# pos

id: cord-241146-j0qperwz
pos: ADD
token:
  https://www.bloomberg.com/opinion/articles/2020-05-01/coronavirus-trillions-in-aid-draws-scams-anddodgy-deals

lemma:
  https://www.bloomberg.com/opinion/articles/2020-05-01/coronavirus-trillions-in-aid-draws-scams-anddodgy-deals


id: cord-291916-5yqc3zcx
pos: NN
token:
  https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance

lemma:
  https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance


id: cord-291916-5yqc3zcx
pos: NNP
token:
  https://www.acc.org/latest-in-cardiology/articles/2020/03/27/14/00/ventricular-arrhythmia-riskdue-to-hydroxychloroquine-azithromycin-treatment-for-covid-19

lemma:
  https://www.acc.org/latest-in-cardiology/articles/2020/03/27/14/00/ventricular-arrhythmia-riskdue-to-hydroxychloroquine-azithromycin-treatment-for-covid-19


id: cord-291916-5yqc3zcx
pos: NNP
token:
  https://investors.modernatx.com/news-releases/news-release-details/moderna-ships-mrnavaccine-against-novel-coronavirus-mrna-1273

lemma:
  https://investors.modernatx.com/news-releases/news-release-details/moderna-ships-mrnavaccine-against-novel-coronavirus-mrna-1273


id: cord-349923-cja8i0hw
pos: NNP
token:
  www.who.int/publications-detail/laboratorytesting-for-2019-novel-coronavirus-in-suspectedhuman-cases-20200117

lemma:
  www.who.int/publications-detail/laboratorytesting-for-2019-novel-coronavirus-in-suspectedhuman-cases-20200117


id: cord-326017-qw4qynqv
pos: NNP
token:
  http://www.iitd.ac.in/content/icmr-approves-probe-freecovid-19-detection-assay-developed-iit-delhi-0

lemma:
  http://www.iitd.ac.in/content/icmr-approves-probe-freecovid-19-detection-assay-developed-iit-delhi-0


id: cord-326017-qw4qynqv
pos: NNP
token:
  https://www.fda.gov/news-events/press-announcements/coronavirusupdate-fda-and-ftc-warn-seven-companies-selling-fraudulent-products-claim-treat-or

lemma:
  https://www.fda.gov/news-events/press-announcements/coronavirusupdate-fda-and-ftc-warn-seven-companies-selling-fraudulent-products-claim-treat-or


id: cord-326017-qw4qynqv
pos: NNP
token:
  https://www.fda.gov/news-events/press-announcements/coronavirus-update-fda-and-ftc-warnseven-companies-selling-fraudulent-products-claim-treat-or

lemma:
  https://www.fda.gov/news-events/press-announcements/coronavirus-update-fda-and-ftc-warnseven-companies-selling-fraudulent-products-claim-treat-or


id: cord-326017-qw4qynqv
pos: NNP
token:
  https://www.euroweeklynews.com/2020/03/16/false-report-of-900k-dead-in-vatican-city-lastnight-i-nearly-fell-off-my-chair-reading-it/

lemma:
  https://www.euroweeklynews.com/2020/03/16/false-report-of-900k-dead-in-vatican-city-lastnight-i-nearly-fell-off-my-chair-reading-it/


id: cord-326017-qw4qynqv
pos: NNP
token:
  https://www.who.int/publications-detail/water-sanitation-hygiene-and-waste-managementfor-the-covid-19-virus-interim-guidance

lemma:
  https://www.who.int/publications-detail/water-sanitation-hygiene-and-waste-managementfor-the-covid-19-virus-interim-guidance


id: cord-326017-qw4qynqv
pos: NNP
token:
  https://health.economictimes.indiatimes.com/news/industry/whosays-over-22000-healthcare-workers-across-52-countries-infected-by-covid-19/75107238

lemma:
  https://health.economictimes.indiatimes.com/news/industry/whosays-over-22000-healthcare-workers-across-52-countries-infected-by-covid-19/75107238


# ent

id: cord-274416-bmvazgj7
type: ORG
entity:
  National Clinical Research Center for Child Health and Disorders and Pediatric Committee of Medical Association of Chinese People s Liberation Army


id: cord-274416-bmvazgj7
type: ORG
entity:
  coronavirus infection Medical Association of Chinese People s Liberation Army Editorial Committee of Chinese Journal of Contemporary Pediatrics


id: cord-294696-pm6pfeeb
type: PROTEIN
entity:
  SARS 20Stellungnahme 20der 20 Desinfektionsmittelkommission 20von 20 DVV 20und 20GfV 20_05032020 BSmodHHMSge2_clean


id: cord-264296-0x90yubt
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 06 03 131987 sha ed6efa757ae5582f4a6108e97d2f40c7cb320584 doc_id 264296 cord_uid 0x90yubt Covid 19 pandemic caused


id: cord-255284-ffh1jl40
type: CHEMICAL
entity:
  cette pathologie En 2 mois une avancée majeure a été réalisée dans la connaissance de cette maladie Il demeure cependant un grand nombre de questions à résoudre Y a t il des porteurs sains


id: cord-268939-ws74xprt
type: WORK_OF_ART
entity:
  Neurologic Manifestations of Hospitalized Patients With Coronavirus Disease Characteristics of ischaemic


id: cord-268822-o86zpu92
type: ORG
entity:
  World Health Organization 2020 Duty to Plan Health Care Crisis Standards of Care and Novel Coronavirus SARS CoV


id: cord-279691-v5kpmk0b
type: PROTEIN
entity:
  Coronavirus Nonstructural Protein 4 Murine Hepatitis Virus Nonstructural Protein 4 Regulates Virus Induced Membrane Modifications and Replication Complex


id: cord-279691-v5kpmk0b
type: PROTEIN
entity:
  NS4A Membrane Curvature and Mechanisms of Dynamic Cell Membrane Remodelling Mechanisms Shaping the Membranes of Cellular Organelles How Proteins Produce Cellular Membrane Curvature Mobility Analysis


id: cord-279691-v5kpmk0b
type: PROTEIN
entity:
  Coronavirus Replication Transcription Complexes Cytoplasmic Dynein Associated Structures Move Bidirectionally


id: cord-279691-v5kpmk0b
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein nsp10 nsp14 Exoribonuclease Complex Identification of Severe Acute Respiratory Syndrome Coronavirus Replicase Products and Characterization of


id: cord-279691-v5kpmk0b
type: ORG
entity:
  the Membrane Rearrangements Induced by Coronavirus Ultrastructure and Origin of Membrane Vesicles Associated


id: cord-279691-v5kpmk0b
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Replication Complex An Electron Microscope Study of the Development of a Mouse Hepatitis Virus in Tissue Culture Cells Proliferative Growth of SARS Coronavirus


id: cord-279691-v5kpmk0b
type: ORG
entity:
  the Mammalian ER Mobility and Interactions of the Coronavirus Nonstructural Protein 4 Murine Hepatitis Virus Nonstructural Protein 4


id: cord-279691-v5kpmk0b
type: WORK_OF_ART
entity:
  Scaffolding Protein Genome Wide Analysis of Protein Protein Interactions and Involvement of Viral Proteins in SARS CoV Replication Analysis of Intraviral Protein Protein Interactions of the SARS


id: cord-279691-v5kpmk0b
type: ORG
entity:
  Membrane Deformation Mechanisms Determining the Morphology of the Peripheral ER Viral Reorganization of the Secretory Pathway Generates


id: cord-279691-v5kpmk0b
type: FAC
entity:
  Infected Mosquito Cells Photobleaching and Photoactivation Following Protein Dynamics in Living Cells Development


id: cord-018078-clxzp1ph
type: PROTEIN
entity:
  Coronaviridae and Arteriviridae A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae High frequency RNA recombination


id: cord-289588-n61gz7pi
type: CHEMICAL
entity:
  Hydroxychloroquine Chloroquine Ribavirin Ritonavir Lopinavir Favipiravir Interferons Bevacizumab Azithromycin


id: cord-280518-2tl0mtb8
type: DISEASE
entity:
  coronavirus Novel coronavirus 2019 nCoV situation report 3 Emergency Committee regarding the outbreak of novel coronavirus 2019 nCoV Geneva Switzerland World


id: cord-028618-kn87q7nb
type: EVENT
entity:
  the Blame Game Patriotism or Opinion Leadership the Nature and Origins of the Rally Round the Flag Effect Italy Critics EU


id: cord-021152-6znmkvy9
type: PROTEIN
entity:
  Coronaviridae family 19 20 21 22 Molecular evidence suggests that the Severe Acute Respiratory Syndrome Betacoronavirus SARS CoV beta CoV


id: cord-278325-ykcd7d59
type: PROTEIN
entity:
  interleukin IL 2R IL 6 IL 1β IL 8 IL 17 granulocyte colony stimulating factor G CSF tumour necrosis factor


id: cord-278325-ykcd7d59
type: ORG
entity:
  the Scientific and Standardization Committee on Perioperative and Critical Care of the International Society on Thrombosis


id: cord-278325-ykcd7d59
type: DISEASE
entity:
  HL Hodgkin lymphoma HSCT haematopoietic stem cell transplantation MM multiple myeloma NHL non Hodgkin lymphoma PD


id: cord-286958-e1ey31eo
type: ORG
entity:
  Notice of the People s Government of Hubei Province on Strengthening the Prevention and Control of Pneumonia Infected


id: cord-031113-moekkw2x
type: ORG
entity:
  the Persistence of Police Legitimacy Obeying the Rules of the Road Procedural Justice Social Identity


id: cord-031113-moekkw2x
type: ORG
entity:
  the Citizen Taxpaying Role and Compliance Practices Centre for Tax System Integrity A New Approach to Tax Compliance Dancing with Tax Authorities Motivational Postures and Non compliant


id: cord-031113-moekkw2x
type: ORG
entity:
  the Ultimate Demonstration of the Real world Impact of Racism Police Occupational Culture Classic Themes Altered Times Status Influences on Perceptions of Procedural Justice A Test of the Group Value Model


id: cord-286683-mettlmhz
type: ORG
entity:
  Cysteine Protease Independent FcγR Pathway Severe Acute Respiratory Syndrome SARS Coronavirus Induced Lung Epithelial Cytokines


id: cord-286683-mettlmhz
type: WORK_OF_ART
entity:
  The Search for Optimal Oxygen Saturation Targets in Critically Ill Patients Observational Data From Large ICU Databases Practical


id: cord-286683-mettlmhz
type: ORG
entity:
  Observational Study of Hydroxychloroquine in Hospitalized Patients with Covid 19 Association of Treatment With Hydroxychloroquine or Azithromycin With In Hospital Mortality in Patients


id: cord-030934-t7akdu6x
type: CELL_LINE
entity:
  China combatting COVID 19 China Novel Coronavirus Investigating and Research Team A novel coronavirus from patients with pneumonia in China Genomic


id: cord-267436-mivxm8oh
type: ORG
entity:
  1 World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis


id: cord-255603-quuju9h4
type: GGP
entity:
  Syndr DOI 10 1016 j dsx 2020 05 008 sha 3211b0da0fdd1240f8538b8a95de7c7e3a9f64d2 doc_id 255603 cord_uid quuju9h4


id: cord-260225-bc1hr0fr
type: WORK_OF_ART
entity:
  Protease Reveals the Critical Role of the Extra Domain in Dimerization of the Enzyme Defining the Extra Domain


id: cord-260225-bc1hr0fr
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein Nsp10 Nsp14 Exoribonuclease Complex Structural Basis


id: cord-260225-bc1hr0fr
type: ORG
entity:
  Coronavirus Infectious Bronchitis Virus Crystal Structure of Its N Terminal Domain and Multimerization Properties Modular Organization of SARS


id: cord-260225-bc1hr0fr
type: FAC
entity:
  the Elderly Cutting Edge Impaired Toll like Receptor Expression and Function in Aging Signaling Pathways


id: cord-260225-bc1hr0fr
type: ORG
entity:
  the Cardiovascular System Implications for Risk Assessment Complement Associated Microvascular Injury and Thrombosis


id: cord-260225-bc1hr0fr
type: ORG
entity:
  A Combined Proteomics Genomics Approach Links Hepatitis C Virus Infection with Nonsense Mediated MRNA Decay Virus Escape and Manipulation of Cellular Nonsense


id: cord-260225-bc1hr0fr
type: EVENT
entity:
  the NMD Resistance of AUG Proximal Nonsense Mutations A Conserved Role for Cytoplasmic Poly A Binding Protein 1 PABPC1


id: cord-260225-bc1hr0fr
type: ORG
entity:
  the Mouse Hepatitis Virus Nucleocapsid Protein Effects of Phosphorylation of Avian Retrovirus Nucleocapsid Protein


id: cord-260225-bc1hr0fr
type: FAC
entity:
  the Crossroads of Many Cellular Pathways Valiente Echeverría F Strategies for Success Viral Infections and Membraneless Organelles


id: cord-260225-bc1hr0fr
type: ORG
entity:
  Concomitant Formation of Stress Granules and Processing Bodies Hypoxic Inhibition of Nonsense Mediated RNA Decay Regulates Gene Expression


id: cord-104500-m0kfom0x
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome Middle East Respiratory Syndrome Coronavirus Disease 19 Super Spread Events


id: cord-104500-m0kfom0x
type: WORK_OF_ART
entity:
  Presymptomatic Phase Japan Emerging Infectious Diseases Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics


id: cord-268561-vq1uhj5i
type: PROTEIN
entity:
  CoV H CoV 229 E H CoV NL63 and H CoV HKU1 rhinovirus enterovirus metapneumovirus adenovirus Mycoplasma pneumoniae Streptococcus


id: cord-268561-vq1uhj5i
type: WORK_OF_ART
entity:
  Neurologic Manifestations of Hospitalized Patients With Coronavirus Disease Relation Between Chest CT Findings and Clinical Conditions of Coronavirus Disease COVID 19 Pneumonia A Multicenter Study Clinical


id: cord-268561-vq1uhj5i
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome Coronavirus 2 Specific Antibody Responses in Coronavirus Disease Clinical


id: cord-268561-vq1uhj5i
type: DISEASE
entity:
  influenza seasonal CoV adenovirus bocavirus human metapneumovirus parainfluenza respiratory syncytial virus rhinovirus Bordetella pertussis


id: cord-256051-87alqfkd
type: ORG
entity:
  Antiphospholipid Antibodies in Patients with Covid 19 Neurologic Manifestations of Hospitalized Patients With Coronavirus Disease Incidence


id: cord-256051-87alqfkd
type: EVENT
entity:
  Diagnosis and Management Relation Between Chest CT Findings and Clinical Conditions of Coronavirus Disease COVID 19


id: cord-266260-t02jngq0
type: ORG
entity:
  A Comparative Study of Clinical Presentation and Risk Factors for Adverse Outcome in Patients Hospitalised with Acute Respiratory Disease Due


id: cord-266260-t02jngq0
type: ORG
entity:
  Saudi Arabia Conveyance Contact Investigation for Imported Middle East Respiratory Syndrome Cases Recovery


id: cord-283215-dgysimh5
type: ORG
entity:
  China American College of Surgeons COVID 19 Guidelines for Triage of Thoracic Cancer Patients American College of Surgeons Committee


id: cord-283215-dgysimh5
type: ORG
entity:
  National Institute for Health and Care Excellence NICE Preliminary Recommendations for Surgical Practice of Neurosurgery Department


id: cord-292751-tk1oggi9
type: DISEASE
entity:
  blood pressure diabetes heart diseases respiratory diseases cerebrovascular diseases endocrine system disorders digestive system disorders


id: cord-302471-all5j2od
type: PROTEIN
entity:
  bovine coronavirus hemagglutinin esterase protein Bovine coronavirus structural proteins Bovine coronavirus hemagglutinin protein


id: cord-297323-l3f12hg4
type: DISEASE
entity:
  cancer immune suppression autoimmune diseases inflammatory disease neurodegenerative diseases obesity


id: cord-241146-j0qperwz
type: CELL_LINE
entity:
  Fake COVID 19 Related Products UK Medicines and Medical Devices Regulator Investigating 14 Cases of Fake or Unlicensed COVID 19 Medical Products


id: cord-253077-61fmul8c
type: PROTEIN
entity:
  colon ACE2 angiotensin converting enzyme 2 BNP B type natriuretic peptide CRP Creactive protein IL interleukin N L neutrophil


id: cord-253077-61fmul8c
type: EVENT
entity:
  a Novel Series of Antiviral Drug Candidates Targeting the SARS CoV Characterization and Quantification of Innate Lymphoid Cell Subsets


id: cord-253077-61fmul8c
type: ORG
entity:
  The Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Inhibits Type I Interferon Production


id: cord-253077-61fmul8c
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame ORF 3b ORF 6 and Nucleocapsid Proteins Function


id: cord-253077-61fmul8c
type: ORG
entity:
  Decade Long Structural Studies of SARS Coronavirus Molecular Mechanism for Antibody Dependent Enhancement of Coronavirus Entry C


id: cord-253077-61fmul8c
type: ORG
entity:
  Camelid Antibodies Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease Neutralizing


id: cord-256688-yy7abob9
type: ORG
entity:
  Department of Defense U S Army U S Air Force Brooke Army Medical Center or SAUSHEC EM Residency Program


id: cord-254446-yxqbe1dj
type: ORG
entity:
  Coronavirus Pneumonia Emergency Response Epidemiology T Clinical Characteristics of Coronavirus Disease 2019


id: cord-254446-yxqbe1dj
type: WORK_OF_ART
entity:
  Prevalence of Underlying Diseases in Hospitalized Patients with COVID 19 a Systematic Review and Meta Analysis Active


id: cord-254446-yxqbe1dj
type: ORG
entity:
  the Coronavirus Disease Review of Emerging Pharmacotherapy for the Treatment of Coronavirus Disease SARS CoV


id: cord-287758-da11ypiy
type: PROTEIN
entity:
  amino acids Proline Leucine Lysine Asparagine Phenylalanine Glycine Threonine Glutamine Alanine Methionine and Tyrosine One


id: cord-287758-da11ypiy
type: CHEBI
entity:
  amino acids Proline Leucine Lysine Asparagine Phenylalanine Glycine Threonine Glutamine Alanine Methionine


id: cord-287758-da11ypiy
type: ORG
entity:
  the Humoral Immune Response Contributes to Virus Spread and Immunopathology in the Airways of Murine Models


id: cord-287758-da11ypiy
type: WORK_OF_ART
entity:
  A Possible Pharmaceutical Treatment for COVID 19 Experimental Treatment with Favipiravir for COVID 19


id: cord-287758-da11ypiy
type: ORG
entity:
  Association of Treatment with Hydroxychloroquine or Azithromycin With In Hospital Mortality in Patients With COVID 19


id: cord-287758-da11ypiy
type: DISEASE
entity:
  cardiovascular issues cerebrovascular chronic pulmonary diseases immunocompromising renal problems hepatic disease hypertension diabetes


id: cord-298156-d0pb1kik
type: EVENT
entity:
  Brussels COVID 19 Outbreak Rights Roles and Responsibilities of Health Workers Including Key Considerations for Occupational Safety and Health


id: cord-303523-m16vlv1q
type: ORG
entity:
  Interim Healthcare Infection Prevention and Control Recommendations for Patients Under Investigation


id: cord-299093-zp07aqpm
type: ORG
entity:
  COVID 19 Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease Clinical


id: cord-299093-zp07aqpm
type: ORG
entity:
  Severe Acute Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the Absence of Encephalitis in Mice Transgenic for Human ACE2


id: cord-258679-rlfsqgm7
type: DNA
entity:
  Arabian Peninsula include Bahrain Iraq Iran Israel Jordan Kuwait Lebanon Oman Palestinian Territories Qatar Saudi Arabia Syria


id: cord-258679-rlfsqgm7
type: CELL_LINE
entity:
  UK London United Kingdom Health Protection Agency European Centre for Disease Prevention and Control Epidemiological update case of severe lower respiratory tract disease associated with a novel coronavirus Further UK case of novel coronavirus London United Kingdom Health Protection Agency Third case of novel coronavirus infection identified in family cluster


id: cord-291916-5yqc3zcx
type: PROTEIN
entity:
  China NHC nonstructural protein 14 nsp14 Northern Hemisphere NH nucleocapsid phosphoprotein N open reading frames


id: cord-291916-5yqc3zcx
type: EVENT
entity:
  Wuhan City Molecular Evolution of Human Coronavirus Genomes A Review of Coronavirus Disease 2019 COVID 19 Genetic Recombination and Pathogenesis of Coronaviruses Coronaviruses in Avian Species Review with Focus on Epidemiology and Diagnosis in Wild Birds


id: cord-291916-5yqc3zcx
type: ORG
entity:
  SARS CoV 2 COVID 19 Infection and Circulating ACE2 Levels Protective Role in Women and Children Front Contact Tracing


id: cord-291916-5yqc3zcx
type: ORG
entity:
  CrossRef 89 National Health Commission of the People s Republic of China Pneumonia Epidemic Situation of New Coronavirus Infection


id: cord-291916-5yqc3zcx
type: ORG
entity:
  Vitro Bionic Digestion and Biomembrane Extraction for Metal Speciation Analysis Bioavailability and Risk Assessment


id: cord-291916-5yqc3zcx
type: WORK_OF_ART
entity:
  Therapeutic Applications of Mesenchymal Stem Cells for Systemic Lupus Erythematosus Mesenchymal Stromal Cells Clinical Challenges and Therapeutic Opportunities


id: cord-262119-s6hc7fxs
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 10 26 356014 sha 7fe7bdc5f8982397c39763159ee63355fca527de doc_id 262119 cord_uid s6hc7fxs We


id: cord-262119-s6hc7fxs
type: WORK_OF_ART
entity:
  Autophagy and Energy Metabolism Canonical and Noncanonical Autophagy as Potential Targets for COVID 19


id: cord-262119-s6hc7fxs
type: WORK_OF_ART
entity:
  The SARS Coronavirus 3a Protein Causes Endoplasmic Reticulum Stress and Induces Ligand Independent Downregulation of the Type 1 Interferon Receptor Accessory


id: cord-262119-s6hc7fxs
type: WORK_OF_ART
entity:
  the NLRP3 Inflammasome in Severe COVID 19 SARS CoV 2 infection and overactivation of Nlrp3 inflammasome


id: cord-262119-s6hc7fxs
type: ORG
entity:
  a Dysregulated Myeloid Cell Compartment Deciphering the Role of Host Genetics in Susceptibility to Severe COVID


id: cord-278668-v530u7h0
type: PROTEIN
entity:
  asparagine residues HexNAc 2 Hex 3 HexNAc 2 Hex 3 dHex 1 HexNAc 2 Hex 3 dHex 2 HexNAc 2 Hex 4 HexNAc 2 Hex 5 HexNAc 2 Hex 6 HexNAc 2 Hex 7 HexNAc 2 Hex 8


id: cord-278668-v530u7h0
type: CHEMICAL
entity:
  asparagine residues HexNAc 2 Hex 3 HexNAc 2 Hex 3 dHex 1 HexNAc 2 Hex 3 dHex 2 HexNAc 2 Hex 4 HexNAc 2 Hex 5 HexNAc 2 Hex 6 HexNAc 2 Hex 7 HexNAc 2 Hex 8 and HexNAc 2 Hex 9


id: cord-312434-yx24golq
type: DNA
entity:
  human coronavirus 229E HCoV 229E human coronavirus OC43 HCoV OC43 human coronavirus NL63 HCoV NL63 and human coronavirus HKU1 HCoV HKU1


id: cord-312434-yx24golq
type: ORG
entity:
  Epidemiology Working Group for NCIP Epidemic Response Chinese Center for Disease Control and Prevention


id: cord-300817-cxc00k0d
type: CELL_LINE
entity:
  India COVID 19 Statewise Status Government of India Domestic fuels indoor air pollution and children s health the case of rural India The SARS MERS


id: cord-274802-7ioiwsd8
type: CELL_TYPE
entity:
  circulating T helper cells CD4 cells Cytotoxic T cells CD8 cells B cells natural killers cells lymphocytes monocytes eosinophils


id: cord-274802-7ioiwsd8
type: PROTEIN
entity:
  activated B cell NF κB Toll like receptors TLRs Mitogen Activated Protein Kinase MAPK Bone Marrow Stromal Cell Antigen 2 BST2 IL


id: cord-274802-7ioiwsd8
type: PROTEIN
entity:
  Intercellular Adhesion Molecule 1 ICAM 1 Intercellular Adhesion Molecule 2 ICAM 2 Matrix Metallopeptidase 9 MMP9 Baculoviral IAP Repeat Containing 3 BIRC3 and Rho Family GTPase 1 RND1


id: cord-274802-7ioiwsd8
type: WORK_OF_ART
entity:
  Activates the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control by the Humoral Immune Response A Transmembrane Serine Protease


id: cord-274802-7ioiwsd8
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Spike Protein S2 Domain with Characteristics of a Viral Fusion Peptide Ultrastructure and Origin of Membrane Vesicles Associated


id: cord-274802-7ioiwsd8
type: FAC
entity:
  Analysis of Constructed E Gene Mutants of Mouse Hepatitis Virus Confirms a Pivotal Role for E Protein in Coronavirus Assembly Infectious Bronchitis Virus E Protein Is Targeted


id: cord-274802-7ioiwsd8
type: ORG
entity:
  Inhibition of Endosomal Lysosomal Degradation Increases the Infectivity of Human Immunodeficiency Virus Hydroxychloroquine


id: cord-274802-7ioiwsd8
type: DISEASE
entity:
  breath chest pain diarrhoea nausea rhinorrhoea runny nose vomiting loss of appetite abdominal pain gastrointestinal bleeding autoimmune haemolytic anaemia


id: cord-318392-r9bbomvk
type: DNA
entity:
  ORF1a n 28 ORF1b n 19 32 kDa non structural protein NSP gene n 6 hemagglutinin esterase HE gene n 2 S gene n 18 4 9 kDa NSP gene n 2 4 8 kDa NSP gene


id: cord-318392-r9bbomvk
type: ORG
entity:
  the International Committee on Taxonomy of Viruses International Union of Microbiological Societies Virology Division Comparative


id: cord-303517-8971aq02
type: FAC
entity:
  Le Centre de Référence Déficits Immunitaires Héréditaires CEREDIH 80 Organization for Primary Immunodeficiencies


id: cord-303517-8971aq02
type: WORK_OF_ART
entity:
  Effect of Dexamethasone in Hospitalized Patients with COVID 19 Preliminary Report Improved Clinical Symptoms and Mortality on Severe Critical COVID 19 Patients Utilizing Convalescent Plasma Transfusion Convalescent


id: cord-303517-8971aq02
type: ORG
entity:
  Pan American Health Organization World Health Organization Centers for Disease Control and Prevention Cancer


id: cord-303517-8971aq02
type: WORK_OF_ART
entity:
  A Trial of Lopinavir Ritonavir in Adults Hospitalized with Severe Covid 19 Centro Nacional de Información de Ciencias Médicas Incidence


id: cord-303517-8971aq02
type: WORK_OF_ART
entity:
  Breathe Pharmacologic Treatment of Transplant Recipients Infected With SARS CoV 2 Considerations Regarding Therapeutic Drug Monitoring and Drug Drug Interactions


id: cord-259229-e8m8m4ut
type: GGP
entity:
  angiotensin I converting enzyme ACE2 angiotensin converting enzyme 2 ACEi ACE inhibitor AT1R angiotensin type 1 receptor AT2R angiotensin type 2 receptor ARBs angiotensin II type I receptor blockers cTnI cardiac troponin I MAS mitochondrial assembly receptor MRAs mineralocorticoid receptor


id: cord-259229-e8m8m4ut
type: WORK_OF_ART
entity:
  Urgent Guidance for Navigating and Circumventing the QTc Prolonging and Torsadogenic Potential of Possible Pharmacotherapies for Coronavirus Disease 19 COVID 19 Role of lopinavir


id: cord-305422-t8azymo7
type: ORG
entity:
  Its Implication for Public Health Interventions Consensus Document on the Epidemiology of SARS Organizaition WH Global Surveillance


id: cord-305422-t8azymo7
type: WORK_OF_ART
entity:
  The World after Ebola An Overview of Ebola Complications Vaccine Development Lessons Learned Financial Losses


id: cord-305422-t8azymo7
type: DISEASE
entity:
  dry cough shortness of breath muscle ache dizziness headache sore throat rhinorrhea chest pain diarrhea nausea and vomiting


id: cord-311847-2czqs84q
type: CELL_TYPE
entity:
  lung kidney vascular endothelia small intestine and human airway epithelia 96 97 98 Conversely MERS CoV


id: cord-311847-2czqs84q
type: GGP
entity:
  Parkinson s disease MS and optic neuritis 129 130 131 132 Therefore it was proposed that a persistent CoV infection might be a pathogenic factor


id: cord-311847-2czqs84q
type: DISEASE
entity:
  diseases like cerebral vasculitis neuromyelitis optica neurosarcoidosis polymyositis myasthenia gravis


id: cord-279255-v861kk0i
type: DISEASE
entity:
  gastrointestinal tract abdominal cavity peritonitis respiratory tract and central nervous system 128 Canines


id: cord-312178-tojgojjf
type: DISEASE
entity:
  illness severe acute respiratory syndrome coronavirus SARS CoV Middle East respiratory syndrome coronavirus MERS CoV


id: cord-308537-i6um5iu2
type: ORG
entity:
  Feline Infectious Peritonitis Current Status Lawrenceville NJ Veterinary Learning Systems Protection


id: cord-319983-e4f2sfl4
type: CELL_LINE
entity:
  Open Label Non Randomized Clinical Trial Treatment of severe acute respiratory syndrome Retrospective comparison


id: cord-319983-e4f2sfl4
type: ORG
entity:
  the National Health Commission of the People s Republic of China on Revising the English Name of Novel Coronavirus Pneumonia Isolation


id: cord-319983-e4f2sfl4
type: ORG
entity:
  Government of India Ministry of Health and Family Welfare Directorate General of Health Services EMR Division 2020 Clinical Management of COVID 19


id: cord-321259-wio2b49i
type: WORK_OF_ART
entity:
  Molecular Evolution of Human Coronavirus Genomes Epidemiology Genetic Recombination and Pathogenesis of


id: cord-323618-d09b65gd
type: PROTEIN
entity:
  Coronaviridae and Arteriviridae A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae


id: cord-323618-d09b65gd
type: DNA
entity:
  human coronavirus strain OC43 phylogenetic relationships to bovine and murine coronaviruses and influenza C virus Analysis of cellular receptors


id: cord-321670-f2d4bykp
type: PROTEIN
entity:
  ein Zwilling wurden symptomatisch 6 Neugeborene hatten eine Atemstörung 3 eine Zyanose 2 Erbrechen und Nahrungsintoleranz 2 Fieber ein


