scholarly journals Automatic Identification of SARS Coronavirus using Compression-Complexity Measures

2020 ◽  
Author(s):  
Karthi Balasubramanian ◽  
Nithin Nagaraj
Keyword(s):  
Distance Measure ◽  
Antiviral Treatment ◽  
Nucleotide Sequences ◽  
Automatic Identification ◽  
Sars Coronavirus ◽  
Complexity Measures ◽  
Medical Practitioners ◽  
Global Pandemic ◽  
Institute Of Technology ◽  
Main Ideas

AbstractFinding vaccine or specific antiviral treatment for global pandemic of virus diseases (such as the ongoing COVID-19) requires rapid analysis, annotation and evaluation of metagenomic libraries to enable a quick and efficient screening of nucleotide sequences. Traditional sequence alignment methods are not suitable and there is a need for fast alignment-free techniques for sequence analysis. Information theory and data compression algorithms provide a rich set of mathematical and computational tools to capture essential patterns in biological sequences. In 2013, our research group (Nagaraj et al., Eur. Phys. J. Special Topics 222(3-4), 2013) has proposed a novel measure known as Effort-To-Compress (ETC) based on the notion of compression-complexity to capture the information content of sequences. In this study, we propose a compression-complexity based distance measure for automatic identification of SARS coronavirus strains from a set of viruses using only short fragments of nucleotide sequences. We also demonstrate that our proposed method can correctly distinguish SARS-CoV-2 from SARS-CoV-1 viruses by analyzing very short segments of nucleotide sequences. This work could be extended further to enable medical practitioners in automatically identifying and characterizing SARS coronavirus strain in a fast and efficient fashion using short and/or incomplete segments of nucleotide sequences. Potentially, the need for sequence assembly can be circumvented.NoteThe main ideas and results of this research were first presented at the International Conference on Nonlinear Systems and Dynamics (CNSD-2013) held at Indian Institute of Technology, Indore, December 12, 2013. In this manuscript, we have extended our preliminary analysis to include SARS-CoV-2 virus as well.

Synthetic and semi-synthetic drugs as promising therapeutic option for the treatment of COVID-19

2020 ◽  
Vol 20 ◽  
Author(s):  
Ekta Shirbhate ◽  
Preeti Patel ◽  
Vijay K Patel ◽  
Ravichandran Veerasamy ◽  
Prabodh C Sharma ◽  
...  
Keyword(s):  
Therapeutic Option ◽  
Antiviral Treatment ◽  
The Novel ◽  
Clinical Experiences ◽  
Synthetic Compounds ◽  
Synthetic Drugs ◽  
Global Pandemic ◽  
The World ◽  
Novel Coronavirus

: The novel coronavirus disease-19 (COVID-19), a global pandemic that emerged from Wuhan, China has today travelled all around the world, so far 216 countries or territories with 21,732,472 people infected and 770,866 deaths globally (as per WHO COVID-19 update dated August 18, 2020). Continuous efforts are being made to repurpose the existing drugs and develop vaccines for combating this infection. Despite, to date, no certified antiviral treatment or vaccine prevails. Although, few candidates have displayed their efficacy in in vitro studies and are being repurposed for COVID-19 treatment. This article summarizes synthetic and semi-synthetic compounds displaying potent activity in their clinical experiences or studies against COVID-19 and also focuses on mode of action of drugs being repositioned against COVID-19.

scholarly journals Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication

2021 ◽  
Author(s):  
Tek Narsingh Malla ◽  
Suraj Pandey ◽  
Ishwor Poudyal ◽  
Luis Aldama ◽  
Dennis Feliz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Vitamin C ◽  
Antiviral Treatment ◽  
Cysteine Proteases ◽  
Vitamin Supplement ◽  
Sars Coronavirus ◽  
Over The Counter ◽  
Main Protease ◽  
Approved Drugs

There is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known as main protease Mpro or 3CLpro. The shortest and the safest path to clinical use is the repurposing of drugs with binding affinity to PLpro or 3CLpro that have an established safety profile in humans. Several studies have reported crystal structures of SARS-CoV-2 main protease in complex with FDA approved drugs such as those used in treatment of hepatitis C. Here, we report the crystal structure of 3CLpro in complex Vitamin C (L-ascorbate) bound to the protein's active site at 2.5 Angstrom resolution. We also demonstrate that L-ascorbate inhibits the 3CLpro in vitro at mmol/L concentrations. The crystal structure of the Vitamin C 3CLpro complex may aid future studies on the effect of Vitamin C not only on the coronavirus main protease but on related proteases of other infectious viruses. Since ascorbate is readily available, as an over-the-counter vitamin supplement, our results have the potential for development of a global and inexpensive antiviral treatment.

