Computational methods and strategies for combating COVID-19.
Ontology highlight
ABSTRACT:
SUBMITTER: Basu S
PROVIDER: S-EPMC9398558 | biostudies-literature | 2022 Oct
REPOSITORIES: biostudies-literature
Publications
Computational methods and strategies for combating COVID-19.
Basu Subhadip S Plewczynski Dariusz D
Methods (San Diego, Calif.) 20220824
Similar Datasets
Project description:Coronavirus disease 2019 (COVID-19) is highly contagious, and thus has become an emerging health crisis worldwide. The optimal strategies to prevent the spread of this disease are inconclusive, and therefore, the adopted measurements to combat COVID-19 varies in different countries. In mid-March and late-August 2020, we performed internet searches to collect relevant information, from sources such as the website of the World Health Organization. The epidemiological data of COVID-19 from several countries were collected and we found that Taiwan had a comparably successful story for combating the pandemic. As of mid-March, Taiwan had high rates of diagnostic testing (688.5 tests per million citizens) with a lower infection rate (49 cases, 2.1 cases per million people). As of late-August, there were 488 cases (20 cases per million people). Furthermore, Taiwanese government-guided strategies and hospital data were also reviewed. We summarized some important strategies to combat COVID-19, which include: (1) border control; (2) official media channel and press conferences; (3) name-based rationing system for medical masks; (4) TOCC-based rapid triage, outdoor clinics, and protective sampling devices; and (5) social distancing, delaying the start of new semesters, and religious assembly restriction. In conclusion, Taiwan had lower rates of COVID-19 compared with other countries, and Taiwan government-guided strategies contributed to the control of the disease's spread.
| S-EPMC7609768 | biostudies-literature
Project description:Experimental approaches are currently used to determine viral-host interactions, but these approaches are both time-consuming and costly. For these reasons, computational-based approaches are recommended. In this study, using computational-based approaches, viral-host interactions of SARS-CoV-2 virus and human proteins were predicted. The study consists of four different stages; in the first stage viral and host protein sequences were obtained. In the second stage, protein sequences were converted into numerical expressions by various protein mapping methods. These methods are entropy-based, AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters, EIIP, AESNN1, Miyazawa energies, Micheletti potentials, Z-scale, and hydrophobicity. In the third stage, a deep learning model was designed and BiLSTM was used for this. In the last stage, the protein sequences were classified, and the viral-host interactions were predicted. The performances of protein mapping methods were determined by accuracy, F1-score, specificity, sensitivity, and AUC scores. According to the classification results, the best classification process was obtained by the entropy-based method. With this method, 94.74% accuracy, and 0.95 AUC score were calculated. Then, the most successful classification process was performed with the Z-scale and 91.23% accuracy, and 0.96 AUC score were obtained. Although other protein mapping methods are not as efficient as Z-scale and entropy-based methods, they have achieved successful classification. AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters and AESNN1 methods showed over 80% accuracy, F1-score, and AUC score. Accuracy scores of EIIP, Miyazawa energies, Micheletti potentials and hydrophobicity methods remained below 80%. When the results were examined in general, it was observed that the computational approaches were successful in predicting viral-host interactions between SARS-CoV-2 virus and human proteins.
| S-EPMC9301933 | biostudies-literature
Project description:The ongoing COVID-19 pandemic triggered by SARS-CoV-2 emerged from Wuhan, China, firstly in December 2019, as well spread to almost all around the world rapidly. The main reason why this disease spreads so many people in a short time is that the virus could be transmitted from an infected person to another by infected droplets. The new emergence of diseases usually may affect multiple organs; moreover, this disease is such an example. Numerous reported studies focus on acute or chronic organ damage caused by the virus. At this point, tissue engineering (TE) strategies can be used to treat the damages with its interdisciplinary approaches. Tissue engineers could design drug delivery systems, scaffolds, and especially biomaterials for the damaged tissue and organs. In this review, brief information about SARS-CoV-2, COVID-19, and epidemiology of the disease will be given at first. After that, the symptoms, the tissue damages in specific organs, and cytokine effect caused by COVID-19 will be described in detail. Finally, it will be attempted to summarize and suggest the appropriate treatments with suitable biomaterials for the damages via TE approaches. The aim of this review is to serve as a summary of currently available tissue damage treatments after COVID-19.
| S-EPMC7677604 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review.
| S-EPMC8894692 | biostudies-literature
Project description: Not available
| S-EPMC7191971 | biostudies-literature
Project description:The COVID-19 disease is caused by a positive stranded RNA virus called SARS-CoV-2. The virus mainly targets the pulmonary epithelial cells as it's initial site of infection by letting its surface spike protein interact and bind to the host ACE2 receptor. The internalization and gradual replication of the virus results in an exaggerated immune response triggering release of many pro-inflammatory cytokines and chemokines. This immune storm is responsible for multiple health hazards in the host ultimately leading to multiple organ failure. Mesenchymal stem cell therapy offers a promising approach towards mitigating the delirious effects of the infection in the COVID-19 patients. This therapy has shown to reduce the expression of pro-inflammatory cytokines as well as repair of damaged tissues in COVID-19 patients. This review has been organized to put forward the positive aruments and implications in support of mesenchymal stem cell therapy as a necessary approach for treating COVID-19 patients.
