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1.
Clin Sci (Lond) ; 134(21): 2851-2871, 2020 11 13.
Article in English | MEDLINE | ID: covidwho-1177131

ABSTRACT

Angiotensin converting enzyme (ACE) is well-known for its role in blood pressure regulation via the renin-angiotensin aldosterone system (RAAS) but also functions in fertility, immunity, haematopoiesis and diseases such as obesity, fibrosis and Alzheimer's dementia. Like ACE, the human homologue ACE2 is also involved in blood pressure regulation and cleaves a range of substrates involved in different physiological processes. Importantly, it is the functional receptor for severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 responsible for the 2020, coronavirus infectious disease 2019 (COVID-19) pandemic. Understanding the interaction between SARS-CoV-2 and ACE2 is crucial for the design of therapies to combat this disease. This review provides a comparative analysis of methodologies and findings to describe how structural biology techniques like X-ray crystallography and cryo-electron microscopy have enabled remarkable discoveries into the structure-function relationship of ACE and ACE2. This, in turn, has enabled the development of ACE inhibitors for the treatment of cardiovascular disease and candidate therapies for the treatment of COVID-19. However, despite these advances the function of ACE homologues in non-human organisms is not yet fully understood. ACE homologues have been discovered in the tissues, body fluids and venom of species from diverse lineages and are known to have important functions in fertility, envenoming and insect-host defence mechanisms. We, therefore, further highlight the need for structural insight into insect and venom ACE homologues for the potential development of novel anti-venoms and insecticides.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/enzymology , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/enzymology , Receptors, Virus/metabolism , Virus Internalization , Angiotensin-Converting Enzyme Inhibitors/therapeutic use , Animals , Antiviral Agents/therapeutic use , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Host-Pathogen Interactions , Humans , Pandemics , Peptidyl-Dipeptidase A/chemistry , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Conformation , Receptors, Virus/chemistry , Structure-Activity Relationship
2.
Methods Mol Biol ; 2203: 241-261, 2020.
Article in English | MEDLINE | ID: covidwho-729911

ABSTRACT

Coronavirus entry encompasses the initial steps of infection, from virion attachment to genome release. Advances in fluorescent labeling of viral and cellular components and confocal imaging enable broad spectrum studies on this process. Here, we describe methods for visualization of coronavirus entry into immortalized cell lines and 3D tissue culture models.


Subject(s)
Coronavirus/pathogenicity , Host-Pathogen Interactions/physiology , Microscopy, Confocal/methods , Cell Line , Coronavirus/isolation & purification , Culture Media/chemistry , Endocytosis , Humans , Nucleocapsid Proteins/metabolism , Triiodobenzoic Acids/chemistry , Virus Internalization
3.
Methods Mol Biol ; 2203: 205-221, 2020.
Article in English | MEDLINE | ID: covidwho-729908

ABSTRACT

We have developed a screening system using the yeast Saccharomyces cerevisiae to identify eukaryotic genes involved in the replication of mammalian viruses. Yeast come with various advantages, but in the context of coronavirus research and the system outlined here, they are simple and easy to work with and can be used at biosafety level 2. The system involves inducible expression of individual viral proteins and identification of detrimental phenotypes in the yeast. Yeast knockout and overexpression libraries can then be used for genome-wide screening of host proteins that provide a suppressor phenotype. From the yeast hits, a narrowed list of candidate genes can be produced to investigate for roles in viral replication. Since the system only requires expression of viral proteins, it can be used for any current or emerging virus, regardless of biocontainment requirements and ability to culture the virus. In this chapter, we will outline the protocols that can be used to take advantage of S. cerevisiae as a tool to advance understanding of how viruses interact with eukaryotic cells.


Subject(s)
Coronavirus/physiology , Coronavirus/pathogenicity , Host-Pathogen Interactions/physiology , Saccharomyces cerevisiae/genetics , Plasmids , Viral Proteins/genetics , Viral Proteins/isolation & purification , Virus Replication
4.
Methods Mol Biol ; 2203: 187-204, 2020.
Article in English | MEDLINE | ID: covidwho-729907

ABSTRACT

Biotin-based proximity labeling circumvents major pitfalls of classical biochemical approaches to identify protein-protein interactions. It consists of enzyme-catalyzed biotin tags ubiquitously apposed on proteins located in close proximity of the labeling enzyme, followed by affinity purification and identification of biotinylated proteins by mass spectrometry. Here we outline the methods by which the molecular microenvironment of the coronavirus replicase/transcriptase complex (RTC), i.e., proteins located within a close perimeter of the RTC, can be determined by different proximity labeling approaches using BirAR118G (BioID), TurboID, and APEX2. These factors represent a molecular signature of coronavirus RTCs and likely contribute to the viral life cycle, thereby constituting attractive targets for the development of antiviral intervention strategies.


Subject(s)
Coronavirus/pathogenicity , Enzymes/genetics , Host-Pathogen Interactions/physiology , Proteomics/methods , Viral Proteins/metabolism , Animals , Ascorbate Peroxidases/genetics , Biotinylation , Carbon-Nitrogen Ligases/genetics , Cell Line , Coronavirus/genetics , Enzymes/metabolism , Escherichia coli Proteins/genetics , Fluorescent Antibody Technique , Microorganisms, Genetically-Modified , Repressor Proteins/genetics , Viral Proteins/chemistry , Viral Proteins/genetics
5.
Int J Mol Sci ; 22(1)2020 Dec 30.
Article in English | MEDLINE | ID: covidwho-1006614

ABSTRACT

Being opportunistic intracellular pathogens, viruses are dependent on the host for their replication. They hijack host cellular machinery for their replication and survival by targeting crucial cellular physiological pathways, including transcription, translation, immune pathways, and apoptosis. Immediately after translation, the host and viral proteins undergo a process called post-translational modification (PTM). PTMs of proteins involves the attachment of small proteins, carbohydrates/lipids, or chemical groups to the proteins and are crucial for the proteins' functioning. During viral infection, host proteins utilize PTMs to control the virus replication, using strategies like activating immune response pathways, inhibiting viral protein synthesis, and ultimately eliminating the virus from the host. PTM of viral proteins increases solubility, enhances antigenicity and virulence properties. However, RNA viruses are devoid of enzymes capable of introducing PTMs to their proteins. Hence, they utilize the host PTM machinery to promote their survival. Proteins from viruses belonging to the family: Togaviridae, Flaviviridae, Retroviridae, and Coronaviridae such as chikungunya, dengue, zika, HIV, and coronavirