A Meta-Analysis on the Safety and Immunogenicity of Covid-19 Vaccines.

OBJECTIVE: The presented meta-analysis (MA) aims at identifying the vaccine safety and immunogenicity in published trials about SARS-CoV-2 vaccines. METHODS: All relevant publications were systematically searched and collected from different databases (Embase, Scopus, EBSCO, MEDLINE central/PubMed, Science Direct, Cochrane Central Register for Clinical Trials (CENTRAL), Clinical Trials.gov, WHO International Clinical Trials Registry Platform (ICTRP), COVID Trial, COVID Inato, Web of Science, ProQuest Thesis, ProQuest Coronavirus Database, SAGE Thesis, Google Scholar, Research Square, and Medxriv) up to January 10, 2021. The pooled vaccine safety and immunogenicity following vaccination in phase 1 and 2 vaccine clinical trials, as well as their 95% confidence intervals (CI), were estimated using the random-effects model. RESULTS: The predefined inclusion criteria were met in 22 out of 8592 articles. The proportion of anti-severe acute respiratory distress coronavirus 2 (SARS-CoV-2) antibody responses after 7 days among 72 vaccinated persons included in 1 study was 81% (95% CI: 70-89), after 14 days among 888 vaccinated persons included in 6 studies was 80% (95% CI: 58-92), after 28 days among 1589 vaccinated persons included in 6 studies was 63% (95% CI: 59-67), after 42 days among 478 vaccinated persons included in 5 studies was 93% (95% CI: 80-98), and after 56 days among 432 vaccinated persons included in 2 studies was 93% (95% CI: 83-97). Meta regression explains more than 80% of this heterogeneity, where the main predictors were; the inactivated vaccine type (ß = 2.027, P = 0.0007), measurement of antibodies at week 1 (ß = -4.327, P < 0.0001) and at week 3 of the first dose (ß = -2.02, P = 0.0025). Furthermore, the pooled proportion adverse effects 7 days after vaccination was 0.01 (0.08-0.14) for fever, headache 0.23 (0.19-0.27), fatigue 0.10 (0.07-0.13), and 0.18 (0.14-0.23) for muscle pain. CONCLUSION: Immunogenicity following vaccination ranged from 63% to 93% depending on the time at which the antibody levels were measured.

COVID-19 Vaccine Booster Dose Acceptance: Systematic Review and Meta-Analysis.

The World Health Organization (WHO) recommended coronavirus disease 2019 (COVID-19) booster dose vaccination after completing the primary vaccination series for individuals ≥18 years and most-at-risk populations. This study aimed to estimate the pooled proportion of COVID-19 vaccine booster dose uptake and intention to get the booster dose among general populations and healthcare workers (HCWs). We searched PsycINFO, Scopus, EBSCO, MEDLINE Central/PubMed, ProQuest, SciELO, SAGE, Web of Science, Google Scholar, and ScienceDirect according to PRISMA guidelines. From a total of 1079 screened records, 50 studies were extracted. Meta-analysis was conducted using 48 high-quality studies according to the Newcastle-Ottawa Scale quality assessment tool. Using the 48 included studies, the pooled proportion of COVID-19 vaccine booster dose acceptance among 198,831 subjects was 81% (95% confidence interval (CI): 75-85%, I2 = 100%). The actual uptake of the booster dose in eight studies involving 12,995 subjects was 31% (95% CI: 19-46%, I2 = 100%), while the intention to have the booster dose of the vaccine was 79% (95% CI: 72-85%, I2 = 100%). The acceptance of the booster dose of COVID-19 vaccines among HCWs was 66% (95% CI: 58-74%), I2 = 99%). Meta-regression revealed that previous COVID-19 infection was associated with a lower intention to have the booster dose. Conversely, previous COVID-19 infection was associated with a significantly higher level of booster dose actual uptake. The pooled booster dose acceptance in the WHO region of the Americas, which did not include any actual vaccination, was 77% (95% CI: 66-85%, I2 = 100%). The pooled acceptance of the booster dose in the Western Pacific was 89% (95% CI: 84-92%, I2 = 100), followed by the European region: 86% (95% CI: 81-90%, I2 = 99%), the Eastern Mediterranean region: 59% (95% CI: 46-71%, I2 = 99%), and the Southeast Asian region: 52% (95% CI: 43-61%, I2 = 95). Having chronic disease and trust in the vaccine effectiveness were the significant predictors of booster dose COVID-19 vaccine acceptance. The global acceptance rate of COVID-19 booster vaccine is high, but the rates vary by region. To achieve herd immunity for the disease, a high level of vaccination acceptance is required. Intensive vaccination campaigns and programs are still needed around the world to raise public awareness regarding the importance of accepting COVID-19 vaccines needed for proper control of the pandemic.