| S-EPMC7224671 | biostudies-literature
Project description:ObjectiveExplore the relevant evidence about stress-related cognitive appraisal and coping strategies among registered nurses in the emergency department (EDRNs) coping with the COVID-19 pandemic.MethodsThis scoping review followed the methodological framework of Arksey and O'Malley to map relevant evidence and synthesize the findings. We searched PubMed, EMBASE, CINAHL, Web of Science, and Scopus electronic databases for related studies from inception through February 2, 2022. This review further conducted study selection based on the PRISMA flow diagram and applied Lazarus and Folkman's Psychological Stress and Coping Theory to systematically organize, summarize, and report the findings.FindingsSixteen studies were included for synthesis. Most of the studies showed that the majority of EDRNs were overwhelmed by the COVID-19 pandemic. Depression, triaging distress, physical exhaustion, and intention to leave ED nursing were cited as major threats to their wellness. Additionally, comprehensive training, a modified triage system, a safe workplace, psychological support, promotion of resilience, and accepting responsibility may help EDRNs cope with pandemic-related challenges effectively.ConclusionThe long-lasting pandemic has affected the physical and mental health of EDRNs because they have increased their effort to respond to the outbreak with dynamically adjusted strategies. Future research should address a modified triage system, prolonged psychological issues, emergency healthcare quality, and solutions facing EDRNs during the COVID-19 or related future pandemics.Clinical relevanceEDRNs have experienced physical and psychological challenges during the pandemic. The ED administrators need to take action to ensure EDRNs' safety in the workplace, an up-to-date triage system, and mental health of frontline nurses to provide high-quality emergency care for combating COVID-19.
| S-EPMC9538970 | biostudies-literature
Project description:Novel coronavirus disease 2019 (COVID-19) has significantly altered the socio-economic status of countries. Although vaccines are now available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent for COVID-19, it continues to transmit and newer variants of concern have been consistently emerging world-wide. Computational strategies involving drug repurposing offer a viable opportunity to choose a medication from a rundown of affirmed drugs against distinct diseases including COVID-19. While pandemics impede the healthcare systems, drug repurposing or repositioning represents a hopeful approach in which existing drugs can be remodeled and employed to treat newer diseases. In this review, we summarize the diverse computational approaches attempted for developing drugs through drug repurposing or repositioning against COVID-19 and discuss their advantages and limitations. To this end, we have outlined studies that utilized computational techniques such as molecular docking, molecular dynamic simulation, disease-disease association, drug-drug interaction, integrated biological network, artificial intelligence, machine learning and network medicine to accelerate creation of smart and safe drugs against COVID-19.
| S-EPMC9043418 | biostudies-literature
Project description:PurposeRecently, the world has been dealing with a new type of coronavirus called COVID-19 that in terms of symptoms is similar to the SARS coronavirus. Unfortunately, researchers could not find a registered therapy to treat the infection related to the virus yet. Regarding the fact that drug repurposing is a good strategy for epidemic viral infection, we applied the drug repurposing strategy using virtual screening to identify therapeutic options for COVID-19. For this purpose, five proteins of COVID-19 (3-chymotrypsin-like protease (3CLpro), Papain-Like protease (PLpro), cleavage site, HR1 and RBD in Spike protein) were selected as target proteins for drug repositioning.MethodsFirst, five proteins of COVID-19 were built by homology modeling. Then FDA-approved drugs (2471 drugs) were screened against cleavage site and RBD in Spike protein via virtual screening. One hundred and twenty-eight FDA-approved drugs with the most favorable free-binding energy were attached to the cleavage site and RBD in Spike protein. Of these 128 drugs, 18 drugs have either been used currently as antiviral or have been reported to possess antiviral effects. Virtual screening was then performed for the 18 selected drugs with ACE2, 3CLpro and PLpro and HR1 and TMPRSS2.ResultsAccording to the results, glecaprevir, paritaprevir, simeprevir, ledipasvir, glycyrrhizic acid, TMC-310911, and hesperidin showed highly favorably free binding energies with all tested target proteins.ConclusionThe above-mentioned drugs can be regarded as candidates to treat COVID-19 infections, but further study on the efficiency of these drugs is also necessary.
| S-EPMC7261216 | biostudies-literature
Project description:Unanticipated pathogenic risk and emerging transmittable diseases can result from interspecies exchanges of viruses among animals and humans. The emergence of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing coronavirus disease-19 (COVID-19) pandemic has recently exemplified this mechanism. Cough, fever, fatigue, headache, sputum production, hemoptysis, dyspnea, diarrhea, and gastrointestinal disorders are the characteristic features of the disease. The most prevalent and serious manifestation of the infection tends to be pneumonia. The new strains of SARS-CoV-2 with more infectivity have been emerging at regular intervals. There is currently no World Health Organization-approved particular drug for COVID-19. Besides, developing novel antivirals would take much time. Thus, repurposing the application of natural products can provide alternatives and can facilitate medication against COVID-19 as well as can slow down the aggressive progression of the disease before the arrival of approved drugs. Probiotics have long been known for their positive effects on the gut microbiome and impact on immune responses. Particularly, their involvement against viral diseases, especially those of the upper and lower respiratory tract, is of current interest for their prospective application against COVID-19. In this review, we comprehensively address the mode of action of probiotics and their possible intervention against coronavirus diseases correlating with their efficacy against viral diseases. In this regard, we explored recently published relevant research and review articles in MEDLINE/PubMed related to COVID-19 and the effects of probiotics on viral infections.
| S-EPMC9020247 | biostudies-literature