id: cord-321194-xi4zy5ow
type: CELL_LINE
entity:
  China Displayed Sign Banning Black People Trump Signs Historic 2 Trillion Stimulus After Congress Passes


id: cord-321194-xi4zy5ow
type: DNA
entity:
  Curb Coronavirus EBRD Unveils V1 Billion Emergency Coronavirus Financing Package Inquiry After 668 of French Aircraft Carrier s Crew Catch Coronavirus Coronavirus Nuggets Report Member of Organization Tested Positive


id: cord-321194-xi4zy5ow
type: ORG
entity:
  Tackle Coronavirus Outbreak Commission Publishes Guidance on Export Requirements for Personal Protective Equipment


id: cord-321194-xi4zy5ow
type: WORK_OF_ART
entity:
  Prisoners to Curb Coronavirus EBRD Unveils V1 Billion Emergency Coronavirus Financing Package Inquiry


id: cord-324198-b8f99z8r
type: PROTEIN
entity:
  Coronavirus COVID 19 in China and Will Influence Future Urban Health Policy Internationally Climate Change and Economic Resilience through Urban and Cultural Heritage The Case of Emerging Small Island Developing States Economies


id: cord-327063-ea7a1xfl
type: ORG
entity:
  the Singapore Novel Coronavirus Outbreak Research T Epidemiologic Features and Clinical Course of Patients Infected With SARS CoV 2


id: cord-327063-ea7a1xfl
type: ORG
entity:
  Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence


id: cord-327063-ea7a1xfl
type: WORK_OF_ART
entity:
  Structure of SARS Coronavirus Spike Receptor Binding Domain Complexed with Receptor Structural Analysis


id: cord-327063-ea7a1xfl
type: DISEASE
entity:
  dyspnea respiratory distress hemoptysis gastrointestinal infection liver central nervous system and lung damage


id: cord-328644-odtue60a
type: DNA
entity:
  protein Nucleocapsid sites 203 and 204 Polyprotein sites 265 3606 and 4715 Spike site 614 and orf8 site 84


id: cord-292912-ufcvecwo
type: WORK_OF_ART
entity:
  the Treatment of Acute Novel Coronavirus Pneumonia COVID 19 Clinical Study for Umbilical Cord Blood Mononuclear Cells in the Treatment of Acute Novel Coronavirus Pneumonia


id: cord-292912-ufcvecwo
type: WORK_OF_ART
entity:
  the Treatment of Acute Novel Coronavirus Pneumonia COVID 19 Clinical Study of Cord Blood NK Cells Combined with Cord Blood Mesenchymal Stem Cells in the Treatment of Acute Novel Coronavirus Pneumonia Immunoregulatory Therapy for Umbilical Cord UC Derived Mesenchymal Stem Cells MSCs Treatment for the


id: cord-322456-5at1euqm
type: ORG
entity:
  Coronavirus Studiengruppe des Internationalen Komitees zur Taxonomie von Viren International Committee on Taxonomy of Viruses


id: cord-326584-io2f52kn
type: WORK_OF_ART
entity:
  Korea The Rate of Underascertainment of Novel Coronavirus 2019 nCoV Infection Estimation Using Japanese Passengers Data on Evacuation Flights Transmission of COVID 19


id: cord-326584-io2f52kn
type: ORG
entity:
  Strategies for Mitigation and Suppression WHO Collaborating Centre for Infectious Disease Modelling MRC Centre for Global Infectious Disease Analysis Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2


id: cord-326584-io2f52kn
type: ORG
entity:
  the Office of the Chief Government Statistician Ministry of Finance and Planning Zanzibar National Population Projections United Republic of Tanzania


id: cord-326584-io2f52kn
type: EVENT
entity:
  New Year Identifying and Interrupting Superspreading Events Implications for Control of Severe Acute Respiratory Syndrome Coronavirus 2


id: cord-320955-xhp96abg
type: ORG
entity:
  COVID 19 A Detailed Chronological Timeline and Extensive Review of Literature Documenting the Pandemic date 2020 07 24


id: cord-325377-g68onkjt
type: CHEMICAL
entity:
  3067 SARS CoV 2 genomes reveals a clonal geo 332 distribution and a rich genetic variations of hotspots mutations Cas12 based


id: cord-325700-f102uk2m
type: WORK_OF_ART
entity:
  Metabolomics Profiling of Critically Ill Coronavirus Disease 2019 Patients Identification of Diagnostic and Prognostic Biomarkers


id: cord-344486-iu5flbcl
type: ORG
entity:
  the Center for Systems Science and Engineering Multicenter Initial Guidance on Use of Antivirals for Children With Coronavirus Disease 2019


id: cord-344486-iu5flbcl
type: ORG
entity:
  the American College of Cardiology American Heart Association Task Force on Clinical Practice Guidelines COVID 19


id: cord-344486-iu5flbcl
type: LAW
entity:
  moderate COVID 19 A Randomized Trial of Hydroxychloroquine as Postexposure Prophylaxis for Covid 19 Clinical


id: cord-344486-iu5flbcl
type: ORG
entity:
  COVID 19 Association of Treatment With Hydroxychloroquine or Azithromycin With In Hospital Mortality in Patients


id: cord-315598-qwh72inx
type: GGP
entity:
  expansión y extensión Colombia reporta a la fecha actual 113 389 casos confirmados y 3984 nuevos casos de COVID 19 confirmados y cerca


id: cord-315598-qwh72inx
type: GGP
entity:
  Ataque cerebrovascular agudo isquémico o hemorrágico con tazas de entre el 5 al 6 por lo que el examen neurológico debe realizarse para documentar


id: cord-315598-qwh72inx
type: PERSON
entity:
  debido al riesgo potencial de contaminación del campo quirúrgico con el aire que sale de la válvula de exhalación


id: cord-315598-qwh72inx
type: PRODUCT
entity:
  con el receptor de la enzima convertidora de angiotensina 2 ACE2 el hemograma puede revelar linfopenia y neutrofilia sin otras anormalidades significativas


id: cord-315598-qwh72inx
type: PERSON
entity:
  además de recibir hidroxicloroquina lopinavir ritonavir y metilprednisolona fueron tratados con plasma


id: cord-315598-qwh72inx
type: ORG
entity:
  Assessment of Self Contamination During Removal of Personal Protective Equipment for Ebola Patient Care


id: cord-315598-qwh72inx
type: ORG
entity:
  Society European Society of Intensive Care Medicine Society of Critical Care Medicine Clinical Practice Guideline Mechanical Ventilation


id: cord-315598-qwh72inx
type: EVENT
entity:
  the Prone Position Outside the Intensive Care Unit Use of Prone Positioning in Nonintubated Patients With COVID 19 and Hypoxemic Acute Respiratory Failure First case


id: cord-315598-qwh72inx
type: ORG
entity:
  CT A Preliminary Study on the Ultrasonic Manifestations of Peripulmonary Lesions of Non Critical Novel Coronavirus Pneumonia Effect of Focused Bedside Ultrasonography


id: cord-315598-qwh72inx
type: EVENT
entity:
  Human Coronaviruses and Other Respiratory Viruses Underestimated Opportunistic Pathogens of the Central Nervous System Viruses Neurological


id: cord-315598-qwh72inx
type: WORK_OF_ART
entity:
  the Acute Disease Quality Initiative ADQI 21 Workgroup Intravascular Volume Assessment in the Critically Ill Patient


id: cord-315598-qwh72inx
type: ORG
entity:
  Dialysis Facilities Additional Guidance for Infection Prevention and Control Recommendations for Patients


id: cord-315598-qwh72inx
type: FAC
entity:
  Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome


id: cord-315598-qwh72inx
type: ORG
entity:
  Covid 19 medRxiv Association of Treatment With Hydroxychloroquine or Azithromycin With In Hospital Mortality in Patients


id: cord-315598-qwh72inx
type: WORK_OF_ART
entity:
  Molecular Mechanism for Antibody Dependent Enhancement of Coronavirus Entry Treatment of 5 Critically Ill Patients With COVID 19 With Convalescent Plasma Effectiveness


id: cord-315598-qwh72inx
type: WORK_OF_ART
entity:
  Treatment With Convalescent Plasma for Critically Ill Patients With Severe Acute Respiratory Syndrome


id: cord-315598-qwh72inx
type: ORG
entity:
  the Difficult Airway Society the Association of Anaesthetists the Intensive Care Society the Faculty of Intensive Care Medicine


id: cord-315598-qwh72inx
type: ORG
entity:
  the Royal College of Anaesthetists Management of Difficult Tracheal Intubation A Closed Claims Analysis Difficult Airway Society


id: cord-315598-qwh72inx
type: WORK_OF_ART
entity:
  Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome and Posterior Probability of Mortality Benefit in a Post


id: cord-315598-qwh72inx
type: ORG
entity:
  Ann Intensive Care Effect of Postextubation High Flow Nasal Cannula vs Noninvasive Ventilation on Reintubation and Postextubation Respiratory Failure in High Risk Patients A Randomized Clinical Trial High


id: cord-315598-qwh72inx
type: ORG
entity:
  American Society for Parenteral and Enteral Nutrition Guidelines for the Provision and Assessment of Nutrition Support Therapy


id: cord-315598-qwh72inx
type: DISEASE
entity:
  acute lung injury acute respiratory distress syndrome Extravascular lung water and pulmonary arterial wedge pressure


id: cord-345503-52kq2u8a
type: ORG
entity:
  National Advance Center for Craniomaxillofacial Reconstruction Tehran Iran 2 Craniomaxillofacial Research Center Tehran University of Medical Sciences


id: cord-326017-qw4qynqv
type: CHEMICAL
entity:
  Chauhan Subhash C title Tomorrow Never Dies Recent Advances in Diagnosis Treatment and Prevention Modalities against


id: cord-326017-qw4qynqv
type: DISEASE
entity:
  HBV hepatitis C virus HCV herpesvirus influenza virus human cytomegalovirus varicellazoster virus respiratory syncytial virus


id: cord-293082-fw7deem8
type: WORK_OF_ART
entity:
  Tracking Changes in SARS CoV 2 Spike Evidence that D614G Increases Infectivity of the COVID 19 Virus


id: cord-293082-fw7deem8
type: ORG
entity:
  Decade Long Structural Studies of SARS Coronavirus Molecular Mechanism for Antibody Dependent Enhancement of Coronavirus Entry Development


id: cord-336775-d4hi9myk
type: DNA
entity:
  CoV genome translated 8 accessory gene 3a 3b 6 7a 7b 8a 8b and 9b MERS CoV encoded 5 accessory genes 3 4a 4b 5 and 8b


id: cord-336775-d4hi9myk
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome Coronavirus Papain Like Protease Ubiquitin Like Domain and Catalytic Domain


id: cord-336775-d4hi9myk
type: WORK_OF_ART
entity:
  Active Replication of Middle East Respiratory Syndrome Coronavirus and Aberrant Induction of Inflammatory Cytokines and Chemokines in Human Macrophages Implications for Pathogenesis A


id: cord-349417-vn7q8wc4
type: PROTEIN
entity:
  Coronaviridae and Arteriviridae A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Topley and Wilson s Microbiology and Microbial Infections Coronavirus mRNA


id: cord-331022-tek4u751
type: GPE
entity:
  Publicly Reported Confirmed Cases Estimation and Application Presymptomatic Transmission of SARS CoV 2


id: cord-331022-tek4u751
type: ORG
entity:
  the Dynamic Changes of Serum Antibody Responses Against Severe Acute Respiratory Syndrome Coronavirus Lack


id: cord-352379-q5inrxcm
type: DNA
entity:
  human coronavirus 229E HCoV 229E porcine transmissible gastroentefitis virus TGEV porcine respiratory coronavirus PRCV feline infectious peritonitis virus


id: cord-344217-kci4uw7u
type: PROTEIN
entity:
  genera alpha coronavirus beta coronavirus gamma coronavirus and delta coronavirus 1 Beta coronaviruses


id: cord-344217-kci4uw7u
type: PROTEIN
entity:
  SARS coronavirus Human coronavirus NL63employs the severe acute respiratory syndrome coronavirus receptor


id: cord-322908-e3gok0ot
type: ORG
entity:
  the Past Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused


id: cord-322908-e3gok0ot
type: WORK_OF_ART
entity:
  Caution Needed on the Use of Chloroquine and Hydroxychloroquine for Coronavirus Disease Controlled Trial of Ebola Virus Disease Therapeutics Coronavirus Susceptibility to the Antiviral Remdesivir GS 5734


id: cord-322908-e3gok0ot
type: WORK_OF_ART
entity:
  Molecular Modeling Evaluation of the Binding Effect of Ritonavir Lopinavir and Darunavir to Severe Acute


id: cord-343021-gqem6bxj
type: ORG
entity:
  Allam Zaheer title Oil Health Equipment and Trade Revisiting Political Economy and International Relations


id: cord-343021-gqem6bxj
type: ORG
entity:
  Coronavirus Pandemic Energy Consumption Economic Growth and Financial Development Exploring the Empirical Linkages for India Hundreds of Doctors


id: cord-347289-3yi5tz04
type: ORG
entity:
  World Health Organization Novel Coronavirus China Epidemiology Genetic Recombination and Pathogenesis of Coronaviruses A Novel Coronavirus Associated


id: cord-347289-3yi5tz04
type: ORG
entity:
  SARS CoV 1 Report of the WHO China Joint Mission on Coronavirus Disease World Health Organization Coronavirus


id: cord-347289-3yi5tz04
type: WORK_OF_ART
entity:
  A Report of 1014 Cases Imaging the Pregnant Patient for Nonobstetric Conditions Algorithms and Radiation Dose Considerations


id: cord-347289-3yi5tz04
type: ORG
entity:
  Pneumonia An Official Clinical Practice Guideline of the Infectious Diseases Society of America American Thoracic Society Consensus Guidelines on the Management of Community Acquired Pneumonia


id: cord-347289-3yi5tz04
type: ORG
entity:
  China Antibodies in Infants Born to Mothers With COVID 19 Pneumonia Possible Vertical Transmission of SARS


id: cord-347289-3yi5tz04
type: ORG
entity:
  Gynecologists Centers for Disease Control and Prevention Considerations for Inpatient Obstetric Healthcare Settings 2020


id: cord-354536-c9v9kbw8
type: DNA
entity:
  Human coronaviruses HCoV NL63 human coronavirus NL63 HCoV 229E human coronavirus 229E HCoV OC43 human coronavirus OC43 and HCoV HKU1 human coronavirus HKU1


id: cord-354536-c9v9kbw8
type: GGP
entity:
  Human coronaviruses HCoV NL63 human coronavirus NL63 HCoV 229E human coronavirus 229E HCoV OC43 human coronavirus OC43


id: cord-354536-c9v9kbw8
type: LOC
entity:
  Middle East Respiratory Syndrome Coronavirus Infection Assessment of Immunoreactive Synthetic Peptides


id: cord-354536-c9v9kbw8
type: DISEASE
entity:
  coronaviruses HCoV NL63 human coronavirus NL63 HCoV 229E human coronavirus 229E HCoV OC43 human coronavirus OC43 and HCoV HKU1 human coronavirus HKU1


id: cord-349287-mwj2qby4
type: ORG
entity:
  Interim Guidelines for Collecting Handling and Testing Clinical Specimens from Patients Under Investigation


id: cord-349287-mwj2qby4
type: ORG
entity:
  the Epidemiology of MERS CoV Infection and Guidance for the Public Clinicians and Public Health Authorities Followup of Contacts of Middle East Respiratory Syndrome Coronavirus


id: cord-349287-mwj2qby4
type: DISEASE
entity:
  human herpesvirus HHV rhinoviruses HRV enteroviruses EV respiratory syncytial virus RSV parainfluenzavirus types 1 2 and 3 PIVs influenzaviruses IFVs endemic HCoVs adenoviruses AdVs metapneumovirus MPV


id: cord-337825-ujq9mxk7
type: CHEMICAL
entity:
  colistin valrubicin icatibant bepotastine epirubicin epoprostenol vapreotide aprepitant caspofungin perphenazine prulifloxacin bictegravir nelfinavir


id: cord-352781-aqh9zxgh
type: WORK_OF_ART
entity:
  The Lancet Infectious Diseases COVID 19 and Thrombotic or Thromboembolic Disease Implications for Prevention Antithrombotic Therapy


id: cord-355758-tk7eturq
type: PROTEIN
entity:
  coronavirus nonstructural proteins 3 and 4 Virology Mobility 574 and Interactions of Coronavirus Nonstructural Protein 4


id: cord-352230-8mazd3eu
type: DISEASE
entity:
  HIV 1 infection Tripterygium wilfordii 197 Bakuchiol phenolic isoprenoid Psoralea corylifolia L 199 Rupestonic acid sesquiterpene Artemisia rupestris L


id: cord-352230-8mazd3eu
type: CHEMICAL
entity:
  nelfinavir lopinavir kaempferol quercetin luteolin 7glucoside demethoxycurcumin naringenin apigenin 7 glucoside oleuropein curcumin catechin epicatechin gallate zingerol gingerol


id: cord-353484-q7d0ysbo
type: ORG
entity:
  SARS CoV 2 Genetic Recombination and Pathogenesis of Coronaviruses Molecular Evolution of Human Coronavirus Genomes Identification


# url

id: cord-241146-j0qperwz
domain: www.bloomberg.com
url:
  http://www.bloomberg.com/opinion/articles/2020-05-01/coronavirus-trillions-in-aid-draws-scams-anddodgy-deals


id: cord-291916-5yqc3zcx
domain: www.who.int
url:
  http://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance


id: cord-291916-5yqc3zcx
domain: www.acc.org
url:
  http://www.acc.org/latest-in-cardiology/articles/2020/03/27/14/00/ventricular-arrhythmia-riskdue-to-hydroxychloroquine-azithromycin-treatment-for-covid-19


id: cord-291916-5yqc3zcx
domain: investors.modernatx.com
url:
  http://investors.modernatx.com/news-releases/news-release-details/moderna-ships-mrnavaccine-against-novel-coronavirus-mrna-1273


id: cord-326017-qw4qynqv
domain: www.fda.gov
url:
  http://www.fda.gov/news-events/press-announcements/coronavirusupdate-fda-and-ftc-warn-seven-companies-selling-fraudulent-products-claim-treat-or


id: cord-326017-qw4qynqv
domain: www.fda.gov
url:
  http://www.fda.gov/news-events/press-announcements/coronavirus-update-fda-and-ftc-warnseven-companies-selling-fraudulent-products-claim-treat-or


id: cord-326017-qw4qynqv
domain: www.euroweeklynews.com
url:
  http://www.euroweeklynews.com/2020/03/16/false-report-of-900k-dead-in-vatican-city-lastnight-i-nearly-fell-off-my-chair-reading-it/


id: cord-326017-qw4qynqv
domain: www.who.int
url:
  http://www.who.int/publications-detail/water-sanitation-hygiene-and-waste-managementfor-the-covid-19-virus-interim-guidance


id: cord-326017-qw4qynqv
domain: health.economictimes.indiatimes.com
url:
  http://health.economictimes.indiatimes.com/news/industry/whosays-over-22000-healthcare-workers-across-52-countries-infected-by-covid-19/75107238


# bib

id: cord-004992-tvpo1kxb
title: Coronavirus-like particles andCampylobacter in marmosets with diarrhea and colitis
author: Russell, R. G.
date: 1985
txt: ./txt/cord-004992-tvpo1kxb.txt
cache: ./cache/cord-004992-tvpo1kxb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087925/
doi: 10.1007/bf01296981
abstract: nan
summary:
  Coronavirus-like particles were found in 24% and Campylobacter fetus subsp, jejuni in 20% of sampled animals with diarrhea. Immunoblotting studies on serum from a small number of animals having diarrhea suggested the presence in the colony of antibodies to a coronavirus antigenically related to the bovine enteric coronavirus but not the porcine transmissible gastroenteritis virus. In an initial attempt to identify the coronaviruslike agents as coronaviruses, serum from 10 marmosets having diarrhea were reacted against viral proteins of the bovine enteric coronavirus and of the porcine transmissible gastroenteritis coronavirus, representatives of the two antigenic subgroups of the mammalian coronaviruses. We describe coronavirus-like particles and Campylobacter in the feces of marmosets suffering diarrhea and colitis. Further investigation is necessary to establish the role of the coronavirus-like particles in both the diarrhea and the colitis observed in the marmosets.


id: cord-018078-clxzp1ph
title: Coronavirus infections in veterinary medicine
author: Weber, Olaf
date: 2005
txt: ./txt/cord-018078-clxzp1ph.txt
cache: ./cache/cord-018078-clxzp1ph.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122866/
doi: 10.1007/3-7643-7339-3_2
abstract: nan
summary:
  Some important viruses that are discussed below belong to group I and include the canine enteric coronavirus (CECoV), the transmissible gastroenteritis virus (TGEV) of swine, the porcine epidemic diarrhoea virus (PEDV), the porcine respiratory coronavirus (PRCoV) and the feline coronaviruses (FCoVs). The clinical symptoms of endemic/enzootic TGE are usually less severe in the older pigs, making a clinical differentiation between TGE and other infectious enteric diseases, like that caused by rotaviruses and/or clostridia, impossible. Bovine coronavirus (BCoV) is an important cause of neonatal calf diarrhea [33] but may also infect the respiratory tract and has been recognized as the causing agent especially for winter dysentery in adult cattle. As for other coronaviruses, seasonal changes in temperature, environmental factors but also the immune status play an important role in the transmission of the virus and the clinical outcome of the infection. Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism


id: cord-021152-6znmkvy9
title: Reproduction of East-African bats may guide risk mitigation for coronavirus spillover
author: Montecino-Latorre, Diego
date: 2020-02-07
txt: ./txt/cord-021152-6znmkvy9.txt
cache: ./cache/cord-021152-6znmkvy9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149079/
doi: 10.1186/s42522-019-0008-8
summary:
  METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. Assuming that higher spillover risk is a function of higher viral shedding [67] and that all coronaviruses with zoonotic potential behave ecologically similarly to coronaviruses detected in this study, managers could target the prevention of human-bat direct (consumption) or indirect (bat droppings) contact specifically during the high-risk season: around and just after weaning, the timing of observable juveniles or individuals smaller than adults. Our proposed risk-driven strategy i) is evidence-based, as it builds upon coronavirus shedding patterns observed across several chiropteran species present around the world; ii) does not require the advanced laboratory capacity often lacking in resource-restricted settings where intense bat-human interfaces usually occur; iii) is a good alternative to the ideal but expensive and resourceintensive longitudinal surveys; and iv) it may prevent the exposure to viruses belonging to other taxa whose observed bat shedding dynamics resemble our findings for coronaviruses (e.g. paramyxoviruses [97] ),

abstract:
  BACKGROUND: Bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the Coronaviridae family. If bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the Severe Acute Respiratory Syndrome virus, spillover may occur. Therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. Past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. We assessed, via Bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. RESULTS: We found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. CONCLUSIONS: These findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. In these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). Our proposed strategy provides an alternative to culling – an ethically questionable practice that may result in higher pathogen levels – and supports the conservation of bats and the delivery of their key ecosystem services.


id: cord-024942-udhajlx2
title: Severe COVID-19 Pneumonia: Assessing Inflammation Burden with Volume-rendered Chest CT
author: Tang, Lei
date: 2020-03-06
txt: ./txt/cord-024942-udhajlx2.txt
cache: ./cache/cord-024942-udhajlx2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233430/
doi: 10.1148/ryct.2020200044
abstract: nan
summary:
  key: cord-024942-udhajlx2 authors: Tang, Lei; Zhang, Xiaoyong; Wang, Yvquan; Zeng, Xianchun title: Severe COVID-19 Pneumonia: Assessing Inflammation Burden with Volume-rendered Chest CT cord_uid: udhajlx2 technique (PULMO 3D software, VB20; Siemens Healthineers, Forchheim, Germany) highlighted the distribution of pulmonary opacities, which was useful to determine the extension of the disease (Fig 2, Movie [supplement] ). The patient was diagnosed with severe COVID-19 pneumonia. This copy is for personal use only. To order printed copies, contact reprints@rsna.org Severe COVID-19 Pneumonia: Assessing Inflammation Burden with Volume-rendered Chest CT Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia A Novel Coronavirus from Patients with Pneumonia in China CT Imaging of the 2019 Novel Coronavirus (2019-nCoV) Pneumonia Novel Coronavirus (2019-nCoV) situation reports Disclosures of Conflicts of Interest: L.T. disclosed no relevant relationships. X. Zhang disclosed no relevant relationships. Y.W. disclosed no relevant relationships. X. Zeng disclosed no relevant relationships.


id: cord-026937-92836tr1
title: Progressive Politics and Humanistic Psychology in the Trump/Coronavirus Era
author: Benjamin, Elliot
date: 2020-06-15
txt: ./txt/cord-026937-92836tr1.txt
cache: ./cache/cord-026937-92836tr1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298060/
doi: 10.1177/0022167820934226
summary:
  The article concludes with the author suggesting that perhaps it may be worthwhile for politically like-minded others to also consider finding ways of merging their progressive politics with humanistic psychology in order to enhance their self-care through these turbulent times in the Trump/Coronavirus era. In the present article, I want to focus on the merging of progressive politics and humanistic psychology during the tremendously stressful and dangerous times in which we are currently living, which I refer to as the Trump/ Coronavirus era. There have been a number of disturbing reports about the significant detrimental effects on the mental health of a large segment of the U.S. population, directly related to our present political climate under what I have referred to as the "dangerous leadership and rhetoric" of President Donald Trump (Benjamin, 2019) . In this way, the five threads of self-care, humanistic psychology, progressive politics, the Resisting Trump movement, and the coronavirus are all woven together for me, with permeable boundaries that are working well to keep me functioning effectively through these trying times.

abstract:
  In this article, the author discusses the relationship of progressive politics to humanistic psychology in the Trump/Coronavirus era. The harsh realities of personal fears and severe challenges to our mental health evoked by both the United States presidency of Donald Trump and the coronavirus pandemic are described initially. Then, a number of self-care practices that are consistent with the basic values of humanistic psychology and that we can undertake to help us meet these harsh realities are illustrated. Next, the author describes his own personal engagement and self-care in the world of progressive politics and humanistic psychology in the context of the Resisting Trump movement. The article concludes with the author suggesting that perhaps it may be worthwhile for politically like-minded others to also consider finding ways of merging their progressive politics with humanistic psychology in order to enhance their self-care through these turbulent times in the Trump/Coronavirus era.


id: cord-028618-kn87q7nb
title: Democracy and the Politics of Coronavirus: Trust, Blame and Understanding
author: Flinders, Matthew
date: 2020-06-23
txt: ./txt/cord-028618-kn87q7nb.txt
cache: ./cache/cord-028618-kn87q7nb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337828/
doi: 10.1093/pa/gsaa013
summary:
  The first is that the Coronavirus crisis emerged at a time of fundamental concern about the global state of democracy; the second is that the limited data that is currently available suggests the existence of a common crisis-linked ''rallying around the flag'' effect; and (third) that this uplift in public confidence and trust may well prove to be short-lived. It is in the context of this core prediction that this sub-section makes three arguments: (i) the analysis of previous pandemics exposes the existence of a powerful socio-political ''negativity bias''; (ii) politicians will try and manage this situation through a mixture of blame-games and self-preservation strategies; and (iii) it is already possible to identify a dominant strategy in the UK context that for the sake of brevity can be labelled ''hugging the experts''.

abstract:
  This article explores the relationship between crises and democracy through a focus on the unfolding coronavirus pandemic. Its central argument is that to interpret the current pandemic purely in terms of its epidemiology and public health implications risks overlooking its potentially more significant socio-political consequences. This is because the challenges posed by the coronavirus crisis have themselves become overlaid or layered-upon a pre-existing set of concerns regarding the performance, efficiency and capacity of democratic political structures. The aim of this article is to try and understand and warn against what might be termed a rather odd form of cross-contamination whereby the cynicism, negativity and frustration concerning politicians, political processes and political institutions that existed before the coronavirus outbreak is allowed to direct, define and automatically devalue how democratic structures are subsequently judged in terms of how they responded to the challenge. As such, this article focuses on the link between the Coronavirus crisis and the democratic crisis; or, more precisely, the risk that the Coronavirus crisis may mutate into and fuel a broader crisis of democracy.


id: cord-030934-t7akdu6x
title: Genetic and pathogenic characterization of SARS-CoV-2: a review
author: Bahrami, Afsane
date: 2020-08-26
txt: ./txt/cord-030934-t7akdu6x.txt
cache: ./cache/cord-030934-t7akdu6x.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451412/
doi: 10.2217/fvl-2020-0129
summary:
  The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. Bioinformatics analysis of the viral genome from one COVID-19 patient shared 89 and 82% sequence similarity with bat SARS-like-CoVZXC21 and human SARS-CoV, respectively [41] . In a recent report it was shown that SARS-CoV-2''s S-protein entry into 293/human ACE2 receptor cells is primarily mediated via endocytosis, and that PIKfyve, a TPC2 and cathepsin L are crucial for virus entry. Findings of an open-label nonrandomized clinical trial among 22 infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in COVID-19 cases and its effectiveness is promoted by azithromycin [99] . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response

abstract:
  The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. This virus belongs to the beta-coronavirus group that contains a single stranded RNA with a nucleoprotein within a capsid. SARS-CoV-2 shares 80% nucleotide identity to SARS-CoV. The virus is disseminated by its binding to the ACE2 receptors on bronchial epithelial cells. The diagnosis of COVID-19 is based on a laboratory-based reverse transcription polymerase chain reaction (RT-PCR) test together with chest computed tomography imaging. To date, no antiviral therapy has been approved, and many aspects of the COVID-19 are unknown. In this review, we will focus on the recent information on genetics and pathogenesis of COVID-19 as well as its clinical presentation and potential treatments.


id: cord-031113-moekkw2x
title: Policing Social Distancing: Gaining and Maintaining Compliance in the Age of Coronavirus
author: Grace, Sara
date: 2020-07-12
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454934/
doi: 10.1093/police/paaa029
abstract:
  Drawing on motivational posturing theory (MPT) and procedural justice theory (PJT), this article makes recommendations for how best to secure compliance with social distancing regulations. Applying those theories to—mostly observational—data from a study on the use and impact of penalty notices for disorder, the influences on cooperation during police–citizen encounters are explored. Whilst focusing on the English data/regulations, as both MPT and PJT have been tested internationally, the conclusions have relevance beyond these shores. The article proposes a sixth posture—compulsion, a form of resistant compliance—to the five set out by MPT. Focusing attention not just on whether compliance is achieved but how recognizes the risk to future legitimacy posed by only achieving compliance through coercion or the threat thereof. Lessons from the research are applied to policing social distancing, with regards to: securing compliance during interactions, self-regulation and enforcement action, and how to preserve police legitimacy.


id: cord-031840-k9l91unc
title: Forum: COVID-19 Dispatches
author: Lu, Li
date: 2020-09-11
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488168/
doi: 10.1177/1532708620953190
abstract:
  COVID-19 pandemic is the first truly global crisis in the digital age. With death count worldwide reaching 586,000 merely 7 months after its first outbreak in China in late December 2019 and 13.6 million cases reported in 188 countries and territories as of July 2020, this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. In addition to causing social and economic disruptions on a scale unseen before, it has turned the world into a site of biopolitical agon where science and reason are forced to betray their impotence against cultish thinking in the planetary endgame depicted in so many dystopian science fictions. It is in this context that this forum offers a set of modest reflections on the current impacts incurred by the COVID-19 virus. Blending ethnographic observations with theory-driven reflections, the five authors address issues made manifest by the crisis across different regions, while keeping their sight on the sociopolitical problems plaguing our life both individually and collectively. Taken together, they provide a grounded documentary for the archive that the COVID-19 virus is making us to construct.


id: cord-034351-5br4faov
author: Xu, Shuang-Fei
date: 2020-10-02
txt: ./txt/cord-034351-5br4faov.txt
cache: ./cache/cord-034351-5br4faov.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7579139/
doi: 10.3390/ijerph17197223
summary:
  (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. Since the first known case of pneumonia infected with the novel coronavirus was reported in the city of Wuhan in late December of 2019, Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and announced by the World Health Organization on 11 February 2020, unexpectedly and quickly spread in China and many other countries with rapid geographical expansion and a sudden increase in the number of cases [1, 2] .

title:
  Cross-Sectional Seroepidemiologic Study of Coronavirus Disease 2019 (COVID-19) among Close Contacts, Children, and Migrant Workers in Shanghai

abstract:
  (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. (2) Method: This is a cross-sectional seroepidemiologic study. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. A multi-stage sampling method will be employed to acquire an adequate sample size. Assessments that include questionnaires and blood, nasopharyngeal specimens, and feces collection will be performed via home-visit survey. (3) Ethics and Dissemination: The study was approved by the Institute Review Board of School of Public Health, Fudan University (IRB#2020-04-0818). Before data collection, written informed consent will be obtained from all participants. The manuscripts from this work will be submitted for publication in quality peer-reviewed journals and presented at national or international conferences.


id: cord-104420-b67xpq12
title: Frequency of diarrhea in novel coronavirus 2019 infection
author: Mungmunpuntipantip, Rujittika
date: 2020
txt: ./txt/cord-104420-b67xpq12.txt
cache: ./cache/cord-104420-b67xpq12.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149807/
doi: nan
abstract: nan
summary:
  title: Frequency of diarrhea in novel coronavirus 2019 infection In additional to respiratory manifestation, atypical clinical presentation of the new disease is possible. Here, the authors performed a summative analysis on available data on 314 cases of novel coronavirus 2019 infections (2 -4) to calculate for frequency of diarrhea. Based on this observation, it can show that diarrhea is a possible atypical clinical presentation of novel coronavirus 2019 infection. in fact, diarrhea is usually a possible but forgotten clinical presentation in new emerging disease such as swine flu (5) . Practitioner should recognize the possibility that diarrhea might be the first clinical presentation of the patient with novel coronavirus 2019 infection. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical features of patients infected with 2019 novel coronavirus in Wuhan Analysis of clinical features of 29 patients with 2019 novel coronavirus pneumonia


id: cord-104500-m0kfom0x
title: The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review
author: Kyriakopoulos, Anthony M.
date: 2020-09-21
txt: ./txt/cord-104500-m0kfom0x.txt
cache: ./cache/cord-104500-m0kfom0x.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587986/
doi: nan
summary:
  A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20(th) of August 2020. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. Following this initial selection stage, further screening was performed by all reviewers, using the previously described search items to identify parameters determining the global impact of COVID-19 due to SSEs. Identified parameters included the global impact of immunity and vaccination, the holy cup and religion transmission, and the austerity caused by COVID-19 and other coronavirus epidemics due to restrictions applied.

abstract:
  Coronaviruses, members of Coronaviridae family, cause extensive epidemics of vast diseases like severe acute respiratory syndrome (SARS) and Coronavirus Disease-19 (COVID-19) in animals and humans. Super spread events (SSEs) potentiate early outbreak of the disease and its constant spread in later stages. Viral recombination events within species and across hosts lead to natural selection based on advanced infectivity and resistance. In this review, the importance of containment of SSEs was investigated with emphasis on stopping COVID-19 spread and its socio-economic consequences. A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the “potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic” and were published before 20(th) of August 2020. Overall, ninety-eight articles were found eligible and reviewed. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. The effect of SSEs on previous SARS epidemics has been documented in detail. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. This is crucial for SARS-COV-2 pandemic containment as the vaccine(s) development process will take considerable time to safely establish its potential usefulness for future clinical usage.


id: cord-139097-deuvq0wf
title: Network structure of COVID-19 spread and the lacuna in India''s testing strategy
author: Sahasranaman, Anand
date: 2020-03-21
txt: ./txt/cord-139097-deuvq0wf.txt
cache: ./cache/cord-139097-deuvq0wf.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2003.09715v1.pdf
doi: nan
summary:
  We characterize the network of COVID-19 spread in India and find that the transmission rate is 0.43, with daily case growth driven by individuals who contracted the virus abroad. Given this bias in testing, it should be no surprise that among the observed cases of COVID-19 in the country, a majority are travellers from high-risk countries and their immediate contacts with local transmission (as reflected in the networks structure of infections, Fig. 2b ). Consolidated data from ICMR tells us that India has so far tested a total of 13,486 samples [35] , or 10 tests people per million population, which is very low compared to other countries that have been testing for community spread [36] , and creates the risk of missing such transmission in case it is already underway in the country. Coronavirus update: 3 more test positive for COVID-19 in Maharashtra, number rises to 5

abstract:
  We characterize the network of COVID-19 spread in India and find that the transmission rate is 0.43, with daily case growth driven by individuals who contracted the virus abroad. We explore the question of whether this represents exponentially decaying dynamics or is simply an artefact of India's testing strategy. Testing has largely been limited to individuals travelling from high-risk countries and their immediate contacts, meaning that the network reflects positive identifications from a biased testing sample. Given generally low levels of testing and an almost complete absence of testing for community spread, there is significant risk that we may be missing out on the actual nature of outbreak. India still has an apparently low current caseload, with possibly a small window of time to act, and should therefore aggressively and systematically expand random testing for community spread, including for asymptomatic cases. This will help understand true transmission characteristics and plan appropriately for the immediate future.


id: cord-241146-j0qperwz
author: Lallie, Harjinder Singh
date: 2020-06-21
url: https://arxiv.org/pdf/2006.11929v1.pdf
doi: nan
title:
  Cyber Security in the Age of COVID-19: A Timeline and Analysis of Cyber-Crime and Cyber-Attacks during the Pandemic

abstract:
  The COVID-19 pandemic was a remarkable unprecedented event which altered the lives of billions of citizens globally resulting in what became commonly referred to as the new-normal in terms of societal norms and the way we live and work. Aside from the extraordinary impact on society and business as a whole, the pandemic generated a set of unique cyber-crime related circumstances which also affected society and business. The increased anxiety caused by the pandemic heightened the likelihood of cyber-attacks succeeding corresponding with an increase in the number and range of cyber-attacks. This paper analyses the COVID-19 pandemic from a cyber-crime perspective and highlights the range of cyber-attacks experienced globally during the pandemic. Cyber-attacks are analysed and considered within the context of key global events to reveal the modus-operandi of cyber-attack campaigns. The analysis shows how following what appeared to be large gaps between the initial outbreak of the pandemic in China and the first COVID-19 related cyber-attack, attacks steadily became much more prevalent to the point that on some days, 3 or 4 unique cyber-attacks were being reported. The analysis proceeds to utilise the UK as a case study to demonstrate how cyber-criminals leveraged key events and governmental announcements to carefully craft and design cyber-crime campaigns.


id: cord-253077-61fmul8c
title: Immunology of COVID-19: current state of the science
author: Vabret, Nicolas
date: 2020-05-06
txt: ./txt/cord-253077-61fmul8c.txt
cache: ./cache/cord-253077-61fmul8c.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32505227/
doi: 10.1016/j.immuni.2020.05.002
summary:
  Lastly, Nonhuman primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific IgG responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into pro-inflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012; Liu et al., 2019) . Collectively, these data suggest that cross-talk with monocytes might impair NK cell recognition and killing of SARS-CoV-2infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients ( Figure 2 ). However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human coronaviruses, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020) .

abstract:
  Abstract The coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of COVID19 pathophysiology. In this review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS-CoV-2 infection.


id: cord-254446-yxqbe1dj
title: A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19
author: Ren, Yunzhao R.
date: 2020-05-29
url: https://www.ncbi.nlm.nih.gov/pubmed/32469437/
doi: 10.1002/jcph.1673
abstract:
  This literature review aims to provide a comprehensive current summary of the pathogenesis, clinical features, disease course, host immune responses, and current investigational antiviral and immunomodulatory pharmacotherapies, in order to facilitate the development of future therapies and measures for prevention and control. This article is protected by copyright. All rights reserved


id: cord-255284-ffh1jl40
title: Syndrome respiratoire aigu sévère
author: Guery, B
date: 2003-06-30
txt: ./txt/cord-255284-ffh1jl40.txt
cache: ./cache/cord-255284-ffh1jl40.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0399077X03002002
doi: 10.1016/s0399-077x(03)00200-2
summary:
  Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d''isoler l''agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l''épidémie. Deux éléments notables sont évoqués dans cette publication, tout d''abord le fait que seuls les patients atteints de SARS ont des anticorps témoignant du fait que ce virus circule pour la première fois. À noter que cette faculté existe chez un Coronavirus porcin entraînant des pathologies respiratoires mais, aucun lien de parenté entre ces deux virus n''a été mis en évidence. Dans le cas du SARS, les premières analyses montrent que la contamination nécessite un contact prolongé et répété avec un malade présentant une symptomatologie pulmonaire. ont montré la présente d''ARN du Coronavirus responsable du SARS dans les selles des patients [4] .

abstract:
  Résumé Le syndrome respiratoire aigu sévère (severe acute respiratory syndrome, SARS) est apparu à l’automne 2002 dans la province de Guangdong en Chine. L’épidémie s’est rapidement propagée à travers le monde pour toucher, courant avril, plus de 26 pays avec un total de cas à cette même date proche de 3500 cas. La symptomatologie associe des formes modérées se manifestant par une fièvre, une hypoxie, avec des formes de gravité majeure responsables de syndrome de détresse aigue nécessitant l’hospitalisation en unité de réanimation. Des formes digestives ont aussi récemment été décrites. Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d’isoler l’agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l’épidémie. Cette revue rassemble l’ensemble des données actuellement disponibles sur le SARS, de l’histoire de l’épidémie aux propositions thérapeutiques disponibles en date d’avril 2003. Abstract In the Fall of 2002 a report from Guangdong Province in China showed the occurrence of an outbreak of atypical pneumonia. This outbreak rapidly progressed from China to Hong Kong, Singapore, Toronto, and the USA, to more than 25 countries worldwide and almost 3500 cases to date in april 2003. The clinical features associate a fever with mild respiratory symptoms which can progress to a typical acute respiratory distress syndrome requiring intensive care unit admission. Enteric forms with diarrhea were recently described in Hong Kong. The medical community responded very rapidly and united in front of this major health crisis. In a couple weeks, the agent, a new Coronavirus was isolated, therapeutic guidelines were proposed and measures to limit the outbreak diffusion were started worldwide. We summarize here the history of the outbreak, the clinical, laboratory and radiological features of SARS. April 2003 therapeutic guidelines are also reported.


id: cord-255603-quuju9h4
title: A review of modern technologies for tackling COVID-19 pandemic
author: Kumar, Aishwarya
date: 2020-05-07
txt: ./txt/cord-255603-quuju9h4.txt
cache: ./cache/cord-255603-quuju9h4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.dsx.2020.05.008
doi: 10.1016/j.dsx.2020.05.008
summary:
  The aim of the present study is to discuss the various aspects of modern technology used to fight against COVID-19 crisis at different scales, including medical image processing, disease tracking, prediction outcomes, computational biology and medicines. For example, early in the outbreak when China initiated its response to virus it focused on artificial intelligence (AI) by relying on like facial recognition cameras to track the infected patients with travel history, robots to deliver food and medicines, drones to disinfect public places, to patrol and broadcast audio messages to public encouraging them to stay at home [1] . In recent writings, it has been discovered that a few research works use artificial intelligence to help analyze computational tomography (CT) scans, while other research works use patient''s clinical information to predict the advancement of the infection [7, 8] .

abstract:
  OBJECTIVE: Science and technology sector constituting of data science, machine learning and artificial intelligence are contributing towards COVID-19. The aim of the present study is to discuss the various aspects of modern technology used to fight against COVID-19 crisis at different scales, including medical image processing, disease tracking, prediction outcomes, computational biology and medicines. METHODS: A progressive search of the database related to modern technology towards COVID-19 is made. Further, a brief review is done on the extracted information by assessing the various aspects of modern technologies for tackling COVID-19 pandemic. RESULTS: We provide a window of thoughts on review of the technology advances used to decrease and smother the substantial impact of the outburst. Though different studies relating to modern technology towards COVID-19 have come up, yet there are still constrained applications and contributions of technology in this fight. CONCLUSIONS: On-going progress in the modern technology has contributed in improving people's lives and hence there is a solid conviction that validated research plans including artificial intelligence will be of significant advantage in helping people to fight this infection.


id: cord-256051-87alqfkd
author: Revzin, Margarita V.
date: 2020-10-01
url: https://www.ncbi.nlm.nih.gov/pubmed/33001783/
doi: 10.1148/rg.2020200149
title:
  Multisystem Imaging Manifestations of COVID-19, Part 1: Viral Pathogenesis and Pulmonary and Vascular System Complications

abstract:
  Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in coronavirus disease 2019 (COVID-19), which was declared an official pandemic by the World Health Organization on March 11, 2020. The infection has been reported in most countries around the world. As of August 2020, there have been over 21 million cases of COVID-19 reported worldwide, with over 800 000 COVID-19–associated deaths. It has become apparent that although COVID-19 predominantly affects the respiratory system, many other organ systems can also be involved. Imaging plays an essential role in the diagnosis of all manifestations of the disease, as well as its related complications, and proper utilization and interpretation of imaging examinations is crucial. With the growing global COVID-19 outbreak, a comprehensive understanding of the diagnostic imaging hallmarks, imaging features, multisystemic involvement, and evolution of imaging findings is essential for effective patient management and treatment. To date, only a few articles have been published that comprehensively describe the multisystemic imaging manifestations of COVID-19. The authors provide an inclusive system-by-system image-based review of this life-threatening and rapidly spreading infection. In part 1 of this article, the authors discuss general aspects of the disease, with an emphasis on virology, the pathophysiology of the virus, and clinical presentation of the disease. The key imaging features of the varied pathologic manifestations of this infection that involve the pulmonary and peripheral and central vascular systems are also described. Part 2 will focus on key imaging features of COVID-19 that involve the cardiac, neurologic, abdominal, dermatologic and ocular, and musculoskeletal systems, as well as pediatric and pregnancy-related manifestations of the virus. Vascular complications pertinent to each system will be also be discussed in part 2. Online supplemental material is available for this article. (©)RSNA, 2020


id: cord-256688-yy7abob9
title: Coronavirus Disease (COVID-19): A primer for emergency physicians
author: Chavez, Summer
date: 2020-03-24
url: https://www.ncbi.nlm.nih.gov/pubmed/32265065/
doi: 10.1016/j.ajem.2020.03.036
abstract:
  INTRODUCTION: Rapid worldwide spread of Coronavirus Disease 2019 (COVID-19) has resulted in a global pandemic. OBJECTIVE: This review article provides emergency physicians with an overview of the most current understanding of COVID-19 and recommendations on the evaluation and management of patients with suspected COVID-19. DISCUSSION: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing COVID-19, is primarily transmitted from person-to-person through close contact (approximately 6 ft) by respiratory droplets. Symptoms of COVID-19 are similar to other viral upper respiratory illnesses. Three major trajectories include mild disease with upper respiratory symptoms, non-severe pneumonia, and severe pneumonia complicated by acute respiratory distress syndrome (ARDS). Emergency physicians should focus on identifying patients at risk, isolating suspected patients, and informing hospital infection prevention and public health authorities. Patients with suspected COVID-19 should be asked to wear a facemask. Respiratory etiquette, hand washing, and personal protective equipment are recommended for all healthcare personnel caring for suspected cases. Disposition depends on patient symptoms, hemodynamic status, and patient ability to self-quarantine. CONCLUSION: This narrative review provides clinicians with an updated approach to the evaluation and management of patients presenting to the emergency department with suspected COVID-19.


id: cord-257824-qz6yxuph
title: Current impact of Covid-19 pandemic on Spanish plastic surgery departments: a multi-center report
author: Fuertes, Víctor
date: 2020-05-19
txt: ./txt/cord-257824-qz6yxuph.txt
cache: ./cache/cord-257824-qz6yxuph.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32836886/
doi: 10.1007/s00238-020-01686-0
summary:
  title: Current impact of Covid-19 pandemic on Spanish plastic surgery departments: a multi-center report The total amount of procedures currently being performed ranged from 0 to 44% of the figures before the coronavirus outbreak, except for one department, with elective surgery mainly affected. The total amount of procedures currently being performed ranged from 0 to 44% of the figures before the coronavirus outbreak (Fig. 1a, b) ; except for one hospital, that was declared to maintain the same surgical activity (100%). Some of the more prevalent measures include screening protocols for Coronavirus among patients and workers, increasing hygiene measures, reducing the number of visitors per patient, directing burn patients who tested positive to other units and trying to apply day-care/ delay surgeries whenever this is possible. This might pose a challenge against the delivery of emergency surgeries and cancer care to our community if this pandemic lasts for a prolonged period long time According to our analysis, reductions of about 20-50% in the total number of consultants per team may lead to this situation.

abstract:
  BACKGROUND: After its initial description in China, Covid-19 is hitting nations across the world, with Spain as the third country in number of deaths, after the USA and Italy. Similarly to what is happening in other countries, an important reduction in available operating rooms is affecting our departments. In this study, we aim to know how Covid-19 pandemic is affecting the delivery of plastic surgery services in Spain. METHODS: A questionnaire addressing some of our concerns about how the Coronavirus crisis might severelyimpact our specialty has been sent to the heads of the divisions of plastic surgery of several hospitals across Spain. RESULTS: A total of 12 plastic surgery departments from different hospitals across the country agreed to participate in the survey. Most plastic surgery teams will need to maintain 50–80% of their staff in order to be able to offer emergency and undelayable oncological procedures. The total amount of procedures currently being performed ranged from 0 to 44% of the figures before the coronavirus outbreak, except for one department, with elective surgery mainly affected. Microsurgical cases have been massively discontinued during this crisis. CONCLUSIONS: Plastic surgery delivery in the Spanish Health System is being severely impacted as a collateral damage from this pandemic. Most of the elective surgery is currently stopped. Our departments seem to be vulnerable regarding their capacity to keep offering emergency care. Level of evidence: not ratable (multi-center survey)


id: cord-258679-rlfsqgm7
title: Update: Severe Respiratory Illness Associated with a Novel Coronavirus — Worldwide, 2012–2013
author: Rha, Brian
date: 2013-03-15
url: https://www.ncbi.nlm.nih.gov/pubmed/23486385/
doi: nan
abstract:
  CDC continues to work closely with the World Health Organization (WHO) and other partners to better understand the public health risk posed by a novel coronavirus that was first reported to cause human infection in September 2012. Genetic sequence analyses have shown that this new virus is different from any other known human coronaviruses, including the one that caused severe acute respiratory syndrome (SARS). As of March 7, 2013, a total of 14 confirmed cases of novel coronavirus infection have been reported to WHO, with eight deaths. Illness onsets have occurred from April 2012 through February 2013. To date, no cases have been reported in the United States.


id: cord-259229-e8m8m4ut
title: Cardiovascular Complications Associated with COVID-19 and Potential Therapeutic Strategies
author: Samidurai, Arun
date: 2020-09-16
url: https://doi.org/10.3390/ijms21186790
doi: 10.3390/ijms21186790
abstract:
  The outbreak of coronavirus disease 2019 (COVID-19), an infectious disease with severe acute respiratory syndrome, has now become a worldwide pandemic. Despite the respiratory complication, COVID-19 is also associated with significant multiple organ dysfunction, including severe cardiac impairment. Emerging evidence reveals a direct interplay between COVID-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. The proposed pathophysiological mechanisms of myocardial impairment include invasion of SARS-CoV-2 virus via angiotensin-converting enzyme 2 to cardiovascular cells/tissue, which leads to endothelial inflammation and dysfunction, de-stabilization of vulnerable atherosclerotic plaques, stent thrombosis, cardiac stress due to diminish oxygen supply and cardiac muscle damage, and myocardial infarction. Several promising therapeutics are under investigation to the overall prognosis of COVID-19 patients with high risk of cardiovascular impairment, nevertheless to date, none have shown proven clinical efficacy. In this comprehensive review, we aimed to highlight the current integrated therapeutic approaches for COVID-19 and we summarized the potential therapeutic options, currently under clinical trials, with their mechanisms of action and associated adverse cardiac events in highly infectious COVID-19 patients.


id: cord-259949-ewcv8m06
author: Xiao, Shu‐Yuan
date: 2020-02-17
url: https://doi.org/10.1002/jmv.25702
doi: 10.1002/jmv.25702
title:
  Evolving status of the 2019 novel coronavirus infection: Proposal of conventional serologic assays for disease diagnosis and infection monitoring

abstract:
  The novel coronavirus (nCoV-2019) outbreak in Wuhan, China has spread rapidly nationwide, with some cases occurring in other parts of the world. Although most patients present with mild febrile illness with patchy pulmonary inflammation, a significant portion develop severe acute respiratory distress syndrome (ARDS), with a current case fatality of 2.3-3%. Diagnosis is based on clinical history and laboratory and chest radiographic findings, but confirmation currently relies on nucleic acid-based assays. The latter are playing an important role in facilitating patient isolation, treatment and assessment of infectious activities. However, due to their limited capacity to handle an epidemic of the current scale and insufficient supply of assay kits, only a portion of suspected cases can be tested, leading to incompleteness and inaccuracy in updating new cases, as well as delayed diagnosis. Furthermore, there has not been enough time to assess specificity and sensitivity. Conventional serological assays, such as enzyme-linked immunoassay (ELISA) for specific IgM and IgG antibodies, should offer a high-throughput alternative, which allows for uniform tests for all suspected patients, and can facilitate more complete identification of infected cases and avoidance of unnecessary cross infection among unselected patients. This article is protected by copyright. All rights reserved.


id: cord-260225-bc1hr0fr
author: Sirpilla, Olivia
date: 2020-07-20
url: https://doi.org/10.1021/acs.jproteome.0c00421
doi: 10.1021/acs.jproteome.0c00421
title:
  SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes

abstract:
  [Image: see text] SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.


id: cord-262119-s6hc7fxs
author: Ostaszewski, Marek
date: 2020-10-27
txt: ./txt/cord-262119-s6hc7fxs.txt
cache: ./cache/cord-262119-s6hc7fxs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.10.26.356014
doi: 10.1101/2020.10.26.356014
summary:
  title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

title:
  COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

abstract:
  We hereby describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied to the contents of the COVID-19 Disease Map for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases.


id: cord-262735-xj9md751
author: Li, Lian Yong
date: 2020-05-12
txt: ./txt/cord-262735-xj9md751.txt
cache: ./cache/cord-262735-xj9md751.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/1751-2980.12862
doi: 10.1111/1751-2980.12862
summary:
  In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. Gastrointestinal manifestation in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection above, by adopting single-cell RNA-sequencing technology from two cohort samples, a recent study has shown that ACE2 is highly expressed in cholangiocytes rather than the hepatocytes or other interstitial cells. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China

title:
  Digestive system involvement of novel coronavirus infection: Prevention and control infection from a gastroenterology perspective

abstract:
  An epidemic of an acute respiratory syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in Wuhan, China, now known as coronavirus disease 2019 (COVID‐19), beginning in December 2019, has attracted an intense amount of attention worldwide. As the natural history and variety of clinical presentations of this disease unfolds, extrapulmonary symptoms of COVID‐19 have emerged, especially in the digestive system. While the respiratory mode of transmission is well known and is probably the principal mode of transmission of this disease, a possibility of the fecal‐oral route of transmission has also emerged in various case series and clinical scenarios. In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. A timely understanding of the relationship between the disease and the digestive system and implementing effective preventive measures are of great importance for a favorable outcome of the disease and can help climnicians to mitigate further transmission by taking appropriate measures.


id: cord-263672-iuo7ukaz
title: What Policies Address Both the Coronavirus Crisis and the Climate Crisis?
author: Engström, Gustav
date: 2020-07-31
url: https://www.ncbi.nlm.nih.gov/pubmed/32836841/
doi: 10.1007/s10640-020-00451-y
abstract:
  The coronavirus pandemic has led many countries to initiate unprecedented economic recovery packages. Policymakers tackling the coronavirus crisis have also been encouraged to prioritize policies which help mitigate a second, looming crisis: climate change. We identify and analyze policies that combat both the coronavirus crisis and the climate crisis. We analyze both the long-run climate impacts from coronavirus-related economic recovery policies, and the impacts of long-run climate policies on economic recovery and public health post-recession. We base our analysis on data on emissions, employment and corona-related layoffs across sectors, and on previous research. We show that, among climate policies, labor-intensive green infrastructure projects, planting trees, and in particular pricing carbon coupled with reduced labor taxation boost economic recovery. Among coronavirus policies, aiding services sectors (leisure services such as restaurants and culture, or professional services such as technology), education and the healthcare sector appear most promising, being labor intensive yet low-emission—if such sectoral aid is conditioned on being directed towards employment and on low-carbon supply chains. Large-scale green infrastructure projects and green R&D investment, while good for the climate, are unlikely to generate enough employment to effectively alleviate the coronavirus crisis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10640-020-00451-y) contains supplementary material, which is available to authorized users.


id: cord-264296-0x90yubt
title: Analyzing hCov genome sequences: Applying Machine Intelligence and beyond
author: Sawmya, Shashata
date: 2020-06-03
txt: ./txt/cord-264296-0x90yubt.txt
cache: ./cache/cord-264296-0x90yubt.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.06.03.131987
doi: 10.1101/2020.06.03.131987
summary:
  We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. C. Several CNN-RNN based models are used to predict mutations at specific Sites of Interest (SoIs) of the sars-cov-2 genome sequence followed by further analyses of the same on several South-Asian countries. D. Overall, we present an analysis pipeline that can be further utilized as well as extended and revised (a) to study where a newly discovered genome sequence lies in relation to its predecessors in different regions of the world; (b) to analyse its virulence with respect to the number of deaths its predecessors have caused in their respective countries and (c) to analyse the mutation at specific important sites of the viral genome.

abstract:
  Covid-19 pandemic, caused by the sars-cov-2 strain of coronavirus, has affected millions of people all over the world and taken thousands of lives. It is of utmost importance that the character of this deadly virus be studied and its nature be analysed. We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. In a nutshell, we have prepared an analysis pipeline for hCov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data.


id: cord-266260-t02jngq0
title: A database of geopositioned Middle East Respiratory Syndrome Coronavirus occurrences
author: Ramshaw, Rebecca E.
date: 2019-12-13
txt: ./txt/cord-266260-t02jngq0.txt
cache: ./cache/cord-266260-t02jngq0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41597-019-0330-0
doi: 10.1038/s41597-019-0330-0
summary:
  As a World Health Organization Research and Development Blueprint priority pathogen, there is a need to better understand the geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and its potential to infect mammals and humans. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) emerged as a global health concern in 2012 when the first human case was documented in Saudi Arabia 1 . Previous literature reviews have looked at healthcare-associated outbreaks 9 , importation events resulting in secondary cases 10, 11 , occurrences among dromedary camels 12, 13 , or to summarize current knowledge and knowledge gaps of MERS-CoV 14, 15 . This database seeks fill gaps in literature and build upon existing notification data by enhancing the geographic resolution of MERS-CoV data and providing occurrences of both mammal and environmental detections in addition to human cases. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission

abstract:
  As a World Health Organization Research and Development Blueprint priority pathogen, there is a need to better understand the geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and its potential to infect mammals and humans. This database documents cases of MERS-CoV globally, with specific attention paid to zoonotic transmission. An initial literature search was conducted in PubMed, Web of Science, and Scopus; after screening articles according to the inclusion/exclusion criteria, a total of 208 sources were selected for extraction and geo-positioning. Each MERS-CoV occurrence was assigned one of the following classifications based upon published contextual information: index, unspecified, secondary, mammal, environmental, or imported. In total, this database is comprised of 861 unique geo-positioned MERS-CoV occurrences. The purpose of this article is to share a collated MERS-CoV database and extraction protocol that can be utilized in future mapping efforts for both MERS-CoV and other infectious diseases. More broadly, it may also provide useful data for the development of targeted MERS-CoV surveillance, which would prove invaluable in preventing future zoonotic spillover.


id: cord-266989-n040i865
title: Coronavirus disease 2019: The harms of exaggerated information and non‐evidence‐based measures
author: Ioannidis, John P. A.
date: 2020-04-09
txt: ./txt/cord-266989-n040i865.txt
cache: ./cache/cord-266989-n040i865.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32191341/
doi: 10.1111/eci.13222
summary:
  • A highly flawed nonpeer-reviewed preprint claiming similarity with HIV-1 drew tremendous attention, and it was withdrawn, but conspiracy theories about the new virus became entrenched • Even major peer-reviewed journals have already published wrong, sensationalist items • Early estimates of the projected proportion of global population that will be infected seem markedly exaggerated • Early estimates of case (infection) fatality rate may be markedly exaggerated • The proportion of undetected infections is unknown but probably varies across countries and may be very large overall • Reported epidemic curves are largely affected by the change in availability of test kits and the willingness to test for the virus over time • Of the multiple measures adopted, a few have strong evidence, and many may have obvious harms • Panic shopping of masks and protective gear and excess hospital admissions may be highly detrimental to health systems without offering any concomitant benefit • Extreme measures such as lockdowns may have major impact on social life and the economy (and those also lives lost), and estimates of this impact are entirely speculative • Comparisons with and extrapolations from the 1918 influenza pandemic are precarious, if not outright misleading and harmful pandemic suggest that early adoption of social distancing measures was associated with lower peak death rates.