Benchmarking a Large Twitter Dataset for Arabic Emotion Analysis (preprint)

Emotion analysis of social media content, e.g., Twitter, is a useful tool forunderstanding people’s reactions during critical events such as Covid-19pandemic. Arabic annotated emotion datasets are nonetheless scarce, whichconsequently affects the accuracy of emotion detection applications, and limittheir usefulness. During the first year of the pandemic, a large Arabic EgyptianCOVID-19 Twitter Dataset (ArECTD) was collected and annotated employing amix of manual annotation and semi-supervised self-learning technique. ArECTDis compromised of approximately 78K tweets and ten emotion labels making itone of the largest available Arabic emotion datasets. The mixed annotationapproach is particularly promising for handling the demanding annotation taskand potentially growing the number of Arabic emotion datasets. The paper aimsto examine the quality of the annotation of ArECTD by measuring the lexicalcorrelates of each emotion. Moreover, content-based analysis was conducted as apractical case study to identify correlations between the detected emotions andthe Egyptian government’s decisions during the pandemic. Furthermore,classification models are developed for ArECTD by fine-tuning thestate-of-the-art Arabic deep learning transformer models, AraBERT andMARBERT, achieving accuracies of 70.01% of 72.5%, respectively. Thegeneralization of the best ArECTD classification model to two other datasetsfrom different domains was studied using transfer learning.

Favipiravir for the Treatment of Coronavirus Disease 2019; a propensity score-matched cohort study (preprint)

Background We investigated clinical outcomes of favipiravir in patients with COVID-19 pneumonia. Methods Patients who between 23 May 2020 and 18 July 2020 received 24 hours or more of favipiravir were assigned to the favipiravir group, while those who did not formed the non-favipiravir group. The primary outcome was 28-day clinical improvement, defined as two-category improvement from baseline on an 8-point ordinal scale. Propensity scores (PS) for favipiravir therapy were used for 1:1 matching. Cox regression was used to examine associations with the primary endpoint. Results The unmatched cohort included 1,493 patients, of which 51.7% were in the favipiravir group, and 48.3% were not receiving supplemental oxygen at baseline. Favipiravir was started within a median of 5 days from symptoms onset. Significant baseline differences between the two unmatched groups existed, but not between the PS-matched groups (N = 774). After PS-matching, there were no significant differences between the two groups in the proportion with 28-day clinical improvement (93.3% versus 92.8%, P 0.780), or 28-day all-cause mortality (2.1% versus 3.1%, P 0.360). Favipiravir was associated with more viral clearance by day 28 (79.8% versus 64.1%, P <0.001). In the adjusted Cox proportional hazards model, favipiravir therapy was not associated 28-day clinical improvement (adjusted hazard ratio 0.978, 95% confidence interval 0.862 to 1.109, P 0.726). Adverse events were common in both groups, but the 93.9% were Grades 1 to 3. Conclusion Favipiravir therapy for COVID-19 pneumonia is well tolerated but is not associated with an increased likelihood of clinical improvement or reduced all-cause mortality by 28 days.

Teledermatology in the time of COVID-19.

AIMS: The enormous spread of the novel Corona virus disease (COVID-19) represents a challenge to dermatological practice. Accumulating evidence has suggested a possible role of teledermatology in facing this challenge. In this article, we aimed to give a general overview of teledermatology in terms of models of practice, modes of delivery, advantages, limitations, ethical considerations and legislative challenges as well as discussing, using examples from literature, how dermatological practice can benefit from teledermatology during the time of the COVID-19 pandemic. DISCUSSION AND CONCLUSION: Teledermatology could be an accessible, accurate and cost-effective substitute for conventional face-to-face dermatological consultations during the COVID-19 pandemic. However, teledermatology practice needs updated legislation and guidelines. More efforts should be done to encourage dermatologists, especially in underserved communities, to provide teledermatology services. Ethical issues and data security related to teledermatology have to be considered.

Can the Rapid Antigen Test for COVID-19 Replace RT-PCR: A Meta-analysis of Test Agreement (preprint)

