Genomics and Evolution of Novel Corona Virus 2019
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ABSTRACT:
SUBMITTER: Kumar A
PROVIDER: S-EPMC7677611 | biostudies-literature | 2020 Sep
REPOSITORIES: biostudies-literature
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Project description:Objective:To assess the knowledge, awareness and attitudes of medical students towards recently discovered coronavirus disease-19 (COVID-19). Methods:This was a cross sectional study conducted on medical students in CMH Lahore Medical College,(LMC), Institute of Dentistry (IOD). A questionnaire containing demographic information, 14 knowledge and eight attitude items was completed by 384 participants. Results:Overall, >90% people were aware about the etiology, mode of transmission and possible symptoms; however, very few of them knew about the in-depth details. Knowledge score revealed that 80% of participants had sufficient knowledge about coronavirus. MBBS students and nursing Students had significantly better knowledge in comparison with other students. In terms of attitude, >80% of students showed positive attitudes among which the nursing students were dominant. Conclusion:The medical students of CMH LMC showed a satisfactory level of awareness and attitudes towards COVID-19 with an obvious difference with regard to disciplines. More educational efforts with periodic educational interventions are still needed about the current pandemic.
| S-EPMC7306955 | biostudies-literature
Project description:In December 2019 a novel coronavirus SARS-CoV-2 emerged in the Hunan seafood market in Wuhan, China, and soon became a global health problem. Since its outbreak, SARS-CoV-2 has had a major impact on clinical diagnostic laboratories. The scientific community has quickly risen to the occasion and reports of new developments have arrived at an unprecedented scale. At present, there is a growing list of over 400 SARC-CoV-2 diagnostic tests either in development or approved for clinical use. This presentation reviews the current laboratory methods available for testing COVID- 19 in microbiology laboratories and also provides an insight into the future diagnostics approaches. Proper respiratory specimen collected at the appropriate time and from the right anatomical site is critical in the accurate and timely diagnosis of SARSCoV2. While oropharyngeal and nasopharyngeal swabs are recommended for the detection of early infection, other lower respiratory tract specimens like the sputum and bronchoalveolar lavage are used for late detection and monitoring of patients with severe COVID-19 pneumonia. Real-time RT-PCR based molecular assay remains the test of choice for the etiological diagnosis of SARS-CoV-2 while serological tests are being introduced as supplementary tools. Finally, there is an urgent need for scaling up the diagnostic capacity by the introduction of reliable and accurate point-of-care tests which will assist in effective control of this outbreak. These assays can be used in the local hospitals and clinics bearing the burden of identifying and treating patients. Highlights • Since its outbreak, SARS-CoV-2 has had a major impact on clinical diagnostic laboratories.• At present, there is a growing list of over 400 SARC-CoV-2 diagnostic tests either in development or approved for clinical use.• Real-time RT-PCR based molecular assay remains the test of choice for the etiological diagnosis of SARS-CoV-2.• Oropharyngeal and nasopharyngeal swabs are recommended for the detection of early infection.• Lower respiratory tract specimens can be used for late detection and monitoring of patients with severe COVID-19 pneumonia.• There is an urgent need for scaling up the diagnostic capacity by the introduction of reliable and accurate point-of-care tests.
| S-EPMC7527305 | biostudies-literature
Project description:The outbreak of Corona Virus Disease 2019 (COVID-19) in Wuhan has significantly impacted the economy and society globally. Countries are in a strict state of prevention and control of this pandemic. In this study, the development trend analysis of the cumulative confirmed cases, cumulative deaths, and cumulative cured cases was conducted based on data from Wuhan, Hubei Province, China from January 23, 2020 to April 6, 2020 using an Elman neural network, long short-term memory (LSTM), and support vector machine (SVM). A SVM with fuzzy granulation was used to predict the growth range of confirmed new cases, new deaths, and new cured cases. The experimental results showed that the Elman neural network and SVM used in this study can predict the development trend of cumulative confirmed cases, deaths, and cured cases, whereas LSTM is more suitable for the prediction of the cumulative confirmed cases. The SVM with fuzzy granulation can successfully predict the growth range of confirmed new cases and new cured cases, although the average predicted values are slightly large. Currently, the United States is the epicenter of the COVID-19 pandemic. We also used data modeling from the United States to further verify the validity of the proposed models.