abstract:
  The evolving coronavirus disease 2019 (COVID-19) epidemic1 is certainly cause for concern. Proper communication and optimal decision-making is an ongoing challenge, as data evolve. The challenge is compounded, however, by exaggerated information. This can lead to inappropriate actions. It is important to differentiate promptly the true epidemic from an epidemic of false claims and potentially harmful actions.


id: cord-267436-mivxm8oh
title: Treatment and vaccines for severe acute respiratory syndrome
author: Groneberg, David A
date: 2005-03-10
txt: ./txt/cord-267436-mivxm8oh.txt
cache: ./cache/cord-267436-mivxm8oh.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1473309905013071
doi: 10.1016/s1473-3099(05)01307-1
summary:
  The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. 31 The results of a randomised clinical study in Guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose (400-600 mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. Search terms were "severe acute respiratory syndrome", "SARS", "treatment", "coronavirus", "infection", "SARS coronavirus", "vaccination", and "antiviral". Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus

abstract:
  The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002–2003 outbreak, is a coronavirus that was unknown before the outbreak. Although many different treatments were used during the outbreak, none were implemented in a controlled fashion. Thus, the optimal treatment for SARS is unknown. Since the outbreak, much work has been done testing new agents against SARS using in-vitro methods and animal models. In addition, global research efforts have focused on the development of vaccines against SARS. Efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another SARS outbreak occur.


id: cord-268483-joiajgs4
title: Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past
author: Shah, Vibhuti Kumar
date: 2020-08-07
url: https://doi.org/10.3389/fimmu.2020.01949
doi: 10.3389/fimmu.2020.01949
abstract:
  After the 1918 flu pandemic, the world is again facing a similar situation. However, the advancement in medical science has made it possible to identify that the novel infectious agent is from the coronavirus family. Rapid genome sequencing by various groups helped in identifying the structure and function of the virus, its immunogenicity in diverse populations, and potential preventive measures. Coronavirus attacks the respiratory system, causing pneumonia and lymphopenia in infected individuals. Viral components like spike and nucleocapsid proteins trigger an immune response in the host to eliminate the virus. These viral antigens can be either recognized by the B cells or presented by MHC complexes to the T cells, resulting in antibody production, increased cytokine secretion, and cytolytic activity in the acute phase of infection. Genetic polymorphism in MHC enables it to present some of the T cell epitopes very well over the other MHC alleles. The association of MHC alleles and its downregulated expression has been correlated with disease severity against influenza and coronaviruses. Studies have reported that infected individuals can, after recovery, induce strong protective responses by generating a memory T-cell pool against SARS-CoV and MERS-CoV. These memory T cells were not persistent in the long term and, upon reactivation, caused local damage due to cross-reactivity. So far, the reports suggest that SARS-CoV-2, which is highly contagious, shows related symptoms in three different stages and develops an exhaustive T-cell pool at higher loads of viral infection. As there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like SARS, MERS, HIV, ebola, malaria, and tuberculosis are being given to COVID-19 patients, and clinical trials for many such drugs have already begun. A classical immunotherapy of convalescent plasma transfusion from recovered patients has also been initiated for the neutralization of viremia in terminally ill COVID-19 patients. Due to the limitations of plasma transfusion, researchers are now focusing on developing neutralizing antibodies against virus particles along with immuno-modulation of cytokines like IL-6, Type I interferons (IFNs), and TNF-α that could help in combating the infection. This review highlights the similarities of the coronaviruses that caused SARS and MERS to the novel SARS-CoV-2 in relation to their pathogenicity and immunogenicity and also focuses on various treatment strategies that could be employed for curing COVID-19.


id: cord-268561-vq1uhj5i
title: Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19
author: da Silva, Severino Jefferson Ribeiro
date: 2020-08-04
url: https://doi.org/10.1021/acsinfecdis.0c00274
doi: 10.1021/acsinfecdis.0c00274
abstract:
  [Image: see text] In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.


id: cord-268822-o86zpu92
author: Anser, Muhammad Khalid
date: 2020-08-18
txt: ./txt/cord-268822-o86zpu92.txt
cache: ./cache/cord-268822-o86zpu92.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33014954/
doi: 10.3389/fpubh.2020.00398
summary:
  In a given scenario, the study focused on the following key variables: communicable diseases, healthcare expenditures, population density, poverty, economic growth, and COVID-19 dummy variable in a panel of 76 selected countries from 2010 through 2019. In a given scenario, the study focused on the following key variables: communicable diseases, healthcare expenditures, population density, poverty, economic growth, and COVID-19 dummy variable in a panel of 76 selected countries from 2010 through 2019. This study intended to explore the answers to the following critical questions: do communicable diseases, including COVID-19, exert a greater magnitude of stress in terms of negatively affecting countries economic growth which then converts into global depression? In a given context, the study prepared a set of research objectives to analyze global depression through some policy instruments, including healthcare expenditures, population density, and poverty incidence in a panel of 76 countries.

title:
  Communicable Diseases (Including COVID-19)—Induced Global Depression: Caused by Inadequate Healthcare Expenditures, Population Density, and Mass Panic

abstract:
  Coronavirus (COVID-19) is spreading at an enormous rate and has caused deaths beyond expectations due to a variety of reasons. These include: (i) inadequate healthcare spending causing, for instance, a shortage of protective equipment, testing swabs, masks, surgical gloves, gowns, etc.; (ii) a high population density that causes close physical contact among community members who reside in compact places, hence they are more likely to be exposed to communicable diseases, including coronavirus; and (iii) mass panic due to the fear of experiencing the loss of loved ones, lockdown, and shortage of food. In a given scenario, the study focused on the following key variables: communicable diseases, healthcare expenditures, population density, poverty, economic growth, and COVID-19 dummy variable in a panel of 76 selected countries from 2010 through 2019. The results show that the impact of communicable diseases on economic growth is positive because the infected countries get a reap of economic benefits from other countries in the form of healthcare technologies, knowledge transfers, cash transfers, international loans, aid, etc., to get rid of the diseases. However, the case is different with COVID-19 as it has seized the whole world together in a much shorter period of time and no other countries are able to help others in terms of funding loans, healthcare facilities, or technology transfers. Thus, the impact of COVID-19 in the given study is negatively impacting countries' economic growth that converts into a global depression. The high incidence of poverty and social closeness increases more vulnerable conditions that spread coronavirus across countries. The momentous increase in healthcare expenditures put a burden on countries' national healthcare bills that stretch the depression phase-out of the boundary. The forecasting relationship suggested the negative impact of the coronavirus pandemic on the global economy would last the next 10 years. Unified global healthcare policies, physical distancing, smart lockdowns, and meeting food challenges are largely required to combat the coronavirus pandemic and escape from global depression.


id: cord-268939-ws74xprt
title: Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic
author: Ozoner, Baris
date: 2020-05-28
txt: ./txt/cord-268939-ws74xprt.txt
cache: ./cache/cord-268939-ws74xprt.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1878875020311669
doi: 10.1016/j.wneu.2020.05.195
summary:
  The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. [5] [6] [7] In neurosurgery practice, intensive modifications were required in surgical scheduling, administration of inpatient and outpatient clinics, management of emergency cases, and even academic & educational activities. 26 A recent study from Wuhan City, China reported that some severe COVID-19 patients developed neurologic manifestations, such as acute cerebrovascular diseases (5.7%), and impaired consciousness (14.8%). 76, 80 Also, a patient with a mass lesion in the sellar region that underwent endonasal endoscopic surgery in Neurosurgery Department, Tongji Medical College, Wuhan City, China was diagnosed with COVID-19 after surgery, and disease was confirmed in 14 healthcare professionals in the same clinic afterwards.

abstract:
  Abstract Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly contagious, life-threatening condition with unprecedented impacts for worldwide societies and healthcare systems. Since the first detection in China, it has spread rapidly worldwide. The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. In some systems, non-overlapping teams were created to minimize transmission among healthcare workers. In case of a massive burden, neurosurgeons may be needed to reassign to the COVID-19 wards, or teams from other regions may be needed to send to severely affected areas. In outpatient practice, if possible, appointments should be turned into telemedicine. All staff assigned in the non-COVID treatment unit should be clothed in level 1 personal protective equipment. If possible, postponement is recommended for operations that do not require urgent or emergent intervention. All patients indicated for surgery must receive a COVID-19 screening, including nasopharyngeal swab, and thorax computed tomography. Level 2 protection measures would be appropriate during COVID-19 negative patients' operations. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. During surgery, the use of high-speed drills and electrocautery should be reduced to minimize aerosol production. Screening is crucial in all patients since the surgical outcome is highly mortal in COVID-19 patients. All educational and academic conferences can be turned into virtual webinars.


id: cord-272902-kdkyzfjv
author: Naghibzadeh, Mahmoud
date: 2020-05-21
txt: ./txt/cord-272902-kdkyzfjv.txt
cache: ./cache/cord-272902-kdkyzfjv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.imu.2020.100356
doi: 10.1016/j.imu.2020.100356
summary:
  An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. Therefore, this research follows two objectives, development of a general microsatellite discoverer which can be used for different genomes, and analysis of the structures of both SARS-CoV-1 and that of Coronavirus-Covid-19 using this tool and revealing their differences. The properties and novelties of the presented method, which is named Fast MicroSatellite Discoverer (FMSD), for finding all microsatellites of a given gene, DNA, RNA, or other genome sequences including the Novel Coronavirus (GenBabk 2019) and SARS (Rota et al. Section 5 details the evaluation, reports the comparison results, and highlights the structural differences with respect to microsatellites between SARS and Coronavirus-Covid-19 as a case study. A software tool called mreps is develop to detect all tandem repeats, including microsatellites, in DNA as well as whole genome.

title:
  Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19

abstract:
  MOTIVATION: Recently, the outbreak of Coronavirus-Covid-19 has forced the World Health Organization to declare a pandemic status. A genome sequence is the core of this virus which interferes with the normal activities of its counterparts within humans. Analysis of its genome may provide clues toward the proper treatment of patients and the design of new drugs and vaccines. Microsatellites are composed of short genome subsequences which are successively repeated many times in the same direction. They are highly variable in terms of their building blocks, number of repeats, and their locations in the genome sequences. This mutability property has been the source of many diseases. Usually the host genome is analyzed to diagnose possible diseases in the victim. In this research, the focus is concentrated on the attacker's genome for discovery of its malicious properties. RESULTS: The focus of this research is the microsatellites of both SARS and Covid-19. An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. The Microsatellite discovery is based on an efficient indexing technique called K-Mer Hash Indexing. The method is called Fast Microsatellite Discovery (FMSD) and it is used for both SARS and Covid-19. A table composed of all microsatellites is reported. There are many differences between SARS and Covid-19, but there is an outstanding difference which requires further investigation. AVAILABILITY: FMSD is freely available at https://gitlab.com/FUM_HPCLab/fmsd_project, implemented in C on Linux-Ubuntu system. Software related contact: hossein_savari@mail.um.ac.ir.


id: cord-274231-2s7ki6g7
title: SARS – Unprecedented global response to a newly emerging disease
author: Ziebuhr, John
date: 2003-12-31
txt: ./txt/cord-274231-2s7ki6g7.txt
cache: ./cache/cord-274231-2s7ki6g7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14503787/
doi: 10.1078/1438-4221-00270
abstract: Abstract No Abstract
summary:
  293, 229 ± 231 (2003) ¹ Urban & Fischer Verlag http://www.urbanfischer.de/journals/ijmm Editorial SARS ± Unprecedented global response to a newly emerging disease Severe acute respiratory syndrome (SARS) is a life-threatening form of pneumonia that is characterized by fever, chills, myalgia, dry cough, and progressing lung infiltrates (Nicholls et al., 2003; Peiris et al., 2003a) . Only few weeks after the outbreak, the concerted global efforts have resulted in the identification of first coronavirus enzyme inhibitors (Anand et al., 2003; Xiong et al., 2003) that are hoped to be useful for the development of anti-SARS drugs. SARS Working Group: A novel coronavirus associated with severe acute respiratory syndrome SARS study group: Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome


id: cord-274416-bmvazgj7
author: Trevisanuto, Daniele
date: 2020-04-24
txt: ./txt/cord-274416-bmvazgj7.txt
cache: ./cache/cord-274416-bmvazgj7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1159/000507935
doi: 10.1159/000507935
summary:
  title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection. Although it is unlikely that neonates born from SARS-CoV-2-infected mothers require an intensive care management related to the maternal infection [18, 19] , coronaviruses may result in adverse outcomes for the fetus and infant (intrauterine growth restriction, preterm delivery, admission to the neonatal intensive care unit (NICU), spontaneous abortion and perinatal death) [16, 17, 25] . Our designated approach for the management of women with suspected or confirmed CO-VID-19 and their infants before, during, and after delivery provides cues to reduce the chance of neonatal infection and therefore potential negative outcomes in the newborn.

title:
  Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan

abstract:
  Coronavirus disease 2019 (COVID-19), caused by the novel SARS-CoV-2 virus, is rapidly spreading across the world. As the number of infections increases, those of infected pregnant women and children will rise as well. Controversy exists whether COVID-19 can be transmitted in utero and lead to disease in the newborn. As this chance cannot be ruled out, strict instructions for the management of mothers and newborn infants are mandatory. This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection.


id: cord-274802-7ioiwsd8
author: Varghese, Praveen Mathews
date: 2020-08-19
txt: ./txt/cord-274802-7ioiwsd8.txt
cache: ./cache/cord-274802-7ioiwsd8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33130519/
doi: 10.1016/j.imbio.2020.152008
summary:
  Proteomic and transcriptomic studies on bronchoalveolar lavage (BAL) samples from COVID-19 patients have also revealed considerable insights into the expression of SARS-CoV-2 receptors, co-receptors, immune responses, as well as risk factors for severe disease e.g. age and co-morbidities. Furthermore, treatment with a recombinant C5a antibody on 2 male COVID-19 patients aged 54 and 67 years showed significant benefit in suppressing complement hyperactivation, which contributes to the excessive immune response causing aggravated inflammatory lung injury, a hallmark of SARS-CoV-2 pathogenesis and lethality (242) . Consistent with endothelial injury, the significantly elevated levels of von Willebrand factor found in the patient with severe COVID-19 has led to the idea that the infection of the ACE2 expressing endothelium by SARS-CoV-2 induces injury and activates the complement , which sets up a feedback loop that maintains a state of inflammation (243, (268) (269) (270) . Initial clinical studies in China involving 100 SARS-CoV-2 infected patients, who were treated with Chloroquine, showed amelioration of pneumonia, shortened disease progression, increased resolution of lung lesions on CT, and a better virus-negative conversion (313, 314) .

title:
  Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies

abstract:
  Abstract The current coronavirus pandemic, COVID-19, is the third outbreak of disease caused by the coronavirus family, after Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. It is an acute infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 Virus (SARS-CoV-2). The severe disease is characterised by acute respiratory distress syndrome, septic shock, metabolic acidosis, coagulation dysfunction, and multiple organ dysfunction syndromes. Currently, no drugs or vaccine exist against the disease and the only course of treatment is symptom management involving mechanical ventilation, immune suppressants, and repurposed drugs. As such the severe form of the disease has a relatively high mortality rate. Last 6 months have seen an explosion of information related to the host receptors, virus transmission, virus structure-function relationships, pathophysiology, co-morbidities, immune response, treatment and most promising vaccines. This review takes a critically comprehensive look at various aspects of host-pathogen interaction in COVID-19. We examine genomic aspects of SARS-CoV-2, modulation of innate and adaptive immunity, complement-triggered microangiopathy, and host transmission modalities. We also examine its pathophysiological impact during pregnancy, in addition to various gaps in our knowledge. The lessons learnt from various clinical trials involving repurposed drugs have been summarised. We also highlight the rationale and likely success of the most promising vaccine candidates.


id: cord-276951-di5n4wyd
author: Venturini, Elisabetta
date: 2020-05-19
txt: ./txt/cord-276951-di5n4wyd.txt
cache: ./cache/cord-276951-di5n4wyd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32444222/
doi: 10.1016/j.jpeds.2020.04.051
abstract: nan
summary:
  title: Severe neutropenia in infants with severe acute respiratory syndrome caused by the novel coronavirus 2019 infection Infection with severe acute respiratory syndrome caused by the novel coronavirus 2019 (SARS-CoV-2) and resulting coronavirus disease 2019 (COVID-19) is a global pandemic. 18, 19 Moreover, the evidence of neutropenia in neonates and infants could be another manifestation of the age-related different immunologic response to SARS-CoV-2 infection. Epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China Laboratory abnormalities in children with novel coronavirus disease 2019 A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Analysis of CT features of 15 children with 2019 novel coronavirus infection Clinical analysis of 31 cases of 2019 novel coronavirus infection in children from six provinces (autonomous region) of northern China A case of children with 2019 novel Coronavirus Infection

title:
  Severe neutropenia in infants with severe acute respiratory syndrome caused by the novel coronavirus 2019 infection


id: cord-278325-ykcd7d59
title: Coronavirus Disease 2019 (COVID-19): A Haematologist's Perspective
author: Cheung, Carmen Ka Man
date: 2020-07-28
url: https://www.ncbi.nlm.nih.gov/pubmed/32721958/
doi: 10.1159/000510178
abstract:
  Coronavirus disease 2019 (COVID-19) is affecting millions of patients worldwide. It is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which belongs to the family Coronaviridae, with 80% genomic similarities to SARS-CoV. Lymphopenia was commonly seen in infected patients and has a correlation to disease severity. Thrombocytopenia, coagulation abnormalities, and disseminated intravascular coagulation were observed in COVID-19 patients, especially those with critical illness and non-survivors. This pandemic has caused disruption in communities and hospital services, as well as straining blood product supply, affecting chemotherapy treatment and haematopoietic stem cell transplantation schedule. In this article, we review the haematological manifestations of the disease and its implication on the management of patients with haematological disorders.


id: cord-278668-v530u7h0
author: Walls, Alexandra C.
date: 2016-09-12
url: https://doi.org/10.1038/nsmb.3293
doi: 10.1038/nsmb.3293
title:
  Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

abstract:
  The threat of a major coronavirus pandemic urges the development of suitable strategies to combat these pathogens. HCoV-NL63 is an α-coronavirus that can cause severe lower respiratory tract infections requiring hospitalization. We report here the 3.4 Å resolution cryo-electron microscopy reconstruction of the HCoV-NL63 coronavirus spike glycoprotein trimer, which is the conformational machine responsible for entry into host cells and the sole target of neutralizing antibodies during infection. The map resolves the extensive glycan shield obstructing the protein surface and, in combination with mass-spectrometry, provides a structural framework to understand accessibility to antibodies. The structure also reveals a remarkable modular architecture of the receptor-binding subunit and the complete architecture of the fusion machinery including the triggering loop and the C-terminal domains, which contribute to anchoring the trimer to the viral membrane. Our data further suggest that HCoV-NL63 and other coronaviruses use molecular trickery, based on masking of epitopes with glycans and activating conformational changes, to evade the immune system of infected hosts.


id: cord-279255-v861kk0i
title: Coronavirus Disease 2019–COVID-19
author: Dhama, Kuldeep
date: 2020-06-24
txt: ./txt/cord-279255-v861kk0i.txt
cache: ./cache/cord-279255-v861kk0i.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32580969/
doi: 10.1128/cmr.00028-20
summary:
  Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . Health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel CoV (originally named 2019-nCoV), which was first identified in Wuhan City, Hubei Province, China, on 12 December 2019.

abstract:
  In recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS-CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus.


id: cord-279363-4almssg6
title: Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión
author: Crespo, Roland Mojica
date: 2020-05-16
txt: ./txt/cord-279363-4almssg6.txt
cache: ./cache/cord-279363-4almssg6.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1138359320301714?v=s5
doi: 10.1016/j.semerg.2020.05.010
summary:
  En ese momento, a este nuevo coronavirus se le llamó 2019-nCoV (del inglés: 2019-novel coronavirus) y fue identificado por las autoridades sanitarias chinas como el agente causal de estos casos de neumonía atípica 1,3,4 . Hacia final de mes, el día 30 de enero la OMS declaró la enfermedad causada por el nuevo coronavirus como una emergencia de salud pública de preocupación internacional, ya que para aquel momento se habían reportado casos en todas las regiones de la OMS en solo un mes 9,11 . Concretamente la RNVE en su informe n°29 del día 7 de mayo enumera los principales síntomas presentados por el conjunto de la población española, hasta la fecha y a base de una muestra de 217,543 casos, de la siguiente manera: Entre estos hallazgos, es comúnmente observar la leucopenia y linfopenia, siendo esta última característica de COVID-19.

abstract:
  Resumen A finales de diciembre del 2019, se reportaron una serie de casos de neumonía atípica, en ese momento, de origen desconocido en Wuhan, China. Días más tarde se identificó al agente etiológico como un nuevo coronavirus. A este nuevo coronavirus, se le llamó SARS-CoV-2 y a la enfermedad que produce se le denominó COVID-19. El origen de este nuevo virus se presume zoonótico siendo los murciélagos su probable vector. Debido al acelerado número de contagios y muertes que se produjeron primero en China y posteriormente alrededor del mundo, la infección de este virus pasó rápidamente de ser un brote aislado en una región china, a convertirse en una emergencia sanitaria de preocupación internacional y posteriormente, en una pandemia. El propósito de esta revisión es estudiar la información más relevante y actual del patógeno, así como la epidemiología, patología, características clínicas, transmisión, prevención y tratamiento de la enfermedad. Abstract In late December 2019, some cases of atypical pneumonia, at that time of unknown origin, were reported in Wuhan, China. Days later, the etiologic agent was identified as a new coronavirus. This new coronavirus was called SARS-CoV-2 and the disease it produces was named COVID-19. The origin of this new virus is presumed zoonotic, with bats being its probable vector. Due to the rapid number of infections and deaths that occurred first in China and later around the world, the infection of this virus quickly went from being an isolated outbreak in a Chinese region to becoming a health emergency of international concern and later, a pandemic. The purpose of this review is to study the most relevant and current information on the pathogen, as well as epidemiology, pathology, clinical features, transmission, prevention, and treatment of the disease.


id: cord-279488-oc0edgd2
author: Nguyen, Trieu
date: 2020-03-14
url: https://doi.org/10.3390/mi11030306
doi: 10.3390/mi11030306
title:
  2019 Novel Coronavirus Disease (COVID-19): Paving the Road for Rapid Detection and Point-of-Care Diagnostics

abstract:
  We believe a point-of-care (PoC) device for the rapid detection of the 2019 novel Coronavirus (SARS-CoV-2) is crucial and urgently needed. With this perspective, we give suggestions regarding a potential candidate for the rapid detection of the coronavirus disease 2019 (COVID-19), as well as factors for the preparedness and response to the outbreak of the COVID-19.


id: cord-279691-v5kpmk0b
title: Biogenesis and Dynamics of the Coronavirus Replicative Structures
author: Hagemeijer, Marne C.
date: 2012-11-21
txt: ./txt/cord-279691-v5kpmk0b.txt
cache: ./cache/cord-279691-v5kpmk0b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23202524/
doi: 10.3390/v4113245
summary:
  Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ).

abstract:
  Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins.


id: cord-280518-2tl0mtb8
author: Xia, Jianhua
date: 2020-03-12
txt: ./txt/cord-280518-2tl0mtb8.txt
cache: ./cache/cord-280518-2tl0mtb8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/jmv.25725
doi: 10.1002/jmv.25725
summary:
  title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. On 7 January 2020, the Chinese Center for Disease Control and Prevention isolated and confirmed this pathogen as a novel type of coronavirus through a throat swab. Study Group of the International Committee on Taxonomy of Viruses named 2019-nCoV severe acute respiratory syndrome-related coronavirus 2, or SARS-CoV-2. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection

title:
  Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection

abstract:
  OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. At an interval of 2 to 3 days, tear and conjunctival secretions were collected twice with disposable sampling swabs for reverse‐transcription polymerase chain reaction (RT‐PCR) assay. RESULTS: Twenty‐one common‐type and nine severe‐type NCP patients were enrolled. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. Fifty‐eight samples from other patents were all negative. CONCLUSION: We speculate that SARS‐CoV‐2 may be detected in the tears and conjunctival secretions in NCP patients with conjunctivitis.


id: cord-281754-auqh3vtr
title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES
author: nan
date: 2017-09-12
txt: ./txt/cord-281754-auqh3vtr.txt
cache: ./cache/cord-281754-auqh3vtr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29737283/
doi: 10.1016/j.disamonth.2017.03.019
abstract: nan
summary:
  As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] .


id: cord-282977-kmj8hj78
title: Battle with COVID-19 Under Partial to Zero Lockdowns in India
author: Babbar, S.
date: 2020-07-04
txt: ./txt/cord-282977-kmj8hj78.txt
cache: ./cache/cord-282977-kmj8hj78.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.07.03.20145664v1?rss=1
doi: 10.1101/2020.07.03.20145664
summary:
  Instead of fixing parameters of the standard SEIR model before simulation, we propose to learn them from the real data set consisting of progression of Corona spread in India. The learning of model is carefully designed by understanding that available data set consist of records of cases under full, partial to zero lockdown phases in India. These two predictions presented in this work provide awareness among citizens of India on importance of control measures such as full, partial and zero lockdown and the spread of Corona disease infection rate. The key motivation to integrate two methods for the predictive task is to use benefits of SEIR model by making its key parameters learn using historical data of confirmed cases under full and partial to zero lockdowns in India. Figures 5 and 6 represents fitting of learned model over actual new cases of Coronavirus data set of India and Delhi respectively.

abstract:
  The cumulative records of COVID-19 are rapidly increasing day by day in India. The key question prevailing in minds of all is when will it get over? There have been several attempts in literature to address this question using time series, Machine learning, epidemiological and statistical models. However due to high level of uncertainty in the domain and lack of big historical data, the performance of these models suffer. In this work, we present an intuitive model that uses a combination of epidemiological model (SEIR) and mathematical curve fitting method to forecast spread of COVID-19 in India in future. By using the combination model, we get characteristics benefits of these models under limited knowledge and historical data about the novel Coronavirus. Instead of fixing parameters of the standard SEIR model before simulation, we propose to learn them from the real data set consisting of progression of Corona spread in India. The learning of model is carefully designed by understanding that available data set consist of records of cases under full, partial to zero lockdown phases in India. Hence, we make two separate predictions by our propose model. One under the situation of full lockdown in India and, other with partial to zero restrictions in India. With continued strict lockdown after May 03, 2020, our model predicted May 14, 2020 as the date of peak of Coronavirus in India. However, in current scenario of partial to zero lockdown phase in India, the peak of Coronavirus cases is predicted to be July 31, 2020. These two predictions presented in this work provide awareness among citizens of India on importance of control measures such as full, partial and zero lockdown and the spread of Corona disease infection rate. In addition to this, it is a beneficial study for the government of India to plan the things ahead.


id: cord-283215-dgysimh5
author: Al-Jabir, Ahmed
date: 2020-05-12
url: https://doi.org/10.1016/j.ijsu.2020.05.002
doi: 10.1016/j.ijsu.2020.05.002
title:
  Impact of the coronavirus (COVID-19) pandemic on surgical practice - Part 2 (surgical prioritisation)

abstract:
  The Coronavirus (COVID-19) Pandemic represents a once in a century challenge to human healthcare with 2.4 million cases and 165,000 deaths thus far. Surgical practice has been significantly impacted with all specialties writing guidelines for how to manage during this crisis. All specialties have had to triage the urgency of their daily surgical procedures and consider non-surgical management options where possible. The Pandemic has had ramifications for ways of working, surgical techniques, open vs minimally invasive, theatre workflow, patient and staff safety, training and education. With guidelines specific to each specialty being implemented and followed, surgeons should be able to continue to provide safe and effective care to their patients during the COVID-19 pandemic. In this comprehensive and up to date review we assess changes to working practices through the lens of each surgical specialty.


id: cord-286683-mettlmhz
author: Ortiz-Prado, Esteban
date: 2020-05-30
txt: ./txt/cord-286683-mettlmhz.txt
cache: ./cache/cord-286683-mettlmhz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.diagmicrobio.2020.115094
doi: 10.1016/j.diagmicrobio.2020.115094
summary:
  Interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in SARS [59] and MERS diseases [60] were also reported in the early study of 41 patients with COVID-19 in Wuhan [41] . A recently published case report of a patient with mild-to-moderate COVID-19 revealed the presence of an increased activated CD4+ T cells and CD8+ T cells, antibody-secreting cells (ASCs), follicular helper T cells (TFH cells), and anti-SARS-CoV-2 IgM and IgG antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [82] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series

title:
  Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review

abstract:
  Abstract Coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. The current classification of coronaviruses recognizes 39 species in 27 subgenera that belong to the family Coronaviridae. From those, at least seven coronaviruses are known to cause respiratory infections in humans. Four of these viruses can cause common cold-like symptoms. Those that infect animals can evolve and become infectious to humans. Three recent examples of these viral jumps include SARS CoV, MERS-CoV and SARS CoV-2 virus. They are responsible for causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the most recently discovered coronavirus disease during 2019 (COVID-19). COVID-19, a respiratory disease caused by the SARS-CoV-2 virus, was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. The rapid spread of the disease has taken the scientific and medical community by surprise. Latest figures from 20th May 2020 show more than 5 million people had been infected with the virus, causing more than 330,000 deaths in over 210 countries worldwide. The large amount of information received daily relating to COVID-19 is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. In order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the SARS CoV-2 Virus and the Coronavirus Diseases 2019 (COVID-19).


id: cord-286958-e1ey31eo
author: Patel, Urvish
date: 2020-08-15
txt: ./txt/cord-286958-e1ey31eo.txt
cache: ./cache/cord-286958-e1ey31eo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.7189/jogh.10.020506
doi: 10.7189/jogh.10.020506
summary:
  We evaluated the global burden of COVID-19 including case fatality rates (CFR), strength of association between deaths and cases to predict CFR, case doubling time, COVID-19 specific mortality rates, and control measures by governments to prevent spread among USA, China, Italy, Iran, Spain, Germany, India, and South Korea. Bavaria declared a state of emergency for 14 days and measures to limit public movement and additional funds for medicine supplies were introduced [71] ; All flights from Iran and China stopped by German Ministry of Transport [72] ; Travelling in coaches, attending religious meetings, visiting playgrounds or engaging in tourism prohibited [73] 17 Finance minister announced US$24 billion stimulus package [88] Infection rate at the beginning of the major intervention (nationwide closure of school or major Table 6 mentions the predicted dates of the peak number of cases based on strict interventions.

