAL: SingleCell, which enables storage, retrieval, and rapid query of single-cell datasets inclusive of millions of cells. The array native database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypotheses. One such example includes identifying the most prevalent cell type annotation tag on returned cells. We used REVEAL: SingleCell to evaluate the expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in < 60 s. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic. Conclusion: In this paper, we introduce the REVEAL: SingleCell database that addresses immediate needs for SARS-CoV-2 research and has the potential to be used more broadly for many precision medicine applications. We used the REVEAL: SingleCell database as a reference to ask questions relevant to drug development and precision medicine regarding cell type and co-expression for genes that encode proteins necessary for SARS-CoV-2 to enter and reproduce in cells. [ABSTRACT FROM AUTHOR]

Background: Since the beginning of the COVID-19 outbreak in December 2019, a substantial body of COVID-19 medical literature has been generated. As of June 2020, gaps and longitudinal trends in the COVID-19 medical literature remain unidentified, despite potential benefits for research prioritisation and policy setting in both the COVID-19 pandemic and future large-scale public health crises.Methods: In this paper, we searched PubMed and Embase for medical literature on COVID-19 between 1 January and 24 March 2020. We characterised the growth of the early COVID-19 medical literature using evidence maps and bibliometric analyses to elicit cross-sectional and longitudinal trends and systematically identify gaps.Results: The early COVID-19 medical literature originated primarily from Asia and focused mainly on clinical features and diagnosis of the disease. Many areas of potential research remain underexplored, such as mental health, the use of novel technologies and artificial intelligence, pathophysiology of COVID-19 within different body systems, and indirect effects of COVID-19 on the care of non-COVID-19 patients. Few articles involved research collaboration at the international level (24.7%). The median submission-to-publication duration was 8 days (interquartile range: 4-16).Conclusions: Although in its early phase, COVID-19 research has generated a large volume of publications. However, there are still knowledge gaps yet to be filled and areas for improvement for the global research community. Our analysis of early COVID-19 research may be valuable in informing research prioritisation and policy planning both in the current COVID-19 pandemic and similar global health crises. [ABSTRACT FROM AUTHOR]

Background: The outbreak of coronavirus disease 2019 (COVID-19) started in December 2020, and is a global problem now. There are several sets of established data regarding computed tomography (CT) findings in COVID-19 pneumonia with many differential diagnoses. During the early days of the pandemic, there was little data regarding lung CT features of COVID-19 in a cancer patient. In this paper, we described a rare case of simultaneous presentation of COVID-19 with pulmonary metastasis.Case Presentation: A Persian patient with a history of chondrosarcoma presented to our clinic during the COVID-19 pandemic with a new-onset cough. He had experienced no recurrence during previous follow-up visits. Chest CT scan revealed numerous bilateral small peripheral and perilymphatic pulmonary nodules, unilateral ground-glass patch, and nodular interlobular septal thickening. Biopsy of the pulmonary nodules established pulmonary metastasis of chondrosarcoma origin, and pharyngeal reverse transcription polymerase chain reaction (RT-PCR) was positive for COVID-19.Conclusion: Pulmonary metastasis should be considered as a differential diagnosis of COVID-19 features in cancer patients in the pandemic era. [ABSTRACT FROM AUTHOR]