scholarly journals ORFhunteR: an accurate approach for the automatic identification and annotation of open reading frames in human mRNA molecules

2021 ◽  
Author(s):  
Vasily V. Grinev ◽  
Mikalai M. Yatskou ◽  
Victor V. Skakun ◽  
Maryna K. Chepeleva ◽  
Petr V. Nazarov
Keyword(s):  
Single Molecule ◽  
Web Application ◽  
R Package ◽  
Nucleotide Sequences ◽  
Open Reading Frames ◽  
Classification Model ◽  
Automatic Identification ◽  
Large Set ◽  
Link Type ◽  
Reading Frames

AbstractMotivationModern methods of whole transcriptome sequencing accurately recover nucleotide sequences of RNA molecules present in cells and allow for determining their quantitative abundances. The coding potential of such molecules can be estimated using open reading frames (ORF) finding algorithms, implemented in a number of software packages. However, these algorithms show somewhat limited accuracy, are intended for single-molecule analysis and do not allow selecting proper ORFs in the case of long mRNAs containing multiple ORF candidates.ResultsWe developed a computational approach, corresponding machine learning model and a package, dedicated to automatic identification of the ORFs in large sets of human mRNA molecules. It is based on vectorization of nucleotide sequences into features, followed by classification using a random forest. The predictive model was validated on sets of human mRNA molecules from the NCBI RefSeq and Ensembl databases and demonstrated almost 95% accuracy in detecting true ORFs. The developed methods and pre-trained classification model were implemented in a powerful ORFhunteR computational tool that performs an automatic identification of true ORFs among large set of human mRNA molecules.Availability and implementationThe developed open-source R package ORFhunteR is available for the community at GitHub repository (https://github.com/rfctbio-bsu/ORFhunteR), from Bioconductor (https://bioconductor.org/packages/devel/bioc/html/ORFhunteR.html) and as a web application (http://orfhunter.bsu.by).

scholarly journals Susceptibility of ferrets, cats, dogs, and different domestic animals to SARS-coronavirus-2

2020 ◽  
Author(s):  
Jianzhong Shi ◽  
Zhiyuan Wen ◽  
Gongxun Zhong ◽  
Huanliang Yang ◽  
Chong Wang ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Severe Acute Respiratory Syndrome ◽  
Close Contact ◽  
Domestic Animals ◽  
Sars Coronavirus ◽  
Animal Management ◽  
Global Pandemic ◽  
Respiratory Droplets ◽  
Animal Reservoirs

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the infectious disease COVID-19, which was first reported in Wuhan, China in December, 2019. Despite the tremendous efforts to control the disease, COVID-19 has now spread to over 100 countries and caused a global pandemic. SARS-CoV-2 is thought to have originated in bats; however, the intermediate animal sources of the virus are completely unknown. Here, we investigated the susceptibility of ferrets and animals in close contact with humans to SARS-CoV-2. We found that SARS-CoV-2 replicates poorly in dogs, pigs, chickens, and ducks, but efficiently in ferrets and cats. We found that the virus transmits in cats via respiratory droplets. Our study provides important insights into the animal reservoirs of SARS-CoV-2 and animal management for COVID-19 control.

scholarly journals Another step toward final call on Remdesivir efficacy as a treatment for hospitalized COVID-19 patients: a multicenter open-label trial

2021 ◽  
Author(s):  
Hamed Hosseini ◽  
Anahita Sadeghi ◽  
Payam Tabarsi ◽  
Azin Etemadimanesh ◽  
Ilad Alavi Darazam ◽  
...  
Keyword(s):  
Treatment Initiation ◽  
Antiviral Treatment ◽  
Respiratory Support ◽  
P Value ◽  
Time Interval ◽  
Start Time ◽  
Open Label ◽  
Non Invasive ◽  
Global Pandemic ◽  
Mean Time