| S-EPMC7535054 | biostudies-literature
Project description: Not available
| S-EPMC7080149 | biostudies-literature
Project description:Background:A recent cluster of pneumonia cases in China was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report the screening and diagnosis of corona virus disease 2019 (COVID-19) in our hospital. Methods:Developed a procedure for the identification of children cases with COVID-19 in outpatient and emergency department of our hospital, then we observed how this process works. Results:(I) There were 56 cases considered suspected cases, and 10 cases were confirmed as COVID-19. (II) Of the 10 confirmed COVID-19 cases admitted in our hospital, 5 were males and 5 were females, aged from 7 months to 11 years, the average age is 6.0±4.2 years, 6 cases were mild pneumonia, the others were upper respiratory tract infection. (III) We followed up 68 patients in isolation at home until symptoms disappeared. Non were missed in the patient's first visit. The sensitivity of this method is 100% and the specificity is 71.3%. Conclusions:Our screening process works well, and it is also necessary to establish a screening network in the hospital.
| S-EPMC7154461 | biostudies-literature
Project description:Background:The present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required. Methods:In this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro. Results:The predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59-HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS-105, 227-LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK-266, 3-DNGPQNQRNAPRITFGGP-20, 29-GERSGARSKQRRPQGL-45. Two other prime vaccine targets, 370-NSASFSTFKCYGVSPTKLNDLCFTNV-395 and 260-AGAAAYYVGYLQPRT-274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins. Conclusions:Taken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2.
| S-EPMC7531350 | biostudies-literature
Project description:The infection epidemic event of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was formally declared a pandemic by World Health Organization on March 11th, 2020. Corona Virus Disease 2019 (COVID-19) is caused by SARS-CoV-2, a new type of coronavirus, which has high contagion and mainly causes respiratory symptoms. With the increase in confirmed cases, however, the infection symptoms turn to be diverse with secondary or first clinical symptoms relating to damage of the cardiovascular system and changes of myocardial enzyme spectrum, cardiac troponin I, electrocardiogram, cardiac function. The occurrence of extra-pulmonary manifestations, including immediately and long-term damage, means that the overall health burden caused by SARS-CoV-2 infection may be under-estimated because COVID-19 patients developed cardiovascular system injury are more likely to become serious. The factors such as directly pathogen-mediated damage to cardiomyocytes, down-regulated angiotensin-converting enzyme 2 (ACE2) expression, excessive inflammatory response, hypoxia and adverse drug reaction, are closely related to the occurrence and development of the course of COVID-19. In combination with recently published medical data of patients having SARS-CoV-2 infection and the latest studies, the manifestations of damage to cardiovascular system by COVID-19, possible pathogenic mechanisms and advances of the treatment are proposed in this article.
| S-EPMC7518803 | biostudies-literature
Project description:Background: Coronavirus disease 2019 (COVID-19), sweeping across the world, has created a worldwide pandemic. Effective treatments of COVID-19 are extremely urgent. Objective: To analyze the efficacy and safety of convalescent plasma (CCP) on patients with COVID-19. Methods: All the relevant studies were searched from PubMed, EMBASE,Cochrane library, Scopus, Web of Science, CBM, CNKI, Wan fang, VIP, Medrxiv, Biorxiv, and SSRN on July 19, 2021. PICOS criteria were as follows: (P) the study interests were human subjects with the infection of COVID-19; (I) the intervention of interest was CCP; (C) comparator treatments contained placebo, sham therapy, and standard treatment; (O) the primary outcome was mortality rates by the novel coronavirus. The secondary outcomes included the incidence of serious adverse events, the rate of ICU admission and mechanical ventilation (MV); the length of hospital stay; the duration of MV and ICU stay; the antibody levels, inflammatory factor levels, and viral loads. (S) Only randomized controlled trials (RCTs) of CCP were included. Subanalysis, quality assessment, sensitive analysis, and publication bias were conducted by two reviewers independently. Results: Sixteen RCTs were included and enrolled a total of 16,296 participants in this meta-analysis. The pooled data showed that no significant difference was observed in reducing the rate of overall mortality between CCP treatment group and placebo group (OR 0.96; 95% CI 0.90 to 1.03; p = 0.30; I 2 = 6%). According to the results of subgroup analysis, severe or critical patients with CCP showed significant difference in reducing the 28-day mortality of compared with placebo (OR 0.58, 95% CI 0.36 to 0.93, p = 0.02, I 2 = 0%). CCP groups have a significantly shorter duration of MV compared with the control group (weighted MD -1.00, 95% CI -1.86 to -0.14 d p = 0.02, I 2 = 0%). No significant difference was observed in the length of hospital stay, the duration of ICU, and the rate of ICU and MV. There is no conclusive evidence about the safety of CCP. Conclusion: Convalescent plasma can significantly reduce the 28-day mortality of severe or critical COVID-19 patients and the duration of MV. However, more evidence was needed to prove the safety of convalescent plasma.