title:
  Early epidemiological indicators, outcomes, and interventions of COVID-19 pandemic: A systematic review

abstract:
  BACKGROUND: Coronavirus disease-2019 (COVID-19), a pandemic that brought the whole world to a standstill, has led to financial and health care burden. We aimed to evaluate epidemiological characteristics, needs of resources, outcomes, and global burden of the disease. METHODS: Systematic review was performed searching PubMed from December 1, 2019, to March 25, 2020, for full-text observational studies that described epidemiological characteristics, following MOOSE protocol. Global data were collected from the JHU-Corona Virus Resource Center, WHO-COVID-2019 situation reports, KFF.org, and Worldometers.info until March 31, 2020. The prevalence percentages were calculated. The global data were plotted in excel to calculate case fatality rate (CFR), predicted CFR, COVID-19 specific mortality rate, and doubling time for cases and deaths. CFR was predicted using Pearson correlation, regression models, and coefficient of determination. RESULTS: From 21 studies of 2747 patients, 8.4% of patients died, 20.4% recovered, 15.4% were admitted to ICU and 14.9% required ventilation. COVID-19 was more prevalent in patients with hypertension (19.3%), smoking (11.3%), diabetes mellitus (10%), and cardiovascular diseases (7.4%). Common complications were pneumonia (82%), cardiac complications (26.4%), acute respiratory distress syndrome (15.7%), secondary infection (11.2%), and septic shock (4.3%). Though CFR and COVID-19 specific death rates are dynamic, they were consistently high for Italy, Spain, and Iran. Polynomial growth models were best fit for all countries for predicting CFR. Though many interventions have been implemented, stern measures like nationwide lockdown and school closure occurred after very high infection rates (>10cases per 100 000population) prevailed. Given the trend of government measures and decline of new cases in China and South Korea, most countries will reach the peak between April 1-20, if interventions are followed. CONCLUSIONS: A collective approach undertaken by a responsible government, wise strategy implementation and a receptive population may help contain the spread of COVID-19 outbreak. Close monitoring of predictive models of such indicators in the highly affected countries would help to evaluate the potential fatality if the second wave of pandemic occurs. The future studies should be focused on identifying accurate indicators to mitigate the effect of underestimation or overestimation of COVID-19 burden.


id: cord-287221-oh7lnxwt
title: Understanding the COVID-19 tourist psyche: The Evolutionary Tourism Paradigm
author: Kock, Florian
date: 2020-09-09
url: https://api.elsevier.com/content/article/pii/S0160738320301973
doi: 10.1016/j.annals.2020.103053
abstract:
  Studies across the social sciences are making increasing use of an evolutionary perspective. Yet, despite its potential, the application of evolutionary psychology in tourism research is scant. Evolutionary psychology is arguably one of the most useful approaches to understanding the effects of the Coronavirus pandemic on the tourist's psyche. This research highlights, explains, and empirically demonstrates the vast untapped potential of this perspective for post-COVID-19 tourism research. The authors develop an Evolutionary Tourism Paradigm, which is based on biological epistemology and theory to address questions in post-COVID-19 tourism research. This paradigm is brought to life through a developed ocean and islands model, and its utility for future research endeavors on the Coronavirus pandemic is empirically demonstrated in two studies.


id: cord-287758-da11ypiy
title: COVID-19 therapy: what weapons do we bring into battle?
author: Mônica Vitalino de Almeida, Sinara
date: 2020-09-10
txt: ./txt/cord-287758-da11ypiy.txt
cache: ./cache/cord-287758-da11ypiy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.bmc.2020.115757
doi: 10.1016/j.bmc.2020.115757
summary:
  The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell.

abstract:
  Urgent treatments, in any modality, to fight SARS-CoV-2 infections are desired by society in general, by health professionals, by Estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding COVID-19: knowledge is the means to discover or to produce an effective treatment against this global disease. Scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of 2020 with over 25,000 published articles related to the new coronavirus. Three great lines of publications related to COVID-19 were identified for building this article: The first refers to knowledge production concerning the virus and pathophysiology of COVID-19; the second regards efforts to produce vaccines against SARS-CoV-2 at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat COVID-19 by drug repurposing. In this review, the drugs that have been repurposed so far are grouped according to their chemical class. Their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. This can help identifying anti-SARS-CoV-2 promising therapeutic agents.


id: cord-289588-n61gz7pi
title: Virology, pathogenesis, diagnosis and in-line treatment of COVID-19
author: Samudrala, Pavan Kumar
date: 2020-07-17
txt: ./txt/cord-289588-n61gz7pi.txt
cache: ./cache/cord-289588-n61gz7pi.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0014299920304672?v=s5
doi: 10.1016/j.ejphar.2020.173375
summary:
  Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. As far as safety is a major concern, 424 Gilead Sciences announced phase III clinical trial of remdesivir to prove its safety and 425 efficacy in COVID-19 infection (Keown, 16 .03.2020). Epidemiology, causes, clinical manifestation and 687 diagnosis, prevention and control of coronavirus disease (COVID-19) during the early 688 outbreak period: a scoping review First known person-to-784 person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 785 the USA Clinical 803 features of patients infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 (COVID-19) Vaccine Development and Production: An 817 Severe acute respiratory 845 syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The 846 epidemic and the challenges Unique epidemiological and clinical features 949 of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control 950 measures

abstract:
  SARS-CoV-2, a newly emerged pathogen in December 2019, marked as one of the highly pathogenic Coronavirus, and altogether this is the third coronavirus attack that crossed the species barrier. As of 1(st) July 2020, it is spreading around 216 countries, areas or territories, and a total of 10,185,374 and 503,862 confirmed cases and death reports, respectively. The SARS-CoV-2 virus entered into the target cells by binding with the hACE2 receptors. Spike glycoprotein promotes the entry of the virus into host target cells. Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. These modifications may be the probable reason for the extreme transmission and pathogenicity of the virus. A hasty spread of COVID-19 throughout the world is highly threatening, but still, scientists do not have a proper therapeutic measure to fight with it. Scientists are endeavoring across the world to find effective therapy to combat COVID 19. Several drugs such as Remdesivir, Hydroxychloroquine, Chloroquine, Ribavirin, Ritonavir, Lopinavir, Favipiravir, Interferons, Bevacizumab, Azithromycin, etc. are currently under clinical trials. Vaccine development from various pharmaceutical companies and research institutes is under progress, and more than ten vaccine candidates are in the various phases of clinical trials. This review work highlighted the origin, emergence, structural features, pathogenesis, and clinical features of COVID-19. We have also discussed the in-line treatment strategies, preventive measures, and vaccines to combat the emergence of COVID-19.


id: cord-289680-pjcskj4m
title: Light in the midst of chaos: COVID-19 and female political representation()
author: Piazza, Kelly Senters
date: 2020-09-02
txt: ./txt/cord-289680-pjcskj4m.txt
cache: ./cache/cord-289680-pjcskj4m.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.worlddev.2020.105125
doi: 10.1016/j.worlddev.2020.105125
summary:
  Research on gender and politics shows that exceptional environments can activate stereotypes of women as honest, trustworthy, and competent lawmakers in public health and, in doing so, can generate increased public support for female political candidates. In line with this research, the Coronavirus Pandemic may increase female representation not due to their perceived trustworthiness or competence in public health but because party leaders are more likely to assign women to leadership positions with high risk of failure in moments of crisis. Reports praising German Chancellor Angela Merkel''s sciencebased response, widespread testing, transparency, stringent social distancing policies, travel restrictions, and relational appeals to the public to induce compliance 6 and New Zealand Prime Minister Jacinda Arden''s clarity, compassion, strict national lockdown, travel restrictions, and pervasive testing (Mahdawi, 2020) 7 have fostered the narrative that female executives have more effectively, efficiently, and impressively handled the coronavirus pandemic (Cherneski, 2020) .

abstract:
  The promotion of gender equality and the empowerment of women are global policy priorities across countries and development institutions. Research on gender and politics shows that exceptional environments can activate stereotypes of women as honest, trustworthy, and competent lawmakers in public health and, in doing so, can generate increased public support for female political candidates. We argue that the 2019–2020 Coronavirus Pandemic has the potential to produce this outcome, as recent public opinion polls highlight widespread discontent with male-led governments’ responses to the pandemic and elevated concerns surrounding public health. Recent positive media reports of female world leaders’ responses to the pandemic provide further reason to suspect a forthcoming increase in political support for female candidates. We posit that such an outcome may prove essential not only for enhancing development and improving long-standing gender inequities but also for alleviating the pandemic’s disproportionately allocated hardships.


id: cord-291916-5yqc3zcx
author: Hozhabri, Hossein
date: 2020-08-05
txt: ./txt/cord-291916-5yqc3zcx.txt
cache: ./cache/cord-291916-5yqc3zcx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/ijerph17165648
doi: 10.3390/ijerph17165648
title:
  The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting

abstract:
  Over the past two decades, there have been two major outbreaks where the crossover of animal Betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In December 2019, a global public health concern started with the emergence of a new strain of coronavirus (SARS-CoV-2 or 2019 novel coronavirus, 2019-nCoV) which has rapidly spread all over the world from its origin in Wuhan, China. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes human SARS-CoV, MERS and two other human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1. The fatality rate of SARS-CoV-2 is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed SARS-CoV-2 to be highly contagious. Based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of SARS-CoV-2 infections in comparison with those caused by SARS-CoV and MERS-CoV. Moreover, the possible impact of weather conditions on the transmission of SARS-CoV-2 is also discussed. Therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches.


id: cord-292751-tk1oggi9
author: Hosseini, Elahe Seyed
date: 2020-09-24
url: https://doi.org/10.1016/j.virol.2020.08.011
doi: 10.1016/j.virol.2020.08.011
title:
  The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies

abstract:
  Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. Early diagnosis of COVID-19 is the most critical step to treat infection. The diagnostic tools are generally molecular methods, serology and viral culture. Recently CRISPR-based method has been investigated to diagnose and treat coronavirus infection. The emergence of 2019-nCoV during the influenza season, has led to the extensive use of antibiotics and neuraminidase enzyme inhibitors, taken orally and intravenously. Currently, antiviral inhibitors of SARS and MERS spike proteins, neuraminidase inhibitors, anti-inflammatory drugs and EK1 peptide are the available therapeutic options for SARS-CoV-2 infected individuals. In addition, Chloroquine, which was previously used for malarial and autoimmune disease, has shown efficacy in the 2019-nCoV infection treatment. In severe hypoxaemia, a combination of antibiotics, α-interferon, lopinavir and mechanical ventilation can effectively mitigate the symptoms. Comprehensive knowledge on the innate and adaptive immune responses, will make it possible to propose potent antiviral drugs with their effective therapeutic measures for the prevention of viral infection. This therapeutic strategy will help patients worldwide to protect themselves against severe and fatal viral infections, that potentially can evolve and develop drug resistance, and to reduce mortality rates.


id: cord-292912-ufcvecwo
author: Qiu, Ruijin
date: 2020-03-08
url: https://doi.org/10.1101/2020.03.04.20031401
doi: 10.1101/2020.03.04.20031401
title:
  Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review

abstract:
  Objectives: To examine heterogeneity of outcomes in protocols of clinical trials of Coronavirus Disease 2019 (COVID-19) and to identify outcomes for prioritization in developing a core outcome set (COS) in this field. Design: This study is a review. Data sources: Databases of ICMJE-accepted clinical trial registry platform were searched on February 14, 2020. Eligibility Criteria: Randomized controlled trials (RCTs) and non-RCTs of COVID-19 were considered.Conditions of patients include common type, severe type or critical type. Interventions include traditional Chinese medicine (TCM) and Western medicine. We excluded trials that for discharged patients, psychological intervention and complications of COVID-19. Data extraction and synthesis: The general information and outcomes, outcome measurement instruments and measurement times were extracted. The results were analysed by descriptive analysis. Results: 19 registry platforms were searched. A total of 97 protocols were included from 160 protocols. For protocols of TCM clinical trials, 76 outcomes from 16 outcome domains were reported, and almost half (34/76, 44.74%) of outcomes were reported only once; the most frequently reported outcome was time of SARS-CoV-2 RNA turns to negative. 27 (27/76, 35.53%) outcomes were provided one or more outcome measurement instruments. 10 outcomes were provided one or more measurement time frame. For protocols of western medicine clinical trials, 126 outcomes from 17 outcome domains were reported; almost half (62/126, 49.21%) of outcomes were reported only once; the most frequently reported outcome was proportion of patients with negative SARS-CoV-2. 27 outcomes were provided one or more outcome measurement instruments. 40 (40/126, 31.75%) outcomes were provided one or more measurement time frame. Conclusion: Outcome reporting in protocols of clinical trials of COVID-19 is inconsistent. Thus, developing a core outcome set is necessary. Keywords: Outcomes; clinical trials, COVID-19; review.


id: cord-293082-fw7deem8
title: Animal coronaviruses and SARS‐CoV‐2
author: Zhang, Guangzhi
date: 2020-08-16
url: https://doi.org/10.1111/tbed.13791
doi: 10.1111/tbed.13791
abstract:
  COVID‐19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). It has rapidly spread to 216 countries and territories since first outbreak in December of 2019, posing a substantial economic losses and extraordinary threats to the public health worldwide. Although bats have been suggested as the natural host of SARS‐CoV‐2, transmission chains of this virus, role of animals during cross‐species transmission, and future concerns remain unclear. Diverse animal coronaviruses have extensively been studied since the discovery of avian coronavirus in 1930s. The current article comprehensively reviews and discusses the current understanding about animal coronaviruses and SARS‐CoV‐2 for their emergence, transmission, zoonotic potential, alteration of tissue/host tropism, evolution, status of vaccines, and surveillance. This study aims at providing guidance for control of COVID‐19 and preventative strategies for possible future outbreaks of zoonotic coronavirus via cross‐species transmission.


id: cord-293166-gkzebyda
author: Hoz, Samer S.
date: 2020-11-03
txt: ./txt/cord-293166-gkzebyda.txt
cache: ./cache/cord-293166-gkzebyda.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1878875020318271
doi: 10.1016/j.wneu.2020.08.060
abstract: nan
summary:
  title: Letter to the Editor: "Beyond Containment: Tracking the Impact of Coronavirus Disease 2019 (COVID-19) on Neurosurgery Services in Iraq" Letter to the Editor: "Beyond Containment: Tracking the Impact of Coronavirus Disease 2019 (COVID-19) on Neurosurgery Services in Iraq" LETTER: The Neurosurgery Teaching Hospital (NTH) in Baghdad, Iraq, provides neurosurgical care for 4.2 million people-approximately 50% of the population in Baghdad, with a total capacity of 102 beds, 16 neurosurgical intensive care unit (NICU) beds, and 7 operating rooms. Cases requiring less immediate care are only admitted if the condition is deemed to be "urgent." This decision is the responsibility of a newly assembled local hospital committee, composed of 3 senior neurosurgeons. As for patients, a total of 25 acute trauma cases have been confirmed to be positive by immediate postoperative polymerase chain reaction. Such situations are hazardous and require urgent legislative change that determines the COVID-19 status of all admitted patients to be positive unless proven otherwise.

title:
  Letter to the Editor: “Beyond Containment: Tracking the Impact of Coronavirus Disease 2019 (COVID-19) on Neurosurgery Services in Iraq”


id: cord-294468-0v4grqa7
author: Kasilingam, Dharun
date: 2020-08-04
url: https://doi.org/10.1111/tbed.13764
doi: 10.1111/tbed.13764
title:
  Exploring the Growth of COVID‐19 Cases using Exponential Modelling Across 42 Countries and Predicting Signs of Early Containment using Machine Learning

abstract:
  COVID‐19 pandemic disease spread by the SARS‐COV‐2 single‐strand structure RNA virus, belongs to the 7(th) generation of the coronavirus family. Following an unusual replication mechanism, it’s extreme ease of transmissivity has put many counties under lockdown. With uncertainty of developing a cure/vaccine for the infection in the near future, the onus currently lies on healthcare infrastructure, policies, government activities, and behaviour of the people to contain the virus. This research uses exponential growth modelling studies to understand the spreading patterns of the COVID‐19 virus and identifies countries that have shown early signs of containment until 26(th) March 2020. Predictive supervised machine learning models are built using infrastructure, environment, policies, and infection‐related independent variables to predict early containment. COVID‐19 infection data across 42 countries are used. Logistic regression results show a positive significant relationship between healthcare infrastructure and lockdown policies, and signs of early containment. Machine learning models based on logistic regression, decision tree, random forest, and support vector machines are developed and show accuracies between 76.2% to 92.9% to predict early signs of infection containment. Other policies and the decisions taken by countries to contain the infection are also discussed.


id: cord-294651-iy0h2pyf
author: Nasrallah, Ali A.
date: 2020-06-08
url: https://doi.org/10.1016/j.jclinepi.2020.06.005
doi: 10.1016/j.jclinepi.2020.06.005
title:
  A large number of COVID-19 interventional clinical trials were registered soon after the pandemic onset: a descriptive analysis

abstract:
  Abstract Background There is a pressing need for evidence-based interventions to address the devastating clinical and public health effects of the Coronavirus disease 2019 (COVID-19) pandemic. The number of registered trials related to COVID-19 is increasing by the day. Objectives To describe the characteristics of the currently registered clinical trials related to COVID-19. Methods We searched the World Health Organization (WHO)’s International Clinical Trials Registry Platform (ICTRP) on May 15, 2020. We included any entry that is related to COVID-19. We abstracted then descriptively analyzed the following characteristics of the registered trials: study design, status, phase, primary endpoints, experimental interventions, and geographic location among other qualifiers. Results We identified 1,308 eligible registered trials. The majority of trials were initially registered with ClinicalTrials.gov (n= 703; 53.7%) and the Chinese Clinical Trial Registry (ChiCTR) (n= 291; 22.2%). The number of participants to be enrolled across these trials was 734,657, with a median of 110 participants per trial. The most-commonly studied intervention category was pharmacologic (n=763; 58.3%), with antiparasitic medications being the most common subcategory. While over half of trials were already recruiting, we identified published peer-reviewed results for only 8 of those trials. Conclusion There is a relatively large number of registered trials but very few results published so far. While our findings suggest an appropriate initial response by the research community, the real challenge will be to get these trials completed, published, and translated into practice and policy.


id: cord-294677-l1b4mw9d
author: Prashantha, C.N.
date: 2020-10-13
url: https://www.sciencedirect.com/science/article/pii/S1093326320305581?v=s5
doi: 10.1016/j.jmgm.2020.107769
title:
  Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus

abstract:
  The Target spike protein docking with antimalarial, antimicrobial, anti-inflammatory and HIV-Protease inhibitors. The docking processed using AutoDock Vina and the binding affinity score is noted based on kcal/mol and estimated inhibitory constant (KI). [Figure: see text]


id: cord-294696-pm6pfeeb
author: Kunz, Y.
date: 2020-10-13
txt: ./txt/cord-294696-pm6pfeeb.txt
cache: ./cache/cord-294696-pm6pfeeb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33048213/
doi: 10.1007/s00120-020-01264-z
summary:
  Ausgelöst wird diese Infektionskrankheit durch das Virus SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), das zur Familie der β-Coronaviridiae bzw. Das SARS-CoV-2 wird im Wesentlichen via Tröpfcheninfektion -und somit über Aerosole -von symptomatischen COVID-19-Patienten übertragen. Es wurde eine Literatursuche in PubMed, bioRxiv und medRxiv sowie den Datenbanken der WHO und des CDC über SARS-CoV-2 und chirurgisches Prozedere bei infizierten Patienten durchgeführt. Das Prostatagewebe scheint demgegenüber nicht von SARS-CoV-2 befallen zu werden, zumindest konnte eine chinesische Gruppe in einer kleinen Studie keine Virus-RNA im Prostatasekret nachweisen [29] . Da basierend auf der oben angesprochenen Studienlage eine SARS-CoV-2-Übertragung mittels Urin denkbar ist, muss bei COVID-19-Patienten und unklaren Verdachtsfällen zusätzlich zur gängigen Schutzkleidung im Operationssaal auf FFP-2-Masken und Schutzbrillen zurückgegriffen werden. Da Aerosole nicht nur während der Operation, sondern bereits zuvor im Rahmen einer OP-Einleitung entstehen können, sollte laut aktuellen Empfehlungen unbedingt auf FFP-2-Masken im Falle eines zu behandelnden Patienten mit Verdacht auf oder einer bestätigten COVID-19-Infektion zurückgegriffen werden.

title:
  Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag

abstract:
  BACKGROUND: COVID-19 poses a challenge to healthcare systems worldwide. Due to the increasing number of cases, surgeons in urology have also been confronted with SARS-CoV‑2 infections. Thus, there is an urgent need for clinical guidance and recommendations. AIM: Our work aims to create a widespread assessment of a possible risk for infection with SARS-CoV‑2 during surgical procedures. Based on current data and current national and international guidelines, we try to assess the risk of infection when handling human tissue and the necessary hygienic measures that are needed. Finally, recommendations for daily urologic work are derived and explained. MATERIALS AND METHODS: The current literature in PubMed, bioRxiv and medRxiv and data available from the WHO and Robert-Koch-Institut on SARS-CoV‑2 and surgical procedures in (potentially) infected patients are reviewed. The endpoint of our research was 21 April 2020. CONCLUSION: Based on our research, general and specific recommendations for clinical urologic praxis can be derived. Although it remains unclear whether SARS-CoV‑2 is transmitted via the aerosols produced, current PPE in operating rooms probably does not offer sufficient protection during surgical interventions during the SARS-CoV‑2 pandemic. Use of FFP‑2 masks, safety goggles and full-body protective suits is crucial. To contain viral spread on surfaces and personnel, complex filter systems (HEPA) should be used as well as closed suction devices during surgery. Combined with consequent disinfection of surfaces and behavioral measures, a safe environment for healthcare workers in urology can be created. Thus, according to current knowledge, we believe that emergency and urgent surgical procedures are not contraindicated, provided that appropriate precautionary safety measures are followed.


id: cord-297168-t6zf5k99
title: The Novel Coronavirus – A Snapshot of Current Knowledge
author: Brüssow, Harald
date: 2020-03-06
txt: ./txt/cord-297168-t6zf5k99.txt
cache: ./cache/cord-297168-t6zf5k99.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32144890/
doi: 10.1111/1751-7915.13557
summary:
  While bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the Huanan food market in Wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. W. Tan and colleagues, who now constitute the China Novel Coronavirus Investigating and Research Team, described subsequently the isolation of further coronaviruses from three patients in Wuhan who tested negative for 18 viral and four bacterial respiratory pathogens. Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients Outside Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series

abstract:
  Another animal to human transmission of a coronavirus occurred in December 2019 on a live animal market in the Chinese city of Wuhan causing an epidemic in China, reaching now different continents. This minireview summarizes the research literature on the virological, clinical and epidemiological aspects of this epidemic published until end of February 2020.


id: cord-297323-l3f12hg4
author: Amor, Sandra
date: 2020-09-26
url: https://doi.org/10.1111/cei.13523
doi: 10.1111/cei.13523
title:
  Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage

abstract:
  Innate immune sensing of viral molecular patterns is essential for development of antiviral responses. Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. Together these strategies allow widespread infection and increased viral load. Despite the efforts of immune subversion, SARS‐CoV‐2 infection activates innate immune pathways inducing a robust type I/III interferon response, production of proinflammatory cytokines, and recruitment of neutrophils and myeloid cells. This may induce hyperinflammation or alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. The dysregulation of the renin‐angiotensin system due to downregulation of angiotensin converting enzyme 2, the receptor for SARS‐CoV‐2, together with the activation of type I/III interferon response, and inflammasome response converge to promote free radical production and oxidative stress. This exacerbates tissue damage in the respiratory system but also leads to widespread activation of coagulation pathways leading to thrombosis. Here, we review the current knowledge of the role of the innate immune response following SARS‐CoV‐2 infection, much of which is based on the knowledge from SARS‐CoV and other coronaviruses. Understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in COVID‐19 may help explain factors that contribute to the variety of clinical manifestations and outcome of SARS‐CoV‐2 infection.


id: cord-298156-d0pb1kik
title: Observed and Potential Impacts of the COVID-19 Pandemic on the Environment
author: Cheval, Sorin
date: 2020-06-10
txt: ./txt/cord-298156-d0pb1kik.txt
cache: ./cache/cord-298156-d0pb1kik.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/ijerph17114140
doi: 10.3390/ijerph17114140
summary:
  Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. The concept of disaster has evolved over time, and here we use an adapted Intergovernmental Panel on Climate Change (IPCC) definition: a disaster is an event, which severely alters the functioning of a community due to hazardous physical, biological or human related impacts leading to widespread adverse effects on multiple scales and systems (environment, economic, social). While negative impacts on the economy and society in general are probably huge, it is very likely that the global-scale reduction of economic activities due to the COVID-19 crisis triggers a lot of sensible improvements in environmental quality and climatic systems.

abstract:
  Various environmental factors influence the outbreak and spread of epidemic or even pandemic events which, in turn, may cause feedbacks on the environment. The novel coronavirus disease (COVID-19) was declared a pandemic on 13 March 2020 and its rapid onset, spatial extent and complex consequences make it a once-in-a-century global disaster. Most countries responded by social distancing measures and severely diminished economic and other activities. Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. This study presents an early overview of the observed and potential impacts of the COVID-19 on the environment. We argue that the effects of COVID-19 are determined mainly by anthropogenic factors which are becoming obvious as human activity diminishes across the planet, and the impacts on cities and public health will be continued in the coming years.


id: cord-299093-zp07aqpm
title: Mechanisms of SARS-CoV-2 transmission and pathogenesis
author: Harrison, Andrew G.
date: 2020-10-14
url: https://www.ncbi.nlm.nih.gov/pubmed/33132005/
doi: 10.1016/j.it.2020.10.004
abstract:
  The emergence of SARS-coronavirus 2 (SARS-CoV-2) marks the third highly pathogenic coronavirus to spill over into the human population. SARS-CoV-2 is highly transmissible with a broad tissue tropism that is likely perpetuating the pandemic. However, important questions remain regarding its transmissibility and pathogenesis. In this review, we summarize current SARS-CoV-2 research, with an emphasis on transmission, tissue tropism, viral pathogenesis, and immune antagonism. We further present advances in animal models that are important for understanding the pathogenesis of SARS-CoV-2, vaccine development, and therapeutic testing. When necessary, comparisons are made from studies with SARS to provide further perspectives on COVID-19, as well as draw inferences for future investigations.


id: cord-300170-s2qthxx4
author: Aven, Terje
date: 2020-10-15
url: https://doi.org/10.1016/j.ress.2020.107270
doi: 10.1016/j.ress.2020.107270
title:
  Globalization and global risk: How risk analysis needs to be enhanced to be effective in confronting current threats

abstract:
  In the last 20-30 years, technological innovation has enabled the advancement of industry at a global scale, giving rise to a truly global society, resting on an interdependent web of transnational technical, economic and social systems. These systems are exposed to scenarios of cascading outbreaks, whose impacts can ripple to very large scales through their strong interdependencies, as recently shown by the pandemic spreading of the Coronavirus. Considerable work has been conducted in recent years to develop frameworks to support the assessment, communication, management and governance of this type of risk, building on concepts like systemic risks, complexity theory, deep uncertainties, resilience engineering, adaptive management and black swans. Yet contemporary risk analysis struggles to provide authoritative societal guidance for adequately handling these types of risks, as clearly illustrated by the Coronavirus case. In this paper, we reflect on this situation. We aim to identify critical challenges in current frameworks of risk assessment and management and point to ways to strengthen these, to be better able to confront threats like the Coronavirus in the future. A set of principles and theses are established, which have the potential to support a common foundation for the many different scientific perspectives and ‘schools’ currently dealing with risk handling issues.


id: cord-300817-cxc00k0d
author: Saha, Jay
date: 2020-07-15
url: https://api.elsevier.com/content/article/pii/S026974912033966X
doi: 10.1016/j.envpol.2020.115250
title:
  Indoor air pollution (IAP) and pre-existing morbidities among under-5 children in India: are risk factors of coronavirus disease (COVID-19)?()

abstract:
  Globally, the Coronavirus disease (COVID-19) outbreak is linked with air pollution of both indoor and outdoor environments and co-morbidities conditions of human beings. To find out the risk factor zones associated with Coronavirus disease among under-five children using pre-existing morbidity conditions and indoor air pollution (IAP) environmental factors and also with current fatality and recovery rate of COVID-19 disease in India. Data was utilized from the 4th round of the National Family Health Survey (NFHS), 2015–16, and from the Ministry of Health and Family Welfare (MoHFW) on 18th May 2020. Mean, standard deviation, and Z-score statistical methods have been employed to find out the risk factor zones i.e. to execute the objective. Findings of this study are, the states and UTs which have more likely to very higher to higher risk factors or zones of Coronavirus disease (COVID-19) are Mizoram (1.4), Meghalaya (1.27), Uttarakhand (0.92), West Bengal (0.73), Uttar Pradesh (0.66), Jammu and Kashmir (0.44), Odisha (0.33), Madhya Pradesh (0.21), Jharkhand (0.20), Bihar (0.19), Maharashtra (0.16 risk score), compared to UTs like Assam (-0.12), Rajasthan (-0.13), Goa (-0.14), Manipur (-0.17), Chandigarh (-0.19), Haryana (-0.22), Delhi (-0.27) have moderate risk factors of COVID-19, and the states and UTs like Daman and Diu (-1.18), Sikkim (-0.98), Andaman and Nicobar Islands (-0.84), Kerala (-0.69), Dadra and Nagar Haveli (-0.68), Arunachal Pradesh ( 0.-53), Karnataka (-0.42), and Nagaland (-0.36) have very low-risk zones of COVID-19 deaths. From a research viewpoint, there is a prerequisite need for epidemiological studies to investigate the connection between indoor air pollution and pre-existing morbidity which are associated with COVID-19. Well-built public health measures, including rapidly searching in high focus areas and testing of COVID-19, should be performed in vulnerable areas of COVID-19.


id: cord-302471-all5j2od
title: Bovine coronavirus
author: Clark, M. A.
date: 1993-12-31
url: https://www.ncbi.nlm.nih.gov/pubmed/8382546/
doi: 10.1016/s0007-1935(05)80210-6
abstract:
  Summary This review aims to summarize current data describing the characteristics of bovine coronavirus (BCV) and the three clinical syndromes with which this virus is associated. The first half of this paper consists of a general description of the virus, commencing with a brief outline of the methods used for in vitro growth. The structure of the virus is then described in more detail, with particular reference to the structure and functions of the four major viral proteins. This is followed by an outline of the unique replication strategy adopted by coronaviruses. The second half of this review discusses the clinical significance of the virus, beginning with a detailed account of BCV-induced neonatal calf diarrhoea, the clinical syndrome with which this virus is most commonly associated. The clinical and epidemiological importance of BCV respiratory tract infection is then discussed, and finally the evidence supporting the aetiological role of BCV in outbreaks of winter dysentery in adult cattle is examined.