Introduction: After emerging the global pandemic of SARS-CoV2 some preliminary studies demonstrated the efficacy of antiviral treatments. But shortly thereafter, inconsistencies in the results of further clinical trials raised doubts on the efficacy of these agents. In this study, we aimed to evaluate the effect of Remdesivir on hospitalized COVID-19 patients' outcomes. Material and methods: This study was an open-label, single-armed, clinical trial on hospitalized patients diagnosed with COVID-19 who had progressive respiratory symptoms despite receiving standard care. All patients received Remdesivir and their characteristics, outcomes, time of treatment initiation, and respiratory support stages during hospitalization were registered and followed up for 14 days. Results: 145 patients with a mean age of 52.89 +- 1.12 years enrolled in this study, 38 (26.2%) died at the end of 14 days period. The mean time interval from the onset of the symptoms to antiviral treatment was 10.63+-0.56 days. Thirty deceased patients (78.9%) were men, showing 2.8 times higher mortality chance compared to women (ORadj=2.77; 95%CI=1.08-7.09). The type of respiratory support on the first day of treatment initiation showed a significantly lower mortality chance in patients receiving O2 only than those who needed non-invasive and/or mechanical ventilation (ORadj=3.91; 95%CI=1.64-9.32). The start time (early vs late administration) and duration (less or more than 7 days) of antiviral treatment had no statistically significant association with mortality or ventilation escalation among the patients (p-value > 0.05). Conclusion: In this study, we showed that Remdesivir probably is not effective on the outcome of hospitalized COVID-19 patients.

Pathophysiology of SARS-CoV-2 (COVID 19) viral infection

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 1809-1814
Author(s):  
Maanya Bhardwaj
Keyword(s):  
Respiratory Infections ◽  
Fungal Infections ◽  
World Health Organisation ◽  
Central China ◽  
World Health ◽  
Medical Practitioners ◽  
Global Pandemic ◽  
Novel Virus ◽  
The City ◽  
Official Status

The city of Wuhan located in Hubei province of central China was burdened with a series of cases presenting with atypical acute respiratory infections in December 2019. Little did people know at that point in time, that a novel virus known as SARS-CoV-2 (COVID-19) or simply corona virus, was responsible for these peculiar presentations. COVID-19 had begun spreading at an alarming rate worldwide, eventually gaining official status as a global pandemic, as affirmed by the World Health Organisation (WHO) on 11 March 2020. By 6 July 2020, globally, there were 1.5 million cases and around 536 893 deaths. As the pandemic took its toll globally, scientists struggled to classify and specify the manifestations of the virus. Medical practitioners, microbiologists and scientists worldwide gradually joined forces to define COVID-19 as an infection characterised by an immense inflammatory reaction or cytokine storm which may cause acute respiratory distress syndrome (ARDS) and multi-organ dysfunction (MODS). During the latter half of 2020, multiple hospitals in India, France, America, Germany and Netherlands reported an increasing incidence of fatal invasive fungal infections in recovered SARS-CoV-2 patients. Increased severity of infections as well as mortality was observed in immunocompromised patients and those with co existing medical illnesses such as diabetes and hypertension. Furthermore, even though many patients recovered from SARS-CoV-2 infection, it was noted that their immunity post recovery was significantly diminished, and it was during this period they were more susceptible to fatal bacterial and fungal co-infections. This review article explores the pathophysiology of COVID 19 infection and difference in response to the infection in adult and paediatric populations.

scholarly journals Risk Perceptions, Attitude and Preventive Practices of Egyptians towards COVID-19

2020 ◽  
Author(s):  
Nadira Mansour Hassan ◽  
Safynaz El Saied Shalaby ◽  
Asmaa Ali EL-Feky ◽  
Eman Ali Younis ◽  
Asmaa Omar Attalla
Keyword(s):  
Perceived Risk ◽  
Risk Perceptions ◽  
Antiviral Treatment ◽  
Good Practice ◽  
Binary Logistic Regression ◽  
Moderate Degree ◽  
Online Questionnaire ◽  
Cross Sectional ◽  
Preventive Practices ◽  
Global Pandemic

Abstract Background: COVID-19 is the latest global pandemic. To date, no antiviral treatment or vaccine has been explicitly recommended for it. Therefore, applying preventive measures to control its spread is the most critical intervention. Perceived risk and attitude determines population’s reaction.Objectives: study perceptions, attitude and practices towards COVID-19 among EgyptiansMethods: The study was cross-sectional using a snowball nonrandom sample from public population of Egyptian Community. They were asked to fulfill predesigned online questionnaire that was available from 16th to 24th March 2020.Results: The study included 1663 participants from all governorates of Egypt. More than half were at age group 21-30 years, 64.3% females and 85.1% students. Main source of information was social media (46.4%). Most of Participants had positive attitude and moderate degree of fear. Only 25.4% of students satisfied with distance learning, 41.4% of participants believe that they are susceptible to infection and 61% believe in seriousness of the disease. About half of participants reported that they follow preventive precautions. Majority of participants (81.3%) believe in effectiveness of these precautions. Participant’s practices were relatively satisfactory except for wearing protective masks, movement of families outside home, reducing touch of nose and eyes, and getting enough sleeping hours. Binary logistic regression identified that significant predictors of good practice were female sex, belief in susceptibility, seriousness, and effectiveness of precautions.On conclusion: Obligatory wearing of masks was an important governmental necessary step and to improve population reaction to control COVID-19, we need to promote realistic risk perceptions and effective attitudes.