| S-EPMC8502818 | biostudies-literature
Project description:Since the first report of SARS-CoV-2 virus in Wuhan, China in December 2019, a global outbreak of Corona Virus Disease 2019 (COVID-19) pandemic has been aroused. In the prevention of this disease, accurate diagnosis of COVID-19 is the center of the problem. However, due to the limitation of detection technology, the test results are impossible to be totally free from pseudo-positive or -negative. Improving the precision of the test results asks for the identification of more biomarkers for COVID-19. On the basis of the expression data of COVID-19 positive and negative samples, we first screened the feature genes through ReliefF, minimal-redundancy-maximum-relevancy, and Boruta_MCFS methods. Thereafter, 36 optimal feature genes were selected through incremental feature selection method based on the random forest classifier, and the enriched biological functions and signaling pathways were revealed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Also, protein-protein interaction network analysis was performed on these feature genes, and the enriched biological functions and signaling pathways of main submodules were analyzed. In addition, whether these 36 feature genes could effectively distinguish positive samples from the negative ones was verified by dimensionality reduction analysis. According to the results, we inferred that the 36 feature genes selected via Boruta_MCFS could be deemed as biomarkers in COVID-19.
| S-EPMC9258782 | biostudies-literature
Project description:The corona virus disease 2019 (COVID-19) pandemic has had a wide-ranging impact on the clinical practice of medicine and emotional well-being of providers. Our aim was to determine the impact of the COVID-19 pandemic on practice and burnout among hepatology providers. From February to March 2021, we conducted an electronic survey of American Association for the Study of Liver Diseases (AASLD) members who were hepatologists, gastroenterologists, and advanced practice providers (APPs). The survey included 26 questions on clinical practice and emotional well-being derived from validated instruments. A total of 230 eligible members completed the survey as follows: 107 (47%) were adult transplant hepatologists, 43 (19%) were adult general hepatologists, 14 (6%) were adult gastroenterologists, 11 (5%) were pediatric hepatologists, 45 (19%) were APPs, and 9 (4%) were other providers. We found that 69 (30%) experienced a reduction in compensation, 92 (40%) experienced a reduction in staff, and 9 (4%) closed their practice; 100 (43%) respondents reported experiencing burnout. In univariate analysis, burnout was more frequently reported in those ≤55 years old (odds ratio [OR], 2.2; 95% confidence interval [CI], 1.2-4.2), women (OR, 2.2; 95% CI, 1.3-3.7), nontransplant hepatology (OR, 2.0; 95% CI, 1.1-3.3), APPs (OR, 2.7; 95% CI, 1.4-5.1), and those less than 10 years in practice (OR, 1.9; 95% CI, 1.1-3.3). In multivariable analysis, only age ≤55 years was associated with burnout (OR, 2.3; 95% CI, 1.1-4.8). The most common ways the respondents suggested the AASLD could help was through virtual platforms for networking, mentoring, and coping with the changes in practice due to the COVID-19 pandemic. Conclusion: The COVID-19 pandemic has had a substantial impact on the clinical practice of hepatology as well as burnout and emotional well-being. Women, APPs, and early and mid-career clinicians more frequently reported burnout. Identified strategies to cope with burnout include virtual platforms to facilitate networking and mentoring.
| S-EPMC8652849 | biostudies-literature