id: cord-303517-8971aq02
title: SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression
author: Cajamarca-Baron, Jairo
date: 2020-10-16
txt: ./txt/cord-303517-8971aq02.txt
cache: ./cache/cord-303517-8971aq02.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S2173574320301295
doi: 10.1016/j.reumae.2020.08.001
summary:
  27, 28 Among other comorbidities, chronic kidney disease is associated with in-hospital mortality, as are cancer and cerebrovascular disease, demonstrated through two meta-analyses that included over fifteen thousand patients ( Table 2) ; studies suggest that superficial fungal infections and psoriasis confer vulnerability to COVID-19; a body mass index (BMI) > 40 kg/m2 is an independent risk factor for complications from the infection; and there are discouraging results regarding underlying neurological disease and SARS-CoV-2. It is even possible that such disease-modifying therapies and their immunosuppressive effect may play a protective role during 19-COVID infection by preventing or dampening hyperimmune activity that, in some cases, could lead to clinical deterioration; there is even a report of a patient with primary progressive multiple sclerosis receiving treatment with ocrelizumab and becoming infected with SARS-CoV-2, in the context of lymphopenia and hypogammaglobulinema expected for this type of treatment, without generating major clinical complications, this hypothesis is obviously limited for now only to academic deductions and limited information.

abstract:
  Background It is not clear whether patients with some degree of immunosuppression have worse outcomes in SARS-CoV-2 infection, compared to healthy people. Objective To carry out a narrative review of the information available on infection by SARS-CoV-2 in immunosuppressed patients, especially patients with cancer, transplanted, neurological diseases, primary and secondary immunodeficiencies. Results Patients with cancer and recent cancer treatment (chemotherapy or surgery) and SARS-CoV-2 infection have a higher risk of worse outcomes. In transplant patients (renal, cardiac and hepatic), with neurological pathologies (multiple sclerosis (MS), neuromyelitis optica (NMODS), myasthenia gravis (MG)), primary immunodeficiencies and infection with human immunodeficiency virus (HIV) in association with immunosuppressants, studies have shown no tendency for worse outcomes. Conclusion Given the little evidence we have so far, the behaviour of SARS-CoV-2 infection in immunosuppressed patients is unclear, but current studies have not shown worse outcomes, except for patients with cancer.


id: cord-303523-m16vlv1q
title: MACHINE LEARNING PREDICTION FOR COVID 19 PANDEMIC IN INDIA
author: Ogundokun, R. O.
date: 2020-05-26
url: https://doi.org/10.1101/2020.05.20.20107847
doi: 10.1101/2020.05.20.20107847
abstract:
  Background: Coronavirus was detected in December 2019 in a bulk seafood shop in Wuhan, China. The original incident of COVID-19 pandemic in India was conveyed on 30th January 2020 instigating from the nation called china. As of 25th April 2020, the Ministry of Health and Family Welfare has established a total of 24, 942 incidents, 5, 210 recuperation including 1 relocation, and 779 demises in the republic. Objective: The objective of the paper is to formulate a simple average aggregated machine learning method to predict the number, size, and length of COVID-19 cases extent and wind-up period crosswise India. Method: This study examined the datasets via the Autoregressive Integrated Moving Average Model (ARIMA). The study also built a simple mean aggregated method established on the performance of 3 regression techniques such as Support Vector Regression (SVR, NN, and LR), Neural Network, and Linear Regression. Result: The results showed that COVID-19 disease can correctly be predicted. The result of the prediction shows that COVID-19 ailment could be conveyed through water and air ecological variables and so preventives measures such as social distancing, wearing of mask and hand gloves, staying at home can help to avert the circulation of the sickness thereby resulting in reduced active cases and even mortality. Conclusion: It was established that the projected method outperformed when likened to previously obtainable practical models on the bases of prediction precision. Hence, putting in place the preventive measures can effectively manage the spread of COVID-19, and also the death rate will be reduced and eventually be over in India and other nations.


id: cord-303917-2tu707ng
title: Potential interventions for novel coronavirus in China: A systematic review
author: Zhang, Lei
date: 2020-03-03
url: https://www.ncbi.nlm.nih.gov/pubmed/32052466/
doi: 10.1002/jmv.25707
abstract:
  An outbreak of a novel coronavirus (COVID‐19 or 2019‐CoV) infection has posed significant threats to international health and the economy. In the absence of treatment for this virus, there is an urgent need to find alternative methods to control the spread of disease. Here, we have conducted an online search for all treatment options related to coronavirus infections as well as some RNA‐virus infection and we have found that general treatments, coronavirus‐specific treatments, and antiviral treatments should be useful in fighting COVID‐19. We suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children's RNA‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. In addition, convalescent plasma should be given to COVID‐19 patients if it is available. In conclusion, we suggest that all the potential interventions be implemented to control the emerging COVID‐19 if the infection is uncontrollable.


id: cord-304295-3mpymd8a
title: Emergence of novel coronavirus and progress toward treatment and vaccine
author: Khan, Muhammad Muzamil
date: 2020-06-04
url: https://doi.org/10.1002/rmv.2116
doi: 10.1002/rmv.2116
abstract:
  In late December 2019, a group of patients was observed with pneumonia‐like symptoms that were linked with a wet market in Wuhan, China. The patients were found to have a novel coronavirus genetically related to a bat coronavirus that was termed SARS‐CoV‐2. The virus gradually spread worldwide and was declared a pandemic by WHO. Scientists have started trials on potential preventive and treatment options. Currently, there is no specific approved treatment for SARS‐CoV‐2, and various clinical trials are underway to explore better treatments. Some previously approved antiviral and other drugs have shown some in vitro activity. Here we summarize the fight against this novel coronavirus with particular focus on the different treatment options and clinical trials exploring treatment as well as work done toward development of vaccines.


id: cord-305266-fuaq4ujb
title: Early Research on COVID-19: A Bibliometric Analysis
author: Gong, Yue
date: 2020-08-05
url: https://www.sciencedirect.com/science/article/pii/S2666675820300278?v=s5
doi: 10.1016/j.xinn.2020.100027
abstract:
  Abstract In December 2019, an outbreak of pneumonia, which was named COVID-2019, emerged as a global health crisis. Scientists worldwide are engaged in attempts to elucidate the transmission and pathogenic mechanisms of the causative coronavirus. COVID-19 was declared a pandemic by the World Health Organization in March 2020, making it critical to track and review the state of research on COVID-19 to provide guidance for further investigations. Here, bibliometric and knowledge mapping analyses of studies on COVID-19 were performed, including more than 1500 papers on COVID-19 available in the PubMed and CNKI databases from January 1, 2020 to March 8, 2020. In this review, we found that because of the rapid response of researchers worldwide, the number of COVID-19-related publications showed a high growth trend in the first ten days of February; among these, the largest number of studies originated in China, the country most affected by pandemic in its early stages. Our findings revealed that the epidemic situation and data accessibility of different research teams have caused obvious difference in emphases of the publications. Besides, there was an unprecedented level of close cooperation and information sharing within the global scientific community relative to previous coronavirus research. We combed and drew the knowledge map of the SARS-CoV-2 literature, explored early status of research on etiology, pathology, epidemiology, treatment, prevention, and control, and discussed knowledge gaps that remain to be urgently addressed. Future perspectives on treatment, prevention, and control were also presented to provide fundamental references for current and future coronavirus research.


id: cord-305422-t8azymo7
title: COVID-19: what has been learned and to be learned about the novel coronavirus disease
author: Yi, Ye
date: 2020-03-15
txt: ./txt/cord-305422-t8azymo7.txt
cache: ./cache/cord-305422-t8azymo7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32226295/
doi: 10.7150/ijbs.45134
summary:
  The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. The virus is highly homologous to the coronavirus (CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003; thus, it was named SARS-CoV-2 by the World Health Organization (WHO) on February 11, 2020, and the associated disease was named CoV Disease-19 (COVID-19) [1] . Whenever possible, we will try to compare COVID-19 with SARS and another CoV-caused disease, Middle East respiratory syndrome (MERS, an outbreak in 2012). Due to the lack of experience with the novel CoV, physicians can mainly provide supportive care to COVID-19 patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other CoVs such as SARS-CoV and MERS-CoV and other viral diseases ( Table 2) .

abstract:
  The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. Similar to its homologous virus, SARS-CoV, which caused SARS in thousands of people in 2003, SARS-CoV-2 might also be transmitted from the bats and causes similar symptoms through a similar mechanism. However, COVID-19 has lower severity and mortality than SARS but is much more transmissive and affects more elderly individuals than youth and more men than women. In response to the rapidly increasing number of publications on the emerging disease, this article attempts to provide a timely and comprehensive review of the swiftly developing research subject. We will cover the basics about the epidemiology, etiology, virology, diagnosis, treatment, prognosis, and prevention of the disease. Although many questions still require answers, we hope that this review helps in the understanding and eradication of the threatening disease.


id: cord-306465-7kevsl1z
title: Study and Overview of the Novel Corona Virus Disease (COVID-19)
author: Agarwal, Krishna Mohan
date: 2020-09-06
txt: ./txt/cord-306465-7kevsl1z.txt
cache: ./cache/cord-306465-7kevsl1z.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S2666351120300371?v=s5
doi: 10.1016/j.sintl.2020.100037
summary:
  In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. The current global pandemic is caused by the "novel coronavirus disease (2019-nCoV) or severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) popularly known as COVID19 Hunan seafood market was sealed, on 7 th January roughly a week after China''s notification of a possible outbreak the disease was confirmed to be the novel coronavirus disease or COVID-19 which has more than 95% homology with bat coronavirus and almost 70% similarity to the SARS CoV-1 Flatten the curve is a statement used during healthcare emergencies, its basic concept is to limit the spread of the virus such that at any given time during a pandemic the total number of patients required to be hospitalized is less than the maximum capacity of the state''s health infrastructure.

abstract:
  In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. Within a span of a few days, this disease became a global threat and was termed as a pandemic by the World Health Organization (WHO) on 11th March 2020, since then the disease has affected more than 1.5 crore people worldwide and around 6.9 lakh people in India as of 5th July 2020. The origin of the COVID-19 disease has been traced back to the bats, but the intermediary contact is unknown. The disease spreads by respiratory droplets and contaminated surfaces. In most cases, the virus shows mild symptoms like fever, fatigue, dyspnea, cough, etc. which may become severe if appropriate precautions are not adhered to. For people with comorbidities (usually elderly) the disease may turn deadly and cause pneumonia, Acute Respiratory Disease Syndrome (ARDS), and multi-organ failure, thereby affecting a person's ability to breathe leading to being put on the ventilator support. The reproduction number (Rℴ) of COVID-19 is much higher than its predecessors and genetically similar diseases like SARS-CoV and MERS-CoV. This paper discusses the epidemiological characteristics of the SARS-CoV-2 virus, its phylogenetic relationship with the previous pandemic causing viruses such as SARS-CoV-1 and MERS-CoV and analyzes the various responses to this global pandemic worldwide, focusing on the actions taken by India and their outcomes.


id: cord-308537-i6um5iu2
title: Coronavirus Infection in Cats
author: Hoskins, Johnny D.
date: 1993-01-31
txt: ./txt/cord-308537-i6um5iu2.txt
cache: ./cache/cord-308537-i6um5iu2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/8380655/
doi: 10.1016/s0195-5616(93)50001-3
summary:
  Cats are susceptible to natural infection with several strains of feline coronavirus that result in either effusive and noneffusive feline infectious peritonitis or enteritis. 33 Most asymptomatic cats with positive coronavirus-antibody titers have been previously infected by strains of feline enteric coronavirus or FIP coronavirus, which usually do not cause fatal disease by natural routes of infection. The susceptibility of cats to FIP disease may involve several predisposing factors, including age at time of exposure, genetic susceptibility, physical condition, stress, presence of concurrent disease (especially feline leukemia virus and feline immunodeficiency virus infections), challenge dose and strain of feline coronavirus, route of infection, previous sensitization with nonprotective corona virus antibodies, and cell-mediated immunocompetence. Cats are susceptible to natural infection with several strains of feline coronavirus that may result in either effusive and noneffusive FIP disease or in subclinical to severe enteritis.

abstract:
  Cats are susceptible to natural infection with several strains of feline coronavirus that result in either effusive and noneffusive feline infectious peritonitis or enteritis. Excretion of coronavirus by infected cats into the environment occurs by way of feces, oronasal secretions, and possibly urine. Clinical diagnosis of coronavirus infection is made by evaluating the case history, physical findings, laboratory results, and coronavirus antibody titers as well as ruling out analogous diseases. An intranasal temperature-sensitive feline infectious peritonitis coronavirus vaccine is available for use in healthy cats 16 weeks of age or older.


id: cord-308857-otsrexqu
author: Goel, Saurav
date: 2020-05-28
url: https://www.sciencedirect.com/science/article/pii/S2468519420300604?v=s5
doi: 10.1016/j.mtchem.2020.100300
title:
  Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic

abstract:
  The world is witnessing tumultuous times as major economic powers including the US, UK, Russia, India, and most of Europe continue to be in a state of lockdown. The worst-hit sectors due to this lockdown are sales, production (manufacturing), transport (aerospace and automotive) and tourism. Lockdowns became necessary as a preventive measure to avoid the spread of the contagious and infectious “Coronavirus Disease 2019” (COVID-19). This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. We also offer perspectives on future considerations on climate change, outsourced versus indigenous manufacturing, automation, and antimicrobial resistance. Overall, this paper attempts to identify key areas where manufacturing can be employed to address societal challenges such as COVID-19.


id: cord-311847-2czqs84q
title: SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms
author: Pennisi, Manuela
date: 2020-07-31
txt: ./txt/cord-311847-2czqs84q.txt
cache: ./cache/cord-311847-2czqs84q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32751841/
doi: 10.3390/ijms21155475
summary:
  Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). Although there are limitations in the epidemiological studies carried on COVID-19, as well as limited case records for determining the actual incidence of these complications, some patients reported neurological symptoms, but clinical findings and pathogenic features have not yet systematically addressed. The aims of this review are i) to summarize the available information on the relationship between CoVs and the nervous system, ii) to identify the potential targets and routes of entry of SARS-CoV-2 into the nervous system, and iii) to describe the range of the neurological features reported to date in patients with COVID-19 and the proposed pathogenic mechanisms. Indeed, no axonal transport of SARS-CoV-2 to the brain has been demonstrated in the hamster model during the first two weeks after infection [89] , and no viral accumulation or persistence has been reported in cerebral olfactory regions of autopsy material from patients with COVID-19 [90] .

abstract:
  Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). However, findings available on its neurological manifestations and their pathogenic mechanisms have not yet been systematically addressed. A literature search on neurological complications reported in patients with COVID-19 until June 2020 produced a total of 23 studies. Overall, these papers report that patients may exhibit a wide range of neurological manifestations, including encephalopathy, encephalitis, seizures, cerebrovascular events, acute polyneuropathy, headache, hypogeusia, and hyposmia, as well as some non-specific symptoms. Whether these features can be an indirect and unspecific consequence of the pulmonary disease or a generalized inflammatory state on the CNS remains to be determined; also, they may rather reflect direct SARS-CoV-2-related neuronal damage. Hematogenous versus transsynaptic propagation, the role of the angiotensin II converting enzyme receptor-2, the spread across the blood-brain barrier, the impact of the hyperimmune response (the so-called “cytokine storm”), and the possibility of virus persistence within some CNS resident cells are still debated. The different levels and severity of neurotropism and neurovirulence in patients with COVID-19 might be explained by a combination of viral and host factors and by their interaction.


id: cord-312178-tojgojjf
title: Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known?
author: Segars, James
date: 2020-04-16
txt: ./txt/cord-312178-tojgojjf.txt
cache: ./cache/cord-312178-tojgojjf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32482250/
doi: 10.1016/j.fertnstert.2020.04.025
summary:
  Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a pandemic of Coronavirus Disease 2019 (COVID-19) across the globe. The novel SARS-CoV-2 virus spreads rapidly, with 2-3 people infected from every index case, a reproduction number (R 0 ) or transmission rate of 2.24 -3.58 (2) . The aim of this review is to summarize what is currently known about the impact of prior coronaviruses and the novel SARS-CoV-2 infection on reproduction and pregnancy. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: Report of two cases & review of the literature An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes

abstract:
  Structured Abstract Objective To summarize current understanding of the effects of novel and prior coronaviruses on human reproduction, specifically male and female gametes, and in pregnancy. Design Review of English publications in PubMed and Embase to April 6, 2020. Methods Manuscripts were screened for reports including coronavirus, reproduction, including pathophysiology and pregnancy. Intervention(s) None. Main Outcome Measure(s) Reproductive outcomes; effects on gametes; pregnancy outcomes; neonatal complications. Results Seventy-nine reports formed the basis of the review. Coronavirus binding to cells involves the S1 domain of the spike protein to receptors present in reproductive tissues, including angiotensin converting enzyme-2 (ACE2), CD26, Ezrin, and cyclophilins. SARS-CoV-1 may cause severe orchitis leading to germ cell destruction in males. Reports indicate decreased sperm concentration and motility for 72-90 days following COVID-19 infection. Gonadotropin-dependent expression of ACE2 was found in human ovaries, but it is unclear whether SARS-CoV-2 adversely affects female gametogenesis. Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. COVID-19 infections in pregnancy are associated with preterm delivery. Postpartum neonatal transmission from mother to child has been reported. Conclusion COVID-19 infection may adversely affect some pregnant women and their offspring. Additional studies are needed to assess effects of SARS-CoV-2 infection on male and female fertility.


id: cord-312434-yx24golq
author: Deng, Ziqin
date: 2020-09-23
url: https://doi.org/10.3389/fcimb.2020.581404
doi: 10.3389/fcimb.2020.581404
title:
  Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research

abstract:
  Human coronaviruses, which can cause a range of infectious diseases, have been studied for nearly 60 years. The field has gained renewed interest from researchers around the world due to the COVID-19 outbreak in late 2019. Despite a large amount of research, little is known about the knowledge structure and developing trends of this topic. Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. The results show that research on human coronavirus is dominated by SARS-CoV. Although there have been many publications, only 626 publications (4.1% of total) have more than 100 citations. The top 20 journals with most publications account for 20.6% of total publications and 41% of total citations. In addition to the United States and some European countries, many Asian and African countries are involved in this research, with China holding an important position in this area. Leading researchers from various fields of human coronavirus research are listed to facilitate collaboration and promote effective disease prevention and control. The keywords co-occurrence analysis reveals that the research focus on virology, public health, drugs and other hotspot fields, and uncovers changes in the direction of coronavirus research. The research map on human coronavirus obtained by our analysis are expected to help researchers to efficiently and effectively explore COVID-19.


id: cord-312741-0au4nctt
title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment
author: Lin, Panpan
date: 2020-10-01
txt: ./txt/cord-312741-0au4nctt.txt
cache: ./cache/cord-312741-0au4nctt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33173860/
doi: 10.1002/mco2.26
summary:
  160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein

abstract:
  Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single‐stranded RNA virus. Human coronavirus (HCoV) strains (HCoV‐229E, HCoV‐OC43, HCoV‐HKU1, HCoV‐NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID‐19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections.


id: cord-315598-qwh72inx
author: Mendoza, Jose Luis Accini
date: 2020-10-06
txt: ./txt/cord-315598-qwh72inx.txt
cache: ./cache/cord-315598-qwh72inx.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5
doi: 10.1016/j.acci.2020.09.004
summary:
  De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400).

title:
  ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19

abstract:
  Antecedentes y objetivos: La enfermedad por coronavirus de 2019 (COVID-19) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (SARS-CoV-2). Se identificó por primera vez en diciembre de 2019 en la ciudad de Wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la Organización Mundial de la Salud (OMS), la reconoció como una pandemia global el 11 de marzo de 2020. La mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. Este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la Asociación Colombiana de Medicina Crítica (AMCI) para el manejo del paciente críticamente enfermo con COVID-19 dentro de las áreas críticas de las instituciones de salud. Métodos: Este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: Delphi modificada y grupos nominales. Se construyeron preguntas por la estrategia PICO. 10 grupos nominales desarrollaron recomendaciones para cada unidad temática. El producto del consenso fue evaluado y calificado en una ronda Delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con COID-19. Resultados: 80 expertos nacionales participaron en la actualización del consenso AMCI, especialistas en Medicina Critica y Cuidados Intensivos, Nefrología, Neurología, Neumología, bioeticistas, Medicina interna, Anestesia, Cirugía General, Cirugía de cabeza y cuello, Cuidados Paliativos, Enfermeras Especialistas en Medicina crítica, Terapeutas respiratorias especialistas en medicina crítica y Fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. La declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de COVID-19 al interior de las unidades de cuidados intensivos en el contexto nacional de Colombia. Conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con COVID-19. Las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. Background and objectives: The 2019 coronavirus disease (COVID-19) is caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2). It was first identified in December 2019 in Wuhan, China. In the following months it spread quickly to all continents and was recognised as a global pandemic by the World Health Organization (WHO) on March 11th, 2020. Most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. This consensus aims to update the initial statement issued by the Colombian Association of Critical Medicine (AMCI) for the management of the critically ill patient with COVID-19 within the critical areas of health institutions. Methods: This study used two formal consensus techniques to construct the final recommendations: modified Delphi and nominal groups. Questions were constructed using the PICO strategy. Recommendations for each thematic unit were developed by 10 nominal groups. The consensus product was evaluated and qualified in a Delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with COVID-19. Results: A total of 80 national experts participated in the update of the AMCI consensus, all specialists in Critical and Intensive Care Medicine, Nephrologists, Neurologists, Chest physician, bioethicists, Internal medicine specialists, Anaesthetists, General Surgeons, head and neck surgery, palliative care, Nurses Specialised in Critical Medicine, Respiratory therapists specialised in critical medicine and Physiotherapy, with clinical experience in the care of critically ill patients. This update issues recommendations in the most relevant areas for health care of COVID-19 patients within the intensive care units, contextualised for Colombia. Conclusions: A significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with COVID-19 through formal consensus techniques. Recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country.


id: cord-315619-gowtohr8
author: Cox, Rebecca C.
date: 2020-09-22
url: https://doi.org/10.1016/j.janxdis.2020.102315
doi: 10.1016/j.janxdis.2020.102315
title:
  Pre-pandemic disgust proneness predicts increased coronavirus anxiety and safety behaviors: Evidence for a diathesis-stress model

abstract:
  Although health anxiety and corresponding safety behaviors can facilitate disease transmission avoidance, they can be maladaptive in excess, including during the coronavirus pandemic. Disgust proneness (i.e., tendency to experience and be sensitive to disgust) is one factor that may predict elevated coronavirus anxiety and safety behaviors during the pandemic, given the role of disgust in avoiding disease transmission. The present study examined the relations between pre-pandemic disgust proneness and coronavirus anxiety and safety behaviors in community adults who completed a 2016 study and were re-contacted on 4/1/2020 (N = 360). Interactions between pre-pandemic disgust proneness and current perceived stress were tested to examine a diathesis-stress model of the role of disgust proneness in anxiety response to the pandemic. Increased pre-pandemic disgust proneness predicted increased coronavirus anxiety and safety behaviors, controlling for number of COVID-19 cases by state. Consistent with a diathesis-stress model, current perceived stress moderated this effect, such that highest coronavirus anxiety and safety behaviors were reported by those with high disgust proneness and high stress. Trait disgust proneness may be a vulnerability factor for anxiety responses to the coronavirus pandemic, particularly among individuals experiencing high stress. Assessing disgust proneness and current stress may facilitate targeted anxiety intervention during the pandemic.


id: cord-318392-r9bbomvk
author: Woo, Patrick CY
date: 2017-06-21
url: https://www.ncbi.nlm.nih.gov/pubmed/28634353/
doi: 10.1038/emi.2017.37
title:
  Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region

abstract:
  Coronavirus HKU15 is a deltacoronavirus that was discovered in fecal samples of pigs in Hong Kong in 2012. Over the past three years, Coronavirus HKU15 has been widely detected in pigs in East/Southeast Asia and North America and has been associated with fatal outbreaks. In all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. In this molecular epidemiology study, we detected Coronavirus HKU15 in 9.6% of the nasopharyngeal samples obtained from 249 pigs in Hong Kong. Samples that tested positive were mostly collected during winter. Complete genome sequencing of the Coronavirus HKU15 in two nasopharyngeal samples revealed quasispecies in one of the samples. Two of the polymorphic sites involved indels, but the other two involved transition substitutions. Phylogenetic analysis showed that the two nasopharyngeal strains in the present study were most closely related to the strains PDCoV/CHJXNI2/2015 from Jiangxi, China, and CH/Sichuan/S27/2012 from Sichuan, China. The outbreak strains in the United States possessed highly similar genome sequences and were clustered monophyletically, whereas the Asian strains were more diverse and paraphyletic. The detection of Coronavirus HKU15 in respiratory tracts of pigs implies that in addition to enteric infections, Coronavirus HKU15 may be able to cause respiratory infections in pigs and that in addition to fecal-oral transmission, the virus could possibly spread through the respiratory route. The presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. Quasispecies were unprecedentedly observed in the 5′-untranslated region of coronavirus genomes.


id: cord-318492-uu1p1rgi
title: COVID-19: Brief Check Point Through The Pathologist's Eye (autopsy archive)
author: Mansueto, Gelsomina
date: 2020-08-28
url: https://www.sciencedirect.com/science/article/pii/S0344033820320501?v=s5
doi: 10.1016/j.prp.2020.153195
abstract:
  During the COVID-19 pandemic many deaths have been caused, especially of patients with cardiovascular comorbidities and old age. Many questions have been asked and few simple answers have been given. The autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (DAD), myocarditis, acute myocardial infarction (AMI), and disseminated intravascular coagulation (DIC); these aspects are not only in COVID-19 but also in other viral infections and associated sepsis. We must not lose sight of the fact that coronavirus with its pathological organ changes have already been described in the years preceding the pandemic.


id: cord-319578-n1ee1688
title: COVID-19 target: A specific target for novel coronavirus detection
author: Kakhki, Reza Kamali
date: 2020-05-30
txt: ./txt/cord-319578-n1ee1688.txt
cache: ./cache/cord-319578-n1ee1688.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.genrep.2020.100740
doi: 10.1016/j.genrep.2020.100740
summary:
  Although molecular methods such as RT-PCR and real-time PCR are among the most common procedures in detecting coronavirus, the use of specific targets still is the first critical step in the accurate diagnosis of the agent. The present study aimed to introduce a novel specific target and evaluate the known target genes in order to analyze COVID-19 bioinformatically. In this study, COVID-19 novel target was detected using the modified comparative genomic analysis (Kakhki, Najafzadeh, Kachuei, & Ghazvini, 2020; Kakhki et al., 2019; Neshani et al., 2018) . Afterwards, the specificity of the primers was determined bioinformatically using BLAST software for all databases to check any cross-reactivity with other bacterial or human genomes. We also designed a specific probe (K_COV-P1) for the novel Coronavirus to differentiate COVID-19 from all other human coronaviruses. The short-chain dehydrogenases/reductases (SDR) gene: A new specific target for rapid detection of Mycobacterium tuberculosis complex by modified comparative genomic analysis.

abstract:
  An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. We, for the first time, detected ORF8 gene as a potential target for the detection of the novel coronavirus. Unlike previous reported genes (RdRP, E and N genes), ORF8 is entirely specific to the novel coronavirus (COVID-19) and has no cross-reactivity with other kinds of coronavirus. Accordingly, ORF8 gene can be used as an additional confirmatory assay.


id: cord-319983-e4f2sfl4
title: The COVID-19: Current understanding
author: Tripathi, Shweta
date: 2020-09-26
txt: ./txt/cord-319983-e4f2sfl4.txt
cache: ./cache/cord-319983-e4f2sfl4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33132617/
doi: 10.14202/vetworld.2020.1998-2005
summary:
  Till the date of writing this article (August 15, 2020), a total number of 2526192+65002 laboratory-confirmed cases of COVID-19 from 35 states and Union Territories, out of which 1,915,580 (71.91%) recovered, while 50,924 (1.93%) deaths are reported in India [8, 10] . According to the Ministry of Family and Health Welfare of India; a suspected case is defined as a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, and shortness of breath) and a history of travel to or residence in a location reporting community transmission of COVID-19, 14 days prior of the beginning of symptoms. However, more clinical trials are needed to prove the safety and effectiveness of convalescent plasma transfusion in SARS-CoV-2 infected patients [48] . Epidemiological and clinical characteristics of 99 cases of 2019 novel Coronavirus pneumonia in Wuhan, China: A descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel Coronavirus-infected pneumonia in Wuhan, China

abstract:
  In December 2019, China reported several cases of a new coronavirus disease (COVID-19). The COVID-19 outbreak, which was initially limited to Wuhan, China, has rapidly spread worldwide. Infection of the disease occurs through exposure to the virus through inhalation of respiratory droplets or if a person touches a mucosal surface after touching an object with the virus on it. The common symptoms of COVID-19 are fever, dry cough, dyspnea (difficult or labored breathing), fatigue, chest pain, and myalgia (muscle pain), etc. Real-time polymerase chain reaction is used to detect the virus in sputum, throat, nasal swabs, and secretion of lower respiratory samples. Early diagnosis, isolation, and supportive care are necessary for the treatment of the patients. The present review aims to provide recent information on COVID-19 related to its epidemiology, clinical symptoms, and management. This article also summarizes the current understanding of severe acute respiratory syndrome coronavirus-2 and its history of origin.


id: cord-320955-xhp96abg
author: Allam, Zaheer
date: 2020-07-24
url: https://api.elsevier.com/content/article/pii/B9780128243138000012
doi: 10.1016/b978-0-12-824313-8.00001-2
title:
  The First 50 days of COVID-19: A Detailed Chronological Timeline and Extensive Review of Literature Documenting the Pandemic

abstract:
  This chapter surveys the global unfolding of events during the first 50 days of the COVID-19 pandemic in China. An extensive review of literature from both academic and popular sources provides a daily overview of the situation covering health, economic, political, and social perspectives and outlines the major course of actions. This chapter surveys, and lays, the chronological timeline of the outbreak, health policy, deaths, recovery, and socioeconomic measures and provides a factual narrative on the unfolding of the pandemic and, while doing so, underlines major milestones and contradictory findings and beliefs on the subject. This supports the perception that data collection varied between research groups, organizations, and national bodies, which later fueled differing viewpoints and policies for combatting the outbreak.