Objectives: Entertainment-education (E-E) media can improve behavioral intent toward health-related practices. In the era of COVID-19, millions of people can be reached by E-E media without requiring any physical contact. We have designed a short, wordless, animated video about COVID-19 hygiene practices-such as social distancing and frequent hand washing-that can be rapidly distributed through social media channels to a global audience. The E-E video's effectiveness, however, remains unclear. The study aims to achieve the following objectives. To: 1.Quantify people's interest in watching a short, animated video about COVID-19 hygiene (abbreviated to CoVideo).2.Establish the CoVideo's effectiveness in increasing behavioural intent toward COVID-19 hygiene.3.Establish the CoVideo's effectiveness in improving COVID-19 hygiene knowledge.Trial Design: The present study is a multi-site, parallel group, randomized controlled trial (RCT) comparing the effectiveness of the CoVideo against an attention placebo control (APC) video or no video. The trial has an intervention arm (CoVideo), placebo arm (APC), and control arm (no video). Nested in each trial arm is a list experiment and questionnaire survey, with the following ordering. Arm 1: the CoVideo, list experiment, and questionnaire survey. Arm 2: the APC video, list experiment, questionnaire survey, and CoVideo. Arm 3: the list experiment, questionnaire survey, and CoVideo. For each list experiment, participants will be randomized to a control or treatment group. The control group will receive a list of five items and the treatment group will receive the same five items plus one item about COVID-19 hygiene. We will use the list experiment to reduce response bias associated with socially desirable answers to COVID-19 questions. The questionnaire survey will include items about the participant's age, sex, country of residence, highest education, and knowledge of COVID-19 spread. After completing the list experiment and questionnaire survey, participants in Arms 2 and 3 will receive the CoVideo to ensure post-trial access to treatment.Participants: This will be an online study setting. We will use Prolific Academic (ProA: https://www.prolific.co) to recruit participants and host our study on the Gorilla™ platform (www.gorilla.sc). To be eligible, participants must be between the age of 18 and 59 years (male, female, or other) and have current residence in the United States, the United Kingdom, Germany, Spain, Mexico, or France. Participants will be excluded from the study if they cannot speak English, German, French, or Spanish (since the instructions and survey questions will be available in these 4 languages only).Intervention and Comparator: The intervention is an E-E video about COVID-19 hygiene (CoVideo). Developed by our co-author (MA) for Stanford Medicine, the CoVideo is animated with sound effects, and has no words, speech, or text. The CoVideo shows how the novel coronavirus is spread (airborne, physical contact) and summarizes the public's response to the COVID-19 outbreak. Key components of the CoVideo are the promotion of five hygiene practices: i) social distancing and avoiding group gatherings, ii) frequently washing hands with soap and water or sanitizer, iii) cleaning surfaces at home (e.g., kitchen counters), iv) not sharing eating utensils, and v) avoidance of stockpiling essential goods (such as toilet paper and face masks). The CoVideo, which was designed for universal reach and optimized for release on social media channels, can be viewed at https://www.youtube.com/watch?v=rAj38E7vrS8. The comparators are an APC video (Arm 2) or no video (Arm 3). The APC video is similar in style to the CoVideo; it is also animated with a duration of 2.30 minutes, has sound effects but no words, speech, or text. The video message is about how small choices become actions, which become habits, which become a way of life. It is available at https://www.youtube.com/watch?v=_HEnohs6yYw. Each list experiment will have a control list as the comparator. The control list is needed to measure the prevalence of behavioral intent toward COVID-19 hygiene.Main Outcomes: This study will measure primary and secondary outcomes related to COVID-19 hygiene. By hygiene, we mean the adoption of behaviors or practices that reduce the chances of being infected or spreading COVID-19. As our primary outcome, we will measure changes in behavioral intent toward five hygiene practices: social distancing, washing hands, cleaning household surfaces, not sharing eating utensils, and not stockpiling essential goods. As a secondary outcome, we will measure knowledge about behaviors that can prevent the spread of COVID-19.Randomization: Using a web-based randomization algorithm, Gorilla will randomly allocate participants to the intervention (CoVideo), placebo (APC), or control (no video) arm (sequence generation) at a 1:1:1 ratio. Within each trial arm, Gorilla will randomly allocate participants at a 1:1 ratio to the control or treatment group. Items in the lists will be randomly ordered to avoid order effects. The presentation order of the list experiments will also be randomized.Blinding: Because ProA handles the interaction between the study investigators and participants, the participants will be completely anonymous to the study investigators. The outcome measures will be self-reported and submitted anonymously. All persons in the study team will be blinded to the group allocation.Numbers To Be Randomized: The Gorilla algorithm will randomize 6,700 participants to each trial arm, giving a total sample size of 20,100.Trial Status: The protocol version number is 1.0 and the date is 18 May 2020. Recruitment is expected to end by 22 June 2020. Thus far, the study investigators have recruited 2,500 participants on ProA. Of these participants, 800 have completed the study on the Gorilla platform.Trial Registration: The study and its outcomes were registered at the German Clinical Trials Register (www.drks.de) on May 12th, 2020, protocol number: #DRKS00021582. The study was registered before any data was collected.Full Protocol: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has the potential to cause high morbidity and mortality in crisis-affected populations. Delivering COVID-19 treatment services in crisis settings will likely entail complex trade-offs between offering services of clinical benefit and minimising risks of nosocomial infection, while allocating resources appropriately and safeguarding other essential services. This paper outlines considerations for humanitarian actors planning COVID-19 treatment services where vaccination is not yet widely available. We suggest key decision-making considerations: allocation of resources to COVID-19 treatment services and the design of clinical services should be based on community preferences, likely opportunity costs, and a clearly articulated package of care across different health system levels. Moreover, appropriate service planning requires information on the expected COVID-19 burden and the resilience of the health system. We explore COVID-19 treatment service options at the patient level (diagnosis, management, location and level of treatment) and measures to reduce nosocomial transmission (cohorting patients, protecting healthcare workers). Lastly, we propose key indicators for monitoring COVID-19 health services. [ABSTRACT FROM AUTHOR]