BackgroundSeveral studies have compared the performance of reverse transcription-polymerase chain reaction (RT-PCR) and antigen rapid diagnostic tests (Ag-RDTs) as tools to diagnose SARS-CoV-2 disease (COVID-19). As the performance of Ag-RDT may vary among different products and viral load scenarios, the clinical utility of the Ag-RDT remains unclear. Our aim is to assess the diagnostic agreement between Ag-RDTs and RT-PCR in testing for COVID-19 across different products and cycle threshold (Ct) values. MethodsAn evidence synthesis and meta-analysis of Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) was conducted after an exhaustive search of five databases to locate published studies that compared Ag-RDT to RT-PCR and reported quantitative comparison results. After the screening, quality assessment, and data extraction, the synthesis of pooled estimates was carried out utilizing the quality-effects (QE) model and Freeman-Tukey double arcsine transformation (FTT) for variance stabilization. Subgroup analysis was also conducted to evaluate the tests diagnostic agreement across distinctive products and Ct-value thresholds. FindingsA total of 420 studies were screened by title and abstract, of which 39 were eventually included in the analysis. The overall NPA was 99.4% (95%CI 98.8-99.8, I2=91.40%). The PPA was higher in lower Ct groups such as groups with Ct <20 and Ct <25, which had an overall PPA of 95.9% (95%CI 92.7-98.2, I2=0%) and 96.8% (95%CI 95.2-98.0, I2=50.1%) respectively. This is in contrast to groups with higher Ct values, which had relatively lower PPA. Panbio and Roche Ag-RDTs had the best consistent overall PPA across different Ct groups especially in groups with Ct <20 and Ct <25. InterpretationThe findings of our meta-analysis support the use of Ag-RDTs in lieu of RT-PCR for decision making regarding COVID-19 control measures, since the enhanced capacity of RT-PCR to detect disease in those that are Ag-RDT negative will be unlikely to have much public health utility. This step will drastically reduce the cost and time in testing for COVID-19. FundingThis research did not receive any specific funding.

Systematic Review and Meta-analysis on COVID-19 Vaccine Hesitancy (preprint)

Background: The presented meta-analysis was developed in response to the publication of several studies addressing COVID-19 vaccines hesitancy. We aimed to identify the proportion of vaccine acceptance and rejection, and factors affecting vaccine hesitancy worldwide especially with the fast emergency approval of vaccines. Methods: Online database search was performed, and relevant studies were included with no language restriction. A meta-analysis was conducted using R software to obtain the random effect model of the pooled prevalence of vaccine acceptance and rejection. Egger regression test was performed to assess publication bias. Quality assessment was assessed using Newcastle-Ottawa Scale quality assessment tool. Results: Thirty-nine out of 12246 articles met the predefined inclusion criteria. All studies were cross-sectional designs. The pooled proportion of COVID-19 vaccine hesitancy was 17% (95% CI: 14-20) while the pooled proportion of COVID-19 vaccine acceptance was 75% (95% CI: 71-79). The vaccine hesitancy and the vaccine acceptance showed high heterogeneity (I 2 =100%). Case fatality ratio and the number of reported cases had significant effect on the vaccine acceptance as the pooled proportion of vaccine acceptance increased by 39.95% (95% CI: 20.1-59.8) for each 1% increase in case fatality (P<0.0001) and decreased by 0.1% (95% CI: -0.2-0.01) for each 1000 reported case of COVID-19, P= 0.0183). Conclusion: Transparency in reporting the number of newly diagnosed COVID-19 cases and deaths is mandatory as these factors are the main determinants of COVID-19 vaccine acceptance.

Knowledge, Attitude and Practice of medical students towards COVID19 in Sudan, 2020: A cross sectional study among 19 universities (preprint)

Introduction: Since December 2019, an outbreak of severe respiratory infection (COVID-19) emerged in the city of Wuhan in China. It quickly spread around the world and is now a pandemic of epic proportions. Medical students are the future generation of doctors who will have to face this and any future similar catastrophe. The knowledge, awareness and practice of medical students toward Covid19 pandemic is of most importance as it demonstrates their preparedness to deal with this pandemic.Objective: To assess the knowledge, awareness and practice of medical students in 19 universities in Sudan about COVID 19.Methodology: This is a cross-sectional study done in 19 universities which have medical schools in Sudan. Data from at least 100 medical students from each university was included in the study. Data was collected using an online questionnaire in April 2020.Results: 2603 medical students from 19 universities were included. Overall good knowledge and practice were demonstrated by the medical students (88.9%) and (78.6%), respectively. Respondents answered that the most common clinical symptoms of COVID-19 were fever (51.9%), dry cough (40.5%). The main combination of clinical symptoms was dry cough, fatigue and fever in (27.7%), and the first initial symptom was headache (48.4%.).(60.2%) wear medical masks, (94.9%) said that avoiding crowded places protects against the spread of Covid19. (50.9%) have confidence that Sudan can win the battle against the COVID-19 with (48.6%) amongst males and (52.2%) amongst females. 69.0% agreed that COVID-19 will finally be successfully controlled.Conclusion: This study showed that medical students in Sudan demonstrated excellent Knowledge and good practice toward Covid19.Recommendations: Although the results were very positive, further education and awareness should be carried out to increase the preparedness of medical students towards such pandemics and public health modules should also focus more on the importance of the knowledge of newly emerging diseases and the practices toward them.

COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation (preprint)

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.