Search

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]