scholarly journals Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2

Science ◽  
2020 ◽  
Vol 368 (6494) ◽  
pp. 1016-1020 ◽  
Author(s):  
Jianzhong Shi ◽  
Zhiyuan Wen ◽  
Gongxun Zhong ◽  
Huanliang Yang ◽  
Chong Wang ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Animal Models ◽  
Severe Acute Respiratory Syndrome ◽  
Close Contact ◽  
Sars Coronavirus ◽  
Airborne Transmission ◽  
Domesticated Animals ◽  
Animal Management ◽  
Global Pandemic

Severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) causes the infectious disease COVID-19 (coronavirus disease 2019), which was first reported in Wuhan, China, in December 2019. Despite extensive efforts to control the disease, COVID-19 has now spread to more than 100 countries and caused a global pandemic. SARS-CoV-2 is thought to have originated in bats; however, the intermediate animal sources of the virus are unknown. In this study, we investigated the susceptibility of ferrets and animals in close contact with humans to SARS-CoV-2. We found that SARS-CoV-2 replicates poorly in dogs, pigs, chickens, and ducks, but ferrets and cats are permissive to infection. Additionally, cats are susceptible to airborne transmission. Our study provides insights into the animal models for SARS-CoV-2 and animal management for COVID-19 control.

scholarly journals Secondary School Teachers Self-Perception of Digital Teaching Competence in Spain Following COVID-19 Confinement

2021 ◽  
Vol 11 (8) ◽  
pp. 407
Author(s):  
Jorge-Manuel Prieto-Ballester ◽  
Francisco-Ignacio Revuelta-Domínguez ◽  
María-Inmaculada Pedrera-Rodríguez
Keyword(s):  
Secondary School ◽  
Secondary School Teachers ◽  
Self Perception ◽  
School Teachers ◽  
Face To Face ◽  
Global Pandemic ◽  
Teaching Competence ◽  
Ict Tools ◽  
Institute Of Technology ◽  
Teaching Learning

The education system has become even more complex following the global pandemic, which saw face-to-face teaching transition to virtual teaching. To cope with this abrupt transition, it is essential that teachers have a sufficient level of digital teaching competence. This article aims to increase awareness of teachers’ self-perception of their digital teaching competences in the educational field. Specifically, this study explores Spanish secondary school teachers’ knowledge and use of different ICT tools by evaluating their competence based on different areas proposed by The National Institute of Technology and Professional Development (Instituto Nacional de Tecnologías Educativas y de Formación del Profesorado, INTEF), Madrid, Spain. From the results of the questionnaires, we have determined that teachers consider themselves to have an upper intermediate level of digital teaching competence, although there are still shortcomings that need to be addressed in order to improve this level of competence, and its true integration in the teaching–learning process.

scholarly journals Identifying Facemask-Wearing Condition Using Image Super-Resolution with Classification Network to Prevent COVID-19

Sensors ◽  
2020 ◽  
Vol 20 (18) ◽  
pp. 5236
Author(s):  
Bosheng Qin ◽  
Dongxiao Li
Keyword(s):  
Super Resolution ◽  
Classification Problem ◽  
Automatic Identification ◽  
Infectious Disease Control ◽  
The Public ◽  
Global Pandemic ◽  
Potential Applications ◽  
Public Dataset ◽  
Image Super Resolution ◽  
Facial Images

The rapid worldwide spread of Coronavirus Disease 2019 (COVID-19) has resulted in a global pandemic. Correct facemask wearing is valuable for infectious disease control, but the effectiveness of facemasks has been diminished, mostly due to improper wearing. However, there have not been any published reports on the automatic identification of facemask-wearing conditions. In this study, we develop a new facemask-wearing condition identification method by combining image super-resolution and classification networks (SRCNet), which quantifies a three-category classification problem based on unconstrained 2D facial images. The proposed algorithm contains four main steps: Image pre-processing, facial detection and cropping, image super-resolution, and facemask-wearing condition identification. Our method was trained and evaluated on the public dataset Medical Masks Dataset containing 3835 images with 671 images of no facemask-wearing, 134 images of incorrect facemask-wearing, and 3030 images of correct facemask-wearing. Finally, the proposed SRCNet achieved 98.70% accuracy and outperformed traditional end-to-end image classification methods using deep learning without image super-resolution by over 1.5% in kappa. Our findings indicate that the proposed SRCNet can achieve high-accuracy identification of facemask-wearing conditions, thus having potential applications in epidemic prevention involving COVID-19.

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