id: cord-321194-xi4zy5ow
author: Allam, Zaheer
date: 2020-07-24
url: https://api.elsevier.com/content/article/pii/B9780128243138000036
doi: 10.1016/b978-0-12-824313-8.00003-6
title:
  The Third 50 Days: A Detailed Chronological Timeline and Extensive Review of Literature Documenting the COVID-19 Pandemic From Day 100 to Day 150

abstract:
  This chapter surveys the global unfolding of events during the third 50 days of the COVID-19 pandemic that originated from China. The third 50 days of the unfolding of the events showcased how city-wide lockdowns were started to be considered globally, the moving of the epicenter from China to Europe, and major industries being impacted worldwide. To document this, an extensive review of the literature provides a daily overview of the situation covering health, economic, political, and social perspectives and outlines key events during the unfolding of the pandemic. This chapter surveys, and establishes a chronological timeline of the outbreak from day 50 to day 100, covering issues appertaining to health policy and dwells into socioeconomic measures and impacts during the unfolding of the pandemic.


id: cord-321259-wio2b49i
title: Digesting the crisis: autophagy and coronaviruses
author: Carmona-Gutierrez, Didac
date: 2020-05-04
txt: ./txt/cord-321259-wio2b49i.txt
cache: ./cache/cord-321259-wio2b49i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.15698/mic2020.05.715
doi: 10.15698/mic2020.05.715
summary:
  Of note, cellular manipulation of autophagic levels during infection may also reflect desperate attempts of the cell to reestablish homeostasis, either through restriction of viral entry by actively shunting endocytosis/endosomal trafficking (possibly resulting in autophagy reduction as a sideeffect) [39] or to counteract virally induced cell death by increasing cytoprotective autophagy. Thus, the group-specific accessory proteins, which by definition are not essential for viral replication but are involved in the modulation of host cells and immune evasion [66, 67] , may represent targets for reducing the autophagy-inhibitory effects of CoVs. The FDA-approved anti-malarial drugs chloroquine and hydroxychloroquine have been suggested to be repurposed for the treatment of COVID-19 [68] [69] [70] , but this remains widely controversial [71] [72] [73] . Intriguingly, another recent preprint presents in vitro data showing that SARS-CoV-2 infection restricts autophagy and that, in turn, pro-autophagic compounds -including spermidine -may inhibit viral propagation [85] .

abstract:
  Autophagy is a catabolic pathway with multifaceted roles in cellular homeostasis. This process is also involved in the antiviral response at multiple levels, including the direct elimination of intruding viruses (virophagy), the presentation of viral antigens, the fitness of immune cells, and the inhibition of excessive inflammatory reactions. In line with its central role in immunity, viruses have evolved mechanisms to interfere with or to evade the autophagic process, and in some cases, even to harness autophagy or constituents of the autophagic machinery for their replication. Given the devastating consequences of the current COVID-19 pandemic, the question arises whether manipulating autophagy might be an expedient approach to fight the novel coronavirus SARS-CoV-2. In this piece, we provide a short overview of the evidence linking autophagy to coronaviruses and discuss whether such links may provide actionable targets for therapeutic interventions.


id: cord-321670-f2d4bykp
title: Perinatale Aspekte der SARS-CoV-2 Infektion
author: Longardt, Ann Carolin
date: 2020-08-24
txt: ./txt/cord-321670-f2d4bykp.txt
cache: ./cache/cord-321670-f2d4bykp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32838447/
doi: 10.1055/a-1192-7437
summary:
  In einer Studie aus den 50 Kliniken in Wuhan wurden 118 Frauen mit COVID-19 zwischen Dezember 2019 und März 2020 erfasst; 109 zeigten einen milden Verlauf und 9 (8 %) einen schweren Verlauf mit Hypoxämie, eine hiervon wurde beatmet. Abgesehen davon, dass das Virus selten im Blut detektiert wurde, stellt sich auch die Frage nach der Expres sion des SARS-CoV-2-Rezeptors ACE2 im Bereich der maternofetalen Grenzfläche beziehungsweise in der Plazenta. Gesichert ist der Infektionsweg durch eine SARS-CoV-2-Übertragung über die Muttermilch damit jedoch nicht. Anzunehmen ist aber auch die Weitergabe von SARSCoV2Antikörpern über die Muttermilch an das Kind, was den klinischen Verlauf einer kindlichen Infektion positiv beeinflussen könnte, ähnlich wie es bei der SARS-Epidemie 2002/2003 berichtet wurde [42] . Vertical Transmission of Coronavirus Disease 19 (COVID-19) from Infected Pregnant Mothers to Neonates: A Review An Analysis of 38 Pregnant Women with COVID19, Their Newborn Infants, and MaternalFetal Transmission of SARS CoV2: Maternal Coronavirus Infections and Pregnancy Outcomes

abstract:
  The novel coronavirus SARS-CoV-2 has developed into a pandemic, yet still has many unknowns. The modalities of transmission, different symptoms and manifestations as well as concomitant circumstances of the disease are insufficiently characterized. Especially patient groups in special situations like pregnant women and newborns have to be considered separately. The current knowledge about pregnancy, labor and the first days of life is characterized by particular uncertainty due to the scarce data available. However, there is currently no evidence of significant unfavorable maternal and perinatal outcome. Many pregnant women with SARS-CoV-2 infection remain asymptomatic. The possibility of vertical transmission to the child cannot be excluded with certainty. However, indications of vertical transmission were detected only in individual cases. Newborn infections are also rather rare, unspecific and usually mild, with respiratory symptoms dominating. In this article, the data available to date are examined in order to provide better information, advice and treatment for pregnant women and newborns with SARS-CoV-2 and to provide suggestions for future research.


id: cord-322456-5at1euqm
title: Die Rolle der Augenheilkunde in der COVID-19-Pandemie
author: Rokohl, Alexander C.
date: 2020-06-09
txt: ./txt/cord-322456-5at1euqm.txt
cache: ./cache/cord-322456-5at1euqm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32519117/
doi: 10.1007/s00347-020-01148-9
summary:
  Im Dezember 2019 wurde Dr. Li Wenliang, ein Augenarzt aus der Volksrepublik China, in seinem Krankenhaus auf 7 Patienten, die alle unter einem schweren akuten Atemnotsyndrom litten und vorher einen Großmarkt in Wuhan besuchten, aufmerksam. Das COVID-19 auslösende Severe-Acute-Respiratory-Syndrome-related Coronavirus-2 (SARS-CoV-2) wurde durch die Coronavirus-Studiengruppe des Internationalen Komitees zur Taxonomie von Viren (International Committee on Taxonomy of Viruses) aufgrund der sehr engen Verwandtschaft zum Sars-Virus (Sars-CoV), an dem 2002/2003 Hunderte Menschen gestorben waren, benannt. Auch Dr. Li Wenliang, der Augenarzt, der die COVID-19 als einer der Ersten entdeckte und später auch an der Krankheit verstarb, könnte von einem asymptomatischen Patienten infiziert worden sein [23] . Zudem konnte in mehreren Studien mit hospitalisierten COVID-19-Patienten SARS-CoV-2-RNA in der Tränenflüssigkeit nachgewiesen werden [2, 28, 30, 32] . Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV-2.

abstract:
  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 19 (COVID-19) has led to a worldwide pandemic. This pandemic presents a huge challenge for the healthcare system and also for ophthalmologists. Previous studies and case reports indicated that SARS-CoV‑2 also infects the conjunctiva resulting in conjunctivitis. In addition, infectious virus particles in the tear fluid can be potential sources of infection; however, the detection of SARS-CoV‑2 RNA in the tear fluid has rarely been successful. Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV‑2. Therefore, protective and hygiene measures should currently be consistently followed to minimize the risk of spreading the virus. Currently, there are no treatment recommendations for conjunctivitis associated with COVID-19. Tear substitutes might be helpful for symptom relief but there is no evidence for a topical antiviral therapy. In the future ophthalmologists could play a decisive role in the screening of maculopathies that might occur during COVID-19 treatment using chloroquine or hydroxychloroquine.


id: cord-322908-e3gok0ot
title: A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19)
author: Huang, Fangfang
date: 2020-05-20
url: https://www.sciencedirect.com/science/article/pii/S1043661820312378?v=s5
doi: 10.1016/j.phrs.2020.104929
abstract:
  The epidemic of pneumonia (COVID-19) caused by novel coronavirus (SARS-CoV-2) infection has been listed as a public health emergency of international concern by the World Health Organization (WHO), and its harm degree is defined as a global “pandemic”. At present, the efforts of various countries focus on the rapid diagnosis and isolation of patients, as well as to find a treatment that can combat the most serious impact of the disease. The number of reported COVID-19 virus infections is still increasing. Unfortunately, no drugs or vaccines have been approved for the treatment of human coronaviruses, but there is an urgent need for in-depth research on emerging human infectious coronaviruses. Clarification transmission routes and pathogenic mechanisms, and identification of potential drug treatment targets will promote the development of effective prevention and treatment measures. In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. This review summarizes the epidemiological characteristics, pathogenesis, virus structure and targeting strategies of COVID-19. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19.


id: cord-322980-rembksdr
title: Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020
author: Talwar, Shivangi
date: 2020-10-22
txt: ./txt/cord-322980-rembksdr.txt
cache: ./cache/cord-322980-rembksdr.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s40495-020-00245-2
doi: 10.1007/s40495-020-00245-2
summary:
  The severe acute respiratory syndrome coronavirus (SARS-CoV-2019) emerged in 2019 in the month of December in Wuhan city of China, which again made the life of humans miserable with numerous fatal health issues and slowly and gradually this virus entrapped the whole world [2, 3] . Before the doctors, scientists, and researchers could study and come up with a cure for treatment, this virus had already infected more than lakhs of people across the world with the human coronavirus pathogens, i.e., HCoV-22E and HCoV-OC43, which affects the upper respiratory tract. Because of broad reach, presently, remdesivir and its in vitro studies against coronavirus help in treating SARS-CoV-2 with EC50 and EC90 estimations of 0.77 μM and 1.76 μM, respectively, and are proved to be a fruitful expected treatment for COVID-19 [ 

abstract:
  PURPOSE OF REVIEW: In the last month of 2019, i.e., December, COVID-19 hit Wuhan city in China. Since then, it has infected more than 210 countries and nearly about 33.4 million people with one million deaths globally. It is a viral disease with flu-like symptoms; hence, prevention and management is the best option to be adopted for its cure. RECENT FINDINGS: Many healthcare systems, scientists, and researchers are fighting for the cure of this pandemic. Ayurvedic and allopathic treatments have been studied extensively and approached for the cure of COVID-19. In addition to ayurvedic treatments, the Ministry of Ayush, India, has also recommended many remedies to boost up immunity. Allopathic studies involved several antiviral drugs which were used in different combinations for the treatment of COVID-19. SUMMARY: Comparative analysis of Ayurveda and allopathic treatment strategies were carried out in the present study. Depending upon the patient’s conditions and symptoms, Ayurveda is useful for the treatment of COVID-19. Allopathic treatments inhibit viral infection by targeting majorly endocytosis, and angiotensin-converting enzyme (Ace) receptor signaling. In this article, we summarize different ayurvedic and allopathic medicines and treatment strategies which have been used for the treatment of COVID-19, a global pandemic.


id: cord-323618-d09b65gd
title: Coronavirus humains (HCoV)
author: Vabret, A.
date: 2008-05-05
txt: ./txt/cord-323618-d09b65gd.txt
cache: ./cache/cord-323618-d09b65gd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18456429/
doi: 10.1016/j.patbio.2008.02.018
summary:
  La survenue récente, en 2002 à 2003, de l''épidémie de SRAS (ou syndrome respiratoire aigu sévère), et l''identification de l''agent pathogène responsable, un coronavirus émergent dans la population humaine, ont conduit à un vif regain d''intérêt et une intensification importante des recherches sur ces virus. Certaines données expérimentales sont inattendues : malgré des séquences en aminoacides conservées au niveau de la protéine S1 des HCoV 229E et NL63, ces deux coronavirus humains utilisent des récepteurs différents (APN et ACE2, respectivement) ; par ailleurs, le SARS-CoV utilise le même récepteur cellulaire que NL63 alors que les séquences S1 sont éloignées, cependant le RBD des deux virus semble proche et il est absent chez les SL-CoV. Une des conséquences biologiques de cette grande délétion est le changement de tropisme du virus qui, d''entérique pour le TGEV, est devenu respiratoire pour le PRCV [36] De nombreuses études ont été menées à la recherche du réservoir animal du SARS-CoV.

abstract:
  Coronaviruses are a large group of viruses and infect a lot of species of mammals and birds. Five coronaviruses currently infect humans: HCoVs 229E and OC43, identified in the 1960s, SARS-CoV identified in March 2003 during the SARS epidemic, and the HCoVs NL63 and HKU1, identified in 2004 and 2005 respectively. The genome of the coronaviruses is a linear, non-segmented, positive-sense single-stranded RNA molecule of approximately 30 kb. The evolution of these viruses occurs through some features: the generation of multiple mutants during the replication resulting on a quasispecies structure of the viral population, the demonstrated ability of coronaviruses to establish persistent infections, the flexibility of the genome due to a high frequency of homologue or heterologue recombinations, the ability to jump barrier species and to adapt to the new environment. Two epidemiologic pictures of HCoV infections have to be distinguished: as suggested by recent studies, HCoVs except SARS-CoV, are distributed worldwide and cocirculate during seasonal outbreaks. The distribution of the different HCoV species varies according to the geographic area and season. In contrast, the SARS-CoV is responsible of the first emerging infectious disease of this millennium, infecting more than 8000 people between November 2002 and July 2003. Its circulation has been stopped by drastic public health policy. Human coronaviruses may be also involved in enteric and neurologic diseases. The detection of these viruses is difficult and mainly based on molecular assays (RT-PCR). There is no established specific therapy to date.


id: cord-324198-b8f99z8r
author: Allam, Zaheer
date: 2020-07-24
url: https://api.elsevier.com/content/article/pii/B9780128243138000103
doi: 10.1016/b978-0-12-824313-8.00010-3
title:
  Underlining the Role of Data Science and Technology in Supporting Supply Chains, Political Stability and Health Networks During Pandemics

abstract:
  This concluding chapter explores how data science and technology has been key in fighting COVID-19 through early detection and in the devising of tools for containing the spread. Interestingly, two precedence constraints are seen to emerge. First, data-driven modeling is the leading policy at an urban and national level, and second, legislations, which are being passed at record speed, will remain as a legacy postvirus. It is expected that those will accelerate the digital transition of communities for decades to come and lead to a resurgence of the smart cities concept which peaked in 2015. This chapter thus outlines the increasing role of data science in health sciences, the need for more robust digital infrastructures, and the role of technology in supporting livability of communities and world order.


id: cord-324324-8ybfiz8f
title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses
author: Decaro, Nicola
date: 2020-04-14
txt: ./txt/cord-324324-8ybfiz8f.txt
cache: ./cache/cord-324324-8ybfiz8f.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113520302935
doi: 10.1016/j.vetmic.2020.108693
summary:
  In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus.

abstract:
  The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.


id: cord-325377-g68onkjt
title: COVID-19: Scientific Overview of the global Pandemic
author: Dey, Anusree
date: 2020-10-28
txt: ./txt/cord-325377-g68onkjt.txt
cache: ./cache/cord-325377-g68onkjt.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.nmni.2020.100800
doi: 10.1016/j.nmni.2020.100800
summary:
  COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics. According to the global data as well as the early estimates from China, both old 69 J o u r n a l P r e -p r o o f age and comorbidities may render the patients at higher risk of developing severe disease or 70 death due to COVID-19 infection, perhaps due to a weaker immune functioning [8, 10] . Interestingly, in an independent study, researchers have found 124 three blood based biomarkers which can predict disease severity at least ten days in advance 125 with more than 90% accuracy, based on a database of 485 infected patients from Wuhan, 126

abstract:
  COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. Genome sequence of the virus revealed that it’s a new zoonotic virus which might have evolved by jumping from bats to humans with one or more intermediate hosts. The immediate availability of the sequence information in public domain has accelerated development of quantitative-reverse-transcription PCR based diagnostics. Besides, numbers of clinical trials have been prioritized globally for testing new vaccines and treatments against this disease. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics.


id: cord-325700-f102uk2m
author: Fraser, Douglas D.
date: 2020-10-21
url: https://doi.org/10.1097/cce.0000000000000272
doi: 10.1097/cce.0000000000000272
title:
  Metabolomics Profiling of Critically Ill Coronavirus Disease 2019 Patients: Identification of Diagnostic and Prognostic Biomarkers

abstract:
  OBJECTIVES: Coronavirus disease 2019 continues to spread rapidly with high mortality. We performed metabolomics profiling of critically ill coronavirus disease 2019 patients to understand better the underlying pathologic processes and pathways, and to identify potential diagnostic/prognostic biomarkers. DESIGN: Blood was collected at predetermined ICU days to measure the plasma concentrations of 162 metabolites using both direct injection-liquid chromatography-tandem mass spectrometry and proton nuclear magnetic resonance. SETTING: Tertiary-care ICU and academic laboratory. SUBJECTS: Patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome coronavirus 2, using standardized hospital screening methodologies, had blood samples collected until either testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until ICU day 10 if the patient tested positive (coronavirus disease 2019 positive). INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Age- and sex-matched healthy controls and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well balanced with the exception that coronavirus disease 2019 positive patients suffered bilateral pneumonia more frequently than coronavirus disease 2019 negative patients. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. Feature selection identified the top-performing metabolites for identifying coronavirus disease 2019 positive patients from healthy control subjects and was dominated by increased kynurenine and decreased arginine, sarcosine, and lysophosphatidylcholines. Arginine/kynurenine ratio alone provided 100% classification accuracy between coronavirus disease 2019 positive patients and healthy control subjects (p = 0.0002). When comparing the metabolomes between coronavirus disease 2019 positive and coronavirus disease 2019 negative patients, kynurenine was the dominant metabolite and the arginine/kynurenine ratio provided 98% classification accuracy (p = 0.005). Feature selection identified creatinine as the top metabolite for predicting coronavirus disease 2019-associated mortality on both ICU days 1 and 3, and both creatinine and creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death with 100% accuracy (p = 0.01). CONCLUSIONS: Metabolomics profiling with feature classification easily distinguished both healthy control subjects and coronavirus disease 2019 negative patients from coronavirus disease 2019 positive patients. Arginine/kynurenine ratio accurately identified coronavirus disease 2019 status, whereas creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death. Administration of tryptophan (kynurenine precursor), arginine, sarcosine, and/or lysophosphatidylcholines may be considered as potential adjunctive therapies.


id: cord-326017-qw4qynqv
author: Laskar, Partha
date: 2020-08-06
url: https://www.ncbi.nlm.nih.gov/pubmed/32781617/
doi: 10.3390/diseases8030030
title:
  “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies

abstract:
  The outbreak of novel coronavirus disease (2019-nCoV or COVID-19) is responsible for severe health emergency throughout the world. The attack of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found to be responsible for COVID-19. The World Health Organization has declared the ongoing global public health emergency as a pandemic. The whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. Enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against COVID-19. Furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. Thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with COVID-19. In this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to COVID-19.


id: cord-326584-io2f52kn
author: Killeen, G.
date: 2020-04-20
txt: ./txt/cord-326584-io2f52kn.txt
cache: ./cache/cord-326584-io2f52kn.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.04.15.20066845v1?rss=1
doi: 10.1101/2020.04.15.20066845
summary:
  Faced with such brutally difficult decisions, it is essential that as many people as possible understand (1) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, (2) why these need to be implemented so early, so aggressively and for such extended periods, and (3) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level. Faced with such brutally difficult decisions, it is essential for policy-makers, health professionals, journalists and the general public that as many people as possible understand (1) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, (2) why these need to be implemented so early, so aggressively and for such extended periods, and (3) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level.

title:
  Why lockdown? Simplified arithmetic tools for decision-makers, health professionals, journalists and the general public to explore containment options for the novel coronavirus

abstract:
  Half the world's population is already under lock-down and the remainder will have to follow if the ongoing novel coronavirus 2019 (COVID-19) virus pandemic is to be contained. Faced with such brutally difficult decisions, it is essential that as many people as possible understand (1) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, (2) why these need to be implemented so early, so aggressively and for such extended periods, and (3) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level. Here we present simplified arithmetic models of COVID-19 transmission, control and elimination in user-friendly Shiny and Excel formats that allow non-specialists to explore, query, critique and understand the containment decisions facing their country and the world at large. Based on parameter values representative of the United Republic of Tanzania, which is still early enough in its epidemic cycle and response to avert a national catastrophe, national containment and elimination with less than 10 deaths is predicted for highly rigorous lock down within 5 weeks of the first confirmed cases and maintained for 15 weeks. However, elimination may only be sustained if case importation from outside the country is comprehensively contained by isolating for three weeks all incoming travellers, except those from countries certified as COVID-free in the future. Any substantive relaxation of these assumptions, specifically shortening the lock-down period, less rigorous lock-down or imperfect importation containment, may facilitate epidemic re-initiation, resulting in over half a million deaths unless rigorously contained a second time. Removing contact tracing and isolation has minimal impact on successful containment trajectories because high incidence of similar mild symptoms caused by other common pathogens attenuates detection success of COVID-19 testing. Nevertheless, contact tracing is recommended as an invaluable epidemiological surveillance platform for monitoring and characterizing the epidemic, and for understanding the influence of interventions on transmission dynamics.


id: cord-327063-ea7a1xfl
author: Dhama, Kuldeep
date: 2020-08-02
url: https://api.elsevier.com/content/article/pii/S1477893920303264
doi: 10.1016/j.tmaid.2020.101830
title:
  SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus

abstract:
  Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome - Coronavirus-2) of the family Coronaviridae, appeared in China in December 2019. This disease was declared as posing Public Health International Emergency by World Health Organization on January 30, 2020, attained the status of a very high-risk category on February 29, and now having a pandemic status (March 11). COVID-19 has presently spread to more than 215 countries/territories while killing nearly 0.62 million humans out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost 15 million as of July 22, 2020, within a short period of just a few months. Researchers worldwide are pacing with high efforts to counter the spread of this virus and to design effective vaccines and therapeutics/drugs. Few of the studies have shown the potential of the animal-human interface and zoonotic links in the origin of SARS-CoV-2. Exploring the possible zoonosis and revealing the factors responsible for its initial transmission from animals to humans will pave ways to design and implement effective preventive and control strategies to counter the COVID-19. The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARS- and MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease.


id: cord-327454-o1mrpgvj
title: Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV
author: Hemmati-Dinarvand, Farshad
date: 2020-05-06
txt: ./txt/cord-327454-o1mrpgvj.txt
cache: ./cache/cord-327454-o1mrpgvj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0188440920305506
doi: 10.1016/j.arcmed.2020.04.022
summary:
  Instead, the extremely pathogenic CoVs, containing Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), mostly contaminate lower airways and lead to pneumonia (5) . Based on the genomic structure and phylogenetic analysis, the family Coronaviridae is currently classified into two subfamilies, Sarbecovirus containing SARS-CoV are two major zoonotic pathogenic coronaviruses (Table 1) . Accordingly, the International Committee on Taxonomy of Viruses named it severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently reported that between the SARS-CoV genome sequence and the novel coronavirus exist 82% similarity, thus, named 2019-nCoV by WHO (18) . This theory may be indicating that 2019-nCoV uses the same SARS-CoV mechanism i.e. through angiotensin-converting enzyme2 (ACE2) receptor and the TMPRSS2 protease to infect the human cells. Sequence analysis has shown that some of the 2019-nCoV clusters and bat-associated SARS76 CoV viruses (SARSr-CoV) can use the ACE2 receptor to enter the host cell.

abstract:
  Abstract At the end of the year 2019, the novel coronavirus (2019-nCoV) was spreading in Wuhan, China, and the outbreak process has a high speed. It was recognized as a pandemic by the World Health Organization (WHO) on 11 March 2020. Coronaviruses are enveloped and single-stranded RNA that have several families including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The pathogenesis mechanism and disease outcomes of SARS and MERS are now clear to some extent, but little information is available for 2019-nCoV. This newly identified corona virus infection represents flu-like symptoms, but usually the first symptoms are fever and dry cough. There has been no specific treatment against 2019-nCoV up to now, and physicians only apply supportive therapy. In the present article, we made an attempt to review the behavior of the virus around the world, epidemiology, a pathway for influx into the host cells, clinical presentation, as well as the treatments currently in use and future approaches; nitazoxanide may be our dream drug. We hope that this review has a positive impact on public knowledge for helping to deal with the 2019-nCoV and move one step forward toward its treatment in the near future.


id: cord-328644-odtue60a
title: Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes
author: Comandatore, Francesco
date: 2020-05-28
txt: ./txt/cord-328644-odtue60a.txt
cache: ./cache/cord-328644-odtue60a.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.30.071027
doi: 10.1101/2020.04.30.071027
summary:
  These variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded RNA viruses -as in the case of SARS-CoV-2 (Sanjuán and Domingo-Calap 2016) , which has a single, positive-strand RNA genome. To have a better insight on the history and spread of the COVID-19 pandemic in Italy and thanks to the sequences deposited in the Gisaid database, we identified 7 non synonymous mutations that are differentially frequent in Italian SARS-CoV-2 strains respect to strains circulating globally. Our analysis allowed us to identify 7 positions in four proteins that present drastic changes in amino acid frequencies when comparing Italian sequences with worldwide sequences available on Gisaid.org on April, 10, 2020 ( Figure 1 ).

abstract:
  The SARS-CoV-2 pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. One of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. Such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. In this work we identified and traced over time 7 amino acid variants that are present with high frequency in Italy and Europe, but that were absent or present at very low frequencies during the first stages of the epidemic in China and the initial reports in Europe. The analysis of these variants helps defining 6 phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. In the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage.


id: cord-331022-tek4u751
title: Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience?
author: Sinderewicz, Emilia
date: 2020-09-09
txt: ./txt/cord-331022-tek4u751.txt
cache: ./cache/cord-331022-tek4u751.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9090739
doi: 10.3390/pathogens9090739
summary:
  The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. The current study reviewed the role of interleukins (ILs) with tumor necrosis factors (TNFs), chemokines and interferons (IFNs) in the immune response to HCoVs. A comparison of the content of proinflammatory Th1 and Th2 cytokines in the serum of SARS patients with healthy controls documented a significantly greater concentration of TNF-α, IL-6, IL-8, IL-10, and IL-12 in the early stage of the SARS-CoV infection [32, 40] .

abstract:
  The global range and high fatality rate of the newest human coronavirus (HCoV) pandemic has made SARS-CoV-2 the focus of the scientific world. Next-generation sequencing of the viral genome and a phylogenetic analysis have shown the high homology of SARS-CoV-2 to other HCoVs that have led to local epidemics in the past. The experience acquired in SARS and MERS epidemics may prove useful in understanding the SARS-CoV-2 pathomechanism and lead to effective treatment and potential vaccine development. This study summarizes the immune response to SARS-CoV, MERS-CoV, and SARS-CoV-2 and focuses on T cell response, humoral immunity, and complement system activation in different stages of HCoVs infections. The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. The role of interferons in the therapy of these infections is also discussed. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated.


id: cord-331822-rsnzyheu
title: Prevention of fogging of protective eyewear for medical staff during the COVID-19 pandemic
author: Hu, Yuli
date: 2020-05-08
txt: ./txt/cord-331822-rsnzyheu.txt
cache: ./cache/cord-331822-rsnzyheu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jen.2020.05.003
doi: 10.1016/j.jen.2020.05.003
abstract: nan
summary:
  title: Prevention of fogging of protective eyewear for medical staff during the COVID-19 pandemic Many studies have noted the importance of wearing goggles to protect the 16 eyes from coronavirus infection when in contact with patients. 8-11 Through 17 interviews with medical staff at our hospital in Wuhan, China, we learnt 18 that fogging of goggles was a problem when caring for COVID-19 patients. Novel Coronavirus disease 2019 92 (COVID-19): The importance of recognising possible early ocular 93 manifestation and using protective eyewear Anti-fog skills for medical goggles during the 110 period of prevention and control of Coronavirus disease 2019 Two simple methods dealing with the 114 problem of fogged goggles during the protection against Coronavirus 115 disease 2019 The Anti-fogging treatments 118 of medical goggles during the Covid-19 The anti-fogging application of the 129 antibacterial hand gel to the reuse goggles during the protection 130 against Covid-19


id: cord-336775-d4hi9myk
author: Kirtipal, Nikhil
date: 2020-08-13
url: https://doi.org/10.1016/j.meegid.2020.104502
doi: 10.1016/j.meegid.2020.104502
title:
  From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses

abstract:
  Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes repaid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this Review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutic against broad spectrum of coronaviruses.


id: cord-337825-ujq9mxk7
title: Overview of lethal human coronaviruses
author: Chen, Bin
date: 2020-06-10
txt: ./txt/cord-337825-ujq9mxk7.txt
cache: ./cache/cord-337825-ujq9mxk7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41392-020-0190-2
doi: 10.1038/s41392-020-0190-2
summary:
  Coronaviruses are the largest +ssRNA viruses and contain at least 14 ORFs, 16 protein combines with viral RNA to form a nucleocapsid, which is involved in the replication of SARS-CoV and is the most abundant protein in virus-infected cells. MERS-CoV can infect T-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, Nanopore Targeted Sequencing, also has the potential for efficiently detecting viruses in a reasonable time. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine

abstract:
  Coronavirus infections of multiple origins have spread to date worldwide, causing severe respiratory diseases. Seven coronaviruses that infect humans have been identified: HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Among them, SARS-CoV and MERS-CoV caused outbreaks in 2002 and 2012, respectively. SARS-CoV-2 (COVID-19) is the most recently discovered. It has created a severe worldwide outbreak beginning in late 2019, leading to date to over 4 million cases globally. Viruses are genetically simple, yet highly diverse. However, the recent outbreaks of SARS-CoV and MERS-CoV, and the ongoing outbreak of SARS-CoV-2, indicate that there remains a long way to go to identify and develop specific therapeutic treatments. Only after gaining a better understanding of their pathogenic mechanisms can we minimize viral pandemics. This paper mainly focuses on SARS-CoV, MERS-CoV, and SARS-CoV-2. Here, recent studies are summarized and reviewed, with a focus on virus–host interactions, vaccine-based and drug-targeted therapies, and the development of new approaches for clinical diagnosis and treatment.