Background: Health workers (HWs) are at increased risk for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection and a possible source of nosocomial transmission clusters. Despite the increased risk, the best surveillance strategy and management of exposed HWs are not yet well known. The aim of this review was to summarize and critically analyze the existing evidence related to this topic in order to support public health strategies aimed at protecting HWs in the hospital setting. Main text: A comprehensive computerized literature research from 1 January 2020 up to 22 May 2020 was made to identify studies analyzing the burden of infection, risk assessment, surveillance and management of HWs exposed to SARS-CoV-2. Among 1623 citation identified using MEDLINE, Embase, Google Scholar and manual search, we included 43 studies, 14 webpages and 5 ongoing trials. Health workers have a high risk of acquiring infection while caring for coronavirus disease 2019 (COVID-19) patients. In particular, some types exposures and their duration, as well as the inadequate or non-use of personal protective equipment (PPE) are associated with increased infection risk. Strict infection prevention and control procedures (IPC), adequate training programs on the appropriate use of PPE and close monitoring of HWs with symptom surveillance and testing are essential to significantly reduce the risk. At the moment there is not enough evidence to provide precise indications regarding pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP). Conclusions: During the spread of COVID-19 outbreak, numerous published papers investigated the epidemiology, risk assessment and prevention and control of SARS-CoV-2. However, more high-quality studies are needed to provide valid recommendations for better management and for the clinical and microbiological surveillance of healthcare personnel. [ABSTRACT FROM AUTHOR]

Introduction: During the COVID-19 pandemic, hospitals faced increasing pressure, where people living with HIV risked to either acquire SARS-CoV-2 and to interrupt the HIV continuum of care. Methods: This is a retrospective, observational study. We compared the numbers of medical visits performed, antiretroviral drugs dispensed and the number of new HIV diagnosis and of hospitalizations in a cohort of people living with HIV (PLWH) followed by the Spedali Civili of Brescia between the bimester of the COVID-19 pandemic peak and the bimester of October–November 2019. Data were retrieved from administrative files and from paper and electronic clinical charts. Categorical variables were described using frequencies and percentages, while continuous variables were described using mean, median, and interquartile range (IQR) values. Means for continuous variables were compared using Student's t-tests and the Mann–Whitney test. Proportions for categorical variables were compared using the χ2 test. Results: As of December 31st, 2019, a total of 3875 PLWH were followed in our clinic. Mean age was 51.4 ± 13 years old, where 28% were females and 18.8% non-Italian. Overall, 98.9% were on ART (n = 3834), 93% were viro-suppressed. A total of 1217 and 1162 patients had their visit scheduled at our out-patient HIV clinic during the two bimesters of 2019 and 2020, respectively. Comparing the two periods, we observed a raise of missed visits from 5 to 8% (p < 0.01), a reduction in the number of new HIV diagnosis from 6.4 in 2019 to 2.5 per month in 2020 (p = 0.01), a drop in ART dispensation and an increase of hospitalized HIV patients due to COVID-19. ART regimens including protease inhibitors (PIs) had a smaller average drop than ART not including PIs (16.6 vs 21.6%, p < 0.05). Whether this may be due to the perception of a possible efficacy of PIs on COVID19 is not known. Conclusions: Our experience highlights the importance of a resilient healthcare system and the need to implement new strategies in order to guarantee the continuum of HIV care even in the context of emergency. [ABSTRACT FROM AUTHOR]