id: cord-338189-j4hnldk4
title: Environmental perspective of COVID-19
author: Saadat, Saeida
date: 2020-08-01
txt: ./txt/cord-338189-j4hnldk4.txt
cache: ./cache/cord-338189-j4hnldk4.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0048969720323871
doi: 10.1016/j.scitotenv.2020.138870
summary:
  The easy spread of this virus made people to wear a mask as precautionary route, use gloves and hand sanitizer on a daily basis that resulted in generation of a massive amount of medical wastes in the environment. However, the lock down of the COVID-19 pandemic caused the air quality in many cities across the globe to improve and drop in water pollutions in some parts of the world. There are some factors that contribute to the risk of COVID-19 but they are probably felt differently by different socioeconomic groups (Lipsitch et al., 2020) -People who have had medical problems of diabetes, chronic respiratory disease, cardiovascular disease, or even high blood pressure and cancer are at higher risk from coronavirus (Giannis et al., 2020; Fang et al., 2020; Zheng et al., 2020) . The major death cases of coronavirus outbreak are happening mainly in old people probably because of a poor immune system that allows rapid growth of viral infections.

abstract:
  The outbreak of COVID-19 has caused concerns globally. On 30 January WHO has declared it as a global health emergency. The easy spread of this virus made people to wear a mask as precautionary route, use gloves and hand sanitizer on a daily basis that resulted in generation of a massive amount of medical wastes in the environment. Millions of people have been put on lockdown in order to reduce the transmission of the virus. This epidemic has also changed the people's life style; caused extensive job losses and threatened the sustenance of millions of people, as businesses have shut down to control the spread of virus. All over the world, flights have been canceled and transport systems have been closed. Overall, the economic activities have been stopped and stock markets dropped along with the falling carbon emission. However, the lock down of the COVID-19 pandemic caused the air quality in many cities across the globe to improve and drop in water pollutions in some parts of the world.


id: cord-340357-gyvvcnuf
title: Being a front-line dentist during the Covid-19 pandemic: a literature review
author: Fallahi, Hamid Reza
date: 2020-04-24
txt: ./txt/cord-340357-gyvvcnuf.txt
cache: ./cache/cord-340357-gyvvcnuf.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s40902-020-00256-5
doi: 10.1186/s40902-020-00256-5
summary:
  This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. The purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the CDC and the ADA guidelines. Due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for 2019-nCoV infection. 2019-nCoV transmission in dental settings occurs through four major routes: (1) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials;

abstract:
  Coronavirus is an enveloped virus with positive-sense single-stranded RNA. Coronavirus infection in humans mainly affects the upper respiratory tract and to a lesser extent the gastrointestinal tract. Clinical symptoms of coronavirus infections can range from relatively mild (similar to the common cold) to severe (bronchitis, pneumonia, and renal involvement). The disease caused by the 2019 novel coronavirus (2019-nCoV) was called Covid-19 by the World Health Organization in February 2020. Face-to-face communication and consistent exposure to body fluids such as blood and saliva predispose dental care workers at serious risk for 2019-nCoV infection. As demonstrated by the recent coronavirus outbreak, information is not enough. During dental practice, blood and saliva can be scattered. Accordingly, dental practice can be a potential risk for dental staff, and there is a high risk of cross-infection. This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus.


id: cord-343021-gqem6bxj
author: Allam, Zaheer
date: 2020-07-24
txt: ./txt/cord-343021-gqem6bxj.txt
cache: ./cache/cord-343021-gqem6bxj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780128243138000097
doi: 10.1016/b978-0-12-824313-8.00009-7
summary:
  The disruptions came just when the consumer demand for different products in other countries from different parts of the world was on a high and rising as depicted in a "United Nations Conference on Trade and Development (UNCTAD)" report showing that exports in 2019 grew by 9.7% in 2018, with China being the world''s leading merchandise trader of the year (UNCTAD, 2020). In other countries such as the United States, it was reported that the government was prompted to force, through an executive order, major companies such as General Motors (GM) to produce ventilators to help bridge the gap that the increasing confirmed cases for coronavirus created (Haynes, 2020) . In other places, such as in the oil-producing countries, including the United States, the impacts of COVID-19 on different economic sectors such as transport and manufacturing saw the demand for oil and oil products plummeting in rates not experienced in recent history.

title:
  Oil, Health Equipment, and Trade: Revisiting Political Economy and International Relations During the COVID-19 Pandemic

abstract:
  The COVID-19 pandemic saw disruptions at an unprecedented global scale with deep societal impacts in cities, countries, and regions. Moreover, in a time of global urgent need for personal protective equipment, ventilators, and other health appliances and gear, both air and sea transport were halted, disconnecting manufacturing nations with consumer nations. With steep rise in demand, and impacted supply chains, nations, which were previously hailing collaborative calls to fight the pandemic, were seen to enter into a trade war of health equipment. With borders closed, nationalist policies were on the rise coupled with fears of tech-powered surveillance states. On the commodities market, the price of oil crashed leading to uncertainties as to the future for oil producing nations as the end point of the pandemic was still unclear. Altogether, the pandemic put on test not only economic structures but also geopolitical ones, where it is seen as the biggest challenge since World War II. This chapter surveys the impacts of the pandemic on the global political landscape and outlines concerns and questions for sustaining a peaceful shared future.


id: cord-344217-kci4uw7u
author: Majid, Sabhiya
date: 2020-08-25
url: https://doi.org/10.1007/s42399-020-00457-z
doi: 10.1007/s42399-020-00457-z
title:
  Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses

abstract:
  Coronavirus disease 2019 (COVID-19), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging in Wuhan, China, in December 2019, it spread widely across the world causing panic—worst ever economic depression is visibly predictable. Coronaviruses (CoVs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-CoV (SARS-CoV) in 2002–2003, Middle East respiratory syndrome-CoV (MERS-CoV) in 2012, and currently this devastating COVID-19. Research strategies focused on understanding the evolutionary origin, transmission, and molecular basis of SARS-CoV-2 and its pathogenesis need to be urgently formulated to manage the current and possible future coronaviral outbreaks. Current response to the COVID-19 outbreak has been largely limited to monitoring/containment. Although frantic global efforts for developing safe and effective prophylactic and therapeutic agents are on, no licensed antiviral treatment or vaccine exists till date. In this review, research strategies for coping with COVID-19 based on evolutionary and molecular aspects of coronaviruses have been proposed.


id: cord-344486-iu5flbcl
title: Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2
author: Chiotos, Kathleen
date: 2020-09-12
txt: ./txt/cord-344486-iu5flbcl.txt
cache: ./cache/cord-344486-iu5flbcl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32918548/
doi: 10.1093/jpids/piaa115
summary:
  In the few months since this initial publication, new evidence has emerged demonstrating the efficacy of the antiviral medication remdesivir in shortening time to clinical recovery in adults with COVID-19, while several other studies have shown ineffectiveness of hydroxychloroquine and lopinavir-ritonavir (4) (5) (6) (7) (8) . Further, additional observational studies have provided insight into the clinical epidemiology of COVID-19 in children, demonstrating that while most young patients experience mild illness, a small proportion develop severe illness associated with adverse clinical outcomes, including need for pediatric intensive care unit (PICU) admission and mortality (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) . Nevertheless, the panel recognizes that pediatric clinicians are likely to consider comorbidities when weighing the risks and benefits of antiviral therapy on a case-bycase basis, and in making these decisions may consider: 1) the available, albeit limited, pediatric COVID-19 literature; 2) risk factors associated with severe COVID-19 in adults; and 3) pre-existing medical conditions in children associated with worse clinical outcomes for other viral infections.

abstract:
  BACKGROUND: Although Coronavirus Disease 2019 (COVID-19) is a mild infection in most children, a small proportion develop severe or critical illness. Data evaluating agents with potential antiviral activity continue to expand, such that updated guidance is needed regarding use of these agents in children. METHODS: A panel of pediatric infectious diseases physicians and pharmacists from 20 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of the best available evidence and expert opinion. RESULTS: Given the typically mild course of COVID-19 in children, supportive care alone is suggested for most cases. For children with severe illness, defined as a supplemental oxygen requirement without need for non-invasive or invasive mechanical ventilation or extra-corporeal membrane oxygenation (ECMO), remdesivir is suggested, preferably as part of a clinical trial if available. Remdesivir should also be considered for critically ill children requiring invasive or non-invasive mechanical ventilation or ECMO. A duration of 5 days is appropriate for most patients. The panel recommends against the use of hydroxychloroquine or lopinavir-ritonavir (or other protease inhibitors) for COVID-19 in children. CONCLUSIONS: Antiviral therapy for COVID-19 is not necessary for the great majority of pediatric patients. For children with severe or critical disease, this guidance offers an approach for decision-making regarding use of remdesivir.


id: cord-344646-wvx6q999
title: Note from the editors: novel coronavirus (2019-nCoV)
author: nan
date: 2020-01-23
txt: ./txt/cord-344646-wvx6q999.txt
cache: ./cache/cord-344646-wvx6q999.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.2807/1560-7917.es.2020.25.3.2001231
doi: 10.2807/1560-7917.es.2020.25.3.2001231
abstract: nan
summary:
  In order to support public health action, viral genome sequences were released by Chinese researchers on 10 January [4] and 2 days later, four further sequences were also made available on the Global Initiative on Sharing All Influenza Data (GISAID) (https://www.gisaid.org/). The other is a rapid communication where researchers based in Hong Kong report on their attempt to estimate the severity among hospitalised cases of 2019-nCoV infection through modelling based on publically available information, mainly from Wuhan health authorities [7] . International health organisations such as the European Centre for Disease Prevention and Control (ECDC) and the WHO are monitoring the situation and provide regular updates. ECDC has set up a dedicated webpage on which updates and risk assessments with focus on Europe are available: https://www.ecdc.europa.eu/en/ novel-coronavirus-china. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases.


id: cord-345014-qp13h0un
title: The 2019 coronavirus: Learning curves, lessons, and the weakest link
author: Stein, Richard Albert
date: 2020-03-13
txt: ./txt/cord-345014-qp13h0un.txt
cache: ./cache/cord-345014-qp13h0un.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/ijcp.13488
doi: 10.1111/ijcp.13488
summary:
  14 In the most recent of the three coronavirus outbreaks, several clusters of patients with pneumonia started to be reported on December 8, 2019 from Wuhan, China, and most of them were epidemiologically linked to the Huanan Seafood Wholesale Market. 24, 25 The virus shares >70% genetic similarity with the 2002-2003 SARS-CoV strain, 5 is most closely related to coronaviruses of bat origin, 17 its spike glycoprotein gene appears to have emerged by recombination between a bat coronavirus and a coronavirus of unknown origins, and relative synonymous codon usage bias analyses indicate that snakes may be a potential reservoir. 26 The SARS-CoV spike protein receptor binds the angiotensin-converting enzyme 2 (ACE2) on host cells, an interaction that shapes cross-species and human-to-human transmission. 10,58-60 Every outbreak brings something new, provides opportunities to reap the benefits gained from past epidemics and pandemics, and provides novel lessons that will shape the framework to manage emerging infectious diseases. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in Wuhan, China

abstract:
  In the space of just six weeks, a new coronavirus, from a family that historically was not viewed as a global health concern, has become daily headline news around the globe. The 21st century marked its arrival with the emergence of three previously unknown coronaviruses. SARS-CoV (severe acute respiratory syndrome coronavirus) was recognized in November 2002 [1, 2], MERS-CoV (Middle East respiratory syndrome coronavirus) in June 2012 [3, 4], and 2019-nCoV in December 2019 [5]. Previously, human coronaviruses, known since the 1960s, were viewed as being only marginally relevant to the clinic, except for infants, the elderly, and immunocompromised individuals [1, 6, 7].


id: cord-345503-52kq2u8a
author: Keyhan, Seied Omid
date: 2020-03-30
txt: ./txt/cord-345503-52kq2u8a.txt
cache: ./cache/cord-345503-52kq2u8a.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32289035/
doi: 10.1186/s40902-020-00254-7
abstract: nan
summary:
  Dysosmia and dysgeusia due to the 2019 Novel Coronavirus; a hypothesis that needs further investigation Seied Omid Keyhan 1,2,3 , Hamid Reza Fallahi 4,5 and Behzad Cheshmi 6* Coronaviruses are known as enveloped viruses with a positive-sense single-stranded RNA genome that their helical symmetry nucleocapsid is about 26-32 kilobases in size, making it the largest investigated genome among RNA viruses. Given that the peripheral trigeminal or olfactory nerves are pathways of penetration of the coronaviruses into the central nervous system, and based on animal studies, it may be hypothesized that complications such as demyelination and stimulation of T cell-mediated autoimmune reactions may occur in the path of the infection spreading, so the occurrence of dysosmia and dysgeusia can be considered potential consequences of these nerve injuries. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

title:
  Dysosmia and dysgeusia due to the 2019 Novel Coronavirus; a hypothesis that needs further investigation


id: cord-347289-3yi5tz04
author: Poon, L. . C.
date: 2020-06-01
txt: ./txt/cord-347289-3yi5tz04.txt
cache: ./cache/cord-347289-3yi5tz04.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32356590/
doi: 10.1002/uog.22061
abstract: nan
summary:
  American College of Obstetricians and Gynecologists (ACOG): https://www.acog.org/clinical-information/phys ician-faqs/covid-19-faqs-for-ob-gyns-obstetrics Centers for Disease Control , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health emergency. A case series of 12 pregnant women with SARS-CoV in Hong Kong, China, reported three maternal deaths, that four of seven patients who presented in the first trimester had spontaneous miscarriage, four of five patients who presented after 24 weeks had preterm birth and two mothers recovered without delivery but their ongoing pregnancies were complicated by FGR 8 . In two studies, with a combined total of 10 pregnant women with COVID-19 in the third trimester, amniotic fluid, cord blood and neonatal throat swab samples tested negative for SARS-CoV-2, suggesting there was no evidence of vertical transmission in women who developed COVID-19 pneumonia in late pregnancy 26, 76 . An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes

title:
  ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update


id: cord-349287-mwj2qby4
title: MERS coronavirus: diagnostics, epidemiology and transmission
author: Mackay, Ian M.
date: 2015-12-22
txt: ./txt/cord-349287-mwj2qby4.txt
cache: ./cache/cord-349287-mwj2qby4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-015-0439-5
doi: 10.1186/s12985-015-0439-5
summary:
  The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Since asymptomatic zoonoses have been posited [72] , an absence of antibodies to MERS-CoV among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering DCs [70] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-tohuman transmission

abstract:
  The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia (KSA). Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels (DC). MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract (LRT) disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute respiratory syndrome (SARS), another sometimes- fatal zoonotic coronavirus disease that has since disappeared, MERS progresses more rapidly to respiratory failure and acute kidney injury (it also has an affinity for growth in kidney cells under laboratory conditions), is more frequently reported in patients with underlying disease and is more often fatal. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Sero-surveys have found widespread evidence of past infection in adult camels and limited past exposure among humans. Sensitive, validated reverse transcriptase real-time polymerase chain reaction (RT-rtPCR)-based diagnostics have been available almost from the start of the emergence of MERS. While the basic virology of MERS-CoV has advanced over the past three years, understanding of the interplay between camel, environment, and human remains limited. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0439-5) contains supplementary material, which is available to authorized users.


id: cord-349313-2gupfqnl
title: Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19)
author: Martinez-Perez, Clara
date: 2020-10-21
url: https://www.ncbi.nlm.nih.gov/pubmed/33096796/
doi: 10.3390/ijerph17207690
abstract:
  Background: The first outbreaks of the new coronavirus disease, named COVID-19, occurred at the end of December 2019. This disease spread quickly around the world, with the United States, Brazil and Mexico being the countries the most severely affected. This study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. Methods: The search for publications was carried out through the Web of Science database using terms such as “COVID-19” and “SARS-CoV-2” for the period between January and July 2020. The Citation Network Explorer software was used for publication analysis. Results: A total of 14,335 publications were found with 42,374 citations generated in the network, with June being the month with the largest number of publications. The most cited publication was “Clinical Characteristics of Coronavirus Disease 2019 in China” by Guan et al., published in April 2020. Nine groups comprising different research areas in this field, including clinical course, psychology, treatment and epidemiology, were found using the clustering functionality. Conclusions: The citation network offers an objective and comprehensive analysis of the main papers on COVID-19 and SARS-CoV-2.


id: cord-349923-cja8i0hw
title: The Novel Coronavirus: A Bird''s Eye View
author: Habibzadeh, Parham
date: 2020-02-05
txt: ./txt/cord-349923-cja8i0hw.txt
cache: ./cache/cord-349923-cja8i0hw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32020915/
doi: 10.15171/ijoem.2020.1921
summary:
  C oronaviruses typically result in respiratory and enteric infections affecting both animals and humans, and were considered relatively benign to humans before the severe acute respiratory syndrome (SARS-CoV) outbreak in 2002 and 2003 in China. [1] [2] [3] [4] A decade later, Middle East respiratory syndrome coronavirus (MERS-CoV), another pathogenic coronavirus with a clinical picture reminiscent of SARS, was isolated in patients presenting with pneumonia in the Middle Eastern countries. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day.

abstract:
  The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. With a death toll exceeding that of the SARS-CoV outbreak back in 2002 and 2003 in China, 2019-nCoV has led to a public health emergency of international concern, putting all health organizations on high alert. Herein, we present on an overview of the currently available information on the pathogenesis, epidemiology, clinical presentation, diagnosis, and treatment of this virus.


id: cord-351707-u8t7h6ri
author: Dammeyer, Jesper
date: 2020-12-01
url: https://www.ncbi.nlm.nih.gov/pubmed/32834285/
doi: 10.1016/j.paid.2020.110263
title:
  An explorative study of the individual differences associated with consumer stockpiling during the early stages of the 2020 Coronavirus outbreak in Europe

abstract:
  There is little existing research on why some people stockpile goods and others do not at a time of crisis. More research on this phenomenon and the individual differences associated with it is needed in order to gain a better understanding of what is a potentially economically and socially disruptive behavior. In this study, 175 adult participants from Denmark and 90 from the United Kingdom responded to a survey about the activity of extra shopping (stockpiling) during the first weeks of the Coronavirus outbreak. Questions exploring the “big five” personality traits, Social Dominance Orientation, Health Literacy, and attitudes to the governmental response to the crisis were included in the survey. The explorative analysis showed that stockpiling was associated with high scores on Extraversion and Neuroticism, and low scores on Conscientiousness and Openness to Experience. Stockpiling was also associated with the view that the government should be doing more to stop the Coronavirus epidemic. An explorative factor analysis of reasons for stockpiling identified the two factors “Panic” and “Action”.


id: cord-352230-8mazd3eu
title: Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status
author: Beeraka, Narasimha M.
date: 2020-09-18
txt: ./txt/cord-352230-8mazd3eu.txt
cache: ./cache/cord-352230-8mazd3eu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3389/fimmu.2020.552925
doi: 10.3389/fimmu.2020.552925
summary:
  Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. COVID-19 is a devastating disease caused by a coronavirus related to the one that caused outbreaks of Severe Acute Respiratory Syndrome (SARS) in the year 2002 (1, 2) .

abstract:
  Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease - 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. The clinical manifestations of this disease are pneumonia, lung injury, inflammation, and severe acute respiratory syndrome (SARS). Currently, there is no vaccine or effective pharmacological agents available for the prevention/treatment of SARS-CoV2 infections. Moreover, development of a suitable vaccine is a challenging task due to antibody-dependent enhancement (ADE) and Th-2 immunopathology, which aggravates infection with SARS-CoV-2. Furthermore, the emerging SARS-CoV-2 strain exhibits several distinct genomic and structural patterns compared to other coronavirus strains, making the development of a suitable vaccine even more difficult. Therefore, the identification of novel small molecule inhibitors (NSMIs) that can interfere with viral entry or viral propagation is of special interest and is vital in managing already infected cases. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, the development of novel inhibitors of ACE2/TMPRSS2 is likely to be beneficial in combating SARS-CoV-2 infections. However, the usage of ACE-2 inhibitors to block the SARS-CoV-2 viral entry requires additional studies as there are conflicting findings and severe health complications reported for these inhibitors in patients. Hence, the current interest is shifted toward the development of NSMIs, which includes natural antiviral phytochemicals and Nrf-2 activators to manage a SARS-CoV-2 infection. It is imperative to investigate the efficacy of existing antiviral phytochemicals and Nrf-2 activators to mitigate the SARS-CoV-2-mediated oxidative stress. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs.


id: cord-352322-tsjwnvkk
title: Coronaviruses in farm animals: Epidemiology and public health implications
author: Khamassi Khbou, Médiha
date: 2020-09-25
txt: ./txt/cord-352322-tsjwnvkk.txt
cache: ./cache/cord-352322-tsjwnvkk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32976707/
doi: 10.1002/vms3.359
summary:
  As consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (TGEV) of swine and the bovine CoV (BCoV) likely originated from the closely related canine coronavirus (CCoV) (Pratelli, 2011) . Coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean CoVs were also considered, as marine mammals are a food source in many countries around the world. Since the first case of human infected by the MERS-CoV was identified in September 2012 in Saudi Arabia (World Health Organization, 2019), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (Omrani, Al-Tawfiq, & Memish, 2015) . Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Infection with a new porcine respiratory coronavirus in Denmark: Serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies

abstract:
  Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross‐species transmission easy. In fact, increasing contact between different animal species fosters cross‐species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human‐animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.


id: cord-352379-q5inrxcm
title: SARS virus: The beginning of the unraveling of a new coronavirus
author: Lai, Michael M. C.
date: 2003-10-17
txt: ./txt/cord-352379-q5inrxcm.txt
cache: ./cache/cord-352379-q5inrxcm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14631105/
doi: 10.1007/bf02256318
summary:
  Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection

abstract:
  Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern China. Its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. However, distinct patterns of several open reading frames in the SARS virus genome may contribute to its severe virulence. The potential mutability of the coronavirus genome may pose problems in the control of future SARS outbreaks. The mechanism of SARS pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. The life cycle of the SARS virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. Vaccines offer an important preventive measure for possible future recurrences of SARS, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in SARS virus pathogenesis. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus.


id: cord-352781-aqh9zxgh
title: Review of Chest CT Manifestations of COVID-19 Infection
author: El Homsi, Maria
date: 2020-06-07
txt: ./txt/cord-352781-aqh9zxgh.txt
cache: ./cache/cord-352781-aqh9zxgh.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S2352047720300289
doi: 10.1016/j.ejro.2020.100239
summary:
  Here, we review the pertinent clinical findings and the current published data describing chest CT findings in COVID-19 pneumonia, the diagnostic performance of CT for diagnosis, including differential diagnosis, as well the evolving role of imaging in this disease. In the US, the Centers for Disease Control and Prevention (CDC), the American College of Radiology (ACR), the Society of Thoracic Radiology (STR), and the American Society of Emergency Radiology (ASER) issued their position statements recommending against the use of CT for widespread screening and diagnosis of COVID-19, instead reserving CT for those cases with clinical suspicion for complications like abscess or empyema [76] [77] [78] . Clinical Features and Chest CT Manifestations of Coronavirus Disease 2019 (COVID-19) in a Single-Center Study in Relation Between Chest CT Findings and Clinical Conditions of Coronavirus Disease (COVID-19) Pneumonia: A Multicenter Study Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases

abstract:
  Coronavirus disease-19 (COVID-19) is a viral pandemic that started in China and has rapidly expanded worldwide. Typical clinical manifestations include fever, cough and dyspnea after an incubation period of 2-14 days. The diagnosis is based on RT-PCR test through a nasopharyngeal swab. Because of the pulmonary tropism of the virus, pneumonia is often encountered in symptomatic patients. Here, we review the pertinent clinical findings and the current published data describing chest CT findings in COVID-19 pneumonia, the diagnostic performance of CT for diagnosis, including differential diagnosis, as well the evolving role of imaging in this disease.


id: cord-352985-5ccrkfsa
author: Putter, Jeffrey S.
date: 2020-09-04
txt: ./txt/cord-352985-5ccrkfsa.txt
cache: ./cache/cord-352985-5ccrkfsa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32948465/
doi: 10.1016/j.transci.2020.102934
summary:
  This communication provides a compilation on aspects of COVID-19 infection control measures, describes the potential role of therapeutic plasma exchange to reduce fatality rates, addresses precautions concerning dexamethasone pharmacotherapy and updates the current status on the availability of vaccines. As the virus can cause excess inflammatory mediators such as cytokines and chemokines to circulate, in theory it would be advantageous to exchange patients with fresh frozen plasma or convalescent plasma containing a fixed dose of coronavirus neutralising antibody, NAb, if available from a donor. Alternatively, the above purer hyperimmune products can be used for upgrading the antibody content of the potential pool of CCP or its cryosupernatant, that will be essential as the carrier of such bioproduct in therapeutic plasma exchange (TPE). Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion as an empirical treatment during outbreaks

title:
  An Update on COVID-19 Infection Control Measures, Plasma-Based Therapeutics, Corticosteroid Pharmacotherapy and Vaccine Research

abstract:
  This communication provides a compilation on aspects of COVID-19 infection control measures, describes the potential role of therapeutic plasma exchange to reduce fatality rates, addresses precautions concerning dexamethasone pharmacotherapy and updates the current status on the availability of vaccines. As part of passive immunotherapy, it focuses on various blood derivatives. These include coronavirus neutralising antibodies extracted from different sources to be administered as a pure hyper concentrate intramuscularly or for upgrading and standardising the specific potency of high affinity antibodies. These processes are intended to compose standardised pooled bioproducts of corona convalescent plasma/cryosupernatant that are pathogen inactivated for additional safety by well-established UV technologies. For the best practice of optimising plasma exchange, hyper concentrate NAb should be added to the cryosupernatant, which contains some of the active principles of corona convalescent plasma. The cryosupernatant apart from the high molecular weight viscous part of cold insoluble proteins that are removed, is equivalent to CCP, but makes it safer for general application. Such a bioproduct is often used routinely for substitution therapy of thrombotic thrombocytopenic purpura. Alternative resources of large-scale specific coronavirus antibodies warrant further exploration such as cadaveric donations. The early uses of therapeutic plasma exchange and low molecular weight heparin, for any clinical trial in development is warranted, in order to interdict the intense inflammatory/kinin driven cascade. Because coronavirus positive patients are highly prone to thrombosis, thromboprophylaxis is necessary, even some time after recovery guided by the laboratory data.


id: cord-353484-q7d0ysbo
title: COVID-19: Progress in diagnostics, therapy and vaccination
author: Liu, Xue
date: 2020-06-19
txt: ./txt/cord-353484-q7d0ysbo.txt
cache: ./cache/cord-353484-q7d0ysbo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.7150/thno.47987
doi: 10.7150/thno.47987
summary:
  Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] .

abstract:
  Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently become a pandemic. As the sudden emergence and rapid spread of SARS-CoV-2 is endangering global health and the economy, the development of strategies to contain the virus's spread are urgently needed. At present, various diagnostic kits to test for SARS-CoV-2 are available for use to initiate appropriate treatment faster and to limit further spread of the virus. Several drugs have demonstrated in vitro activity against SARS-CoV-2 or potential clinical benefits. In addition, institutions and companies worldwide are working tirelessly to develop treatments and vaccines against COVID-19. However, no drug or vaccine has yet been specifically approved for COVID-19. Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic.


id: cord-354536-c9v9kbw8
title: Advances and challenges in the prevention and treatment of COVID-19
author: Han, Yan-Jie
date: 2020-07-09
txt: ./txt/cord-354536-c9v9kbw8.txt
cache: ./cache/cord-354536-c9v9kbw8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32714083/
doi: 10.7150/ijms.47836
summary:
  This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro.

abstract:
  Since the end of 2019, a new type of coronavirus pneumonia (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading rapidly throughout the world. Previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19.


id: cord-355238-wl53z9l7
author: Putrino, Alessandra
date: 2020-07-10
txt: ./txt/cord-355238-wl53z9l7.txt
cache: ./cache/cord-355238-wl53z9l7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32650753/
doi: 10.1186/s12903-020-01187-3
summary:
  Due to the increasing involvement of a large part of the population in the global epidemic situation in Italy, the present study aimed to assess the knowledge about the new coronavirus, the perception of risk and the clinical management of the risk related to infection during the first month of the Italian epidemic in an online survey of Italian dentists. Six questions were intended to evaluate the direct influence of the coronavirus epidemic on the dentist''s clinical activity (presence or absence of infected cases in their region; questions of patients about coronavirus; patients appearing to be worried or not about possible infections with coronavirus during dental procedures; effective decrease or not in patient appointment number since the coronavirus outbreak onset; adoption of special measures taken during professional activity since the coronavirus emergency started in Italy; and which prevention methods are possibly used).

title:
  Coronavirus (COVID-19) in Italy: knowledge, management of patients and clinical experience of Italian dentists during the spread of contagion

abstract:
  BACKGROUND: The coronavirus infection that emerged in China in the last few months of 2019 has now spread globally. Italy registered its first case in the second half of February, and in a short time period, it became the top country in Europe in terms of the number of infected people and the first in the world in terms of deaths. The medical and scientific community has been called upon to manage the emergency and to take measures. Dentists also need to take new precautions during their clinical activity to protect themselves, coworkers and patients from the risks of contagion and to avoid further spread of infection. METHODS: Following the data published in the international literature as well as the guidelines and directives constantly updated by the WHO and by the national health authorities, a questionnaire to be completed anonymously was submitted online to Italian dentists using social tools and online professional platforms. The collected data were processed statistically, providing descriptive data and analysis of correlations of the most significant parameters using the Pearson’s χ2, the Likelihood-Ratio χ2, Cramér’s V, Fisher’s exact test, Goodman and Kruskal’s γ, and Kendall’s τb (p < 0.05). RESULTS: A total of 535 dentists from Italy participated in the survey. A good level of scientific knowledge about coronavirus and the extra precautionary measures needed to limit the spread was related to the age of respondents and their sex. Coming from areas with higher concentrations of cases affected knowledge, level of attention and perception of risk related to dental activity. CONCLUSIONS: At the moment, there are no therapies or vaccines to contain the infection with the new coronavirus that is causing many infections, many of which are fatal, worldwide. Dentists are one of the categories at highest risk of encountering diseases and infections because they work in close proximity with patients, and in their procedures, there is always contact with aerosols with high bacterial and viral potential. Therefore, during this COVID-19 emergency, it is important that dentists are properly informed and take the appropriate precautionary measures.


id: cord-355758-tk7eturq
author: Berrio, Alejandro
date: 2020-09-22
txt: ./txt/cord-355758-tk7eturq.txt
cache: ./cache/cord-355758-tk7eturq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.09.16.300038
doi: 10.1101/2020.09.16.300038
summary:
  Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses.

title:
  Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

abstract:
  Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. Thermodynamic modeling of RNA stability and structure, however, indicates that RNA secondary structure within both genes in the SARS-CoV-2 genome differs from those of RaTG13, the reconstructed common ancestor, and Pan-CoV-GD (Guangdong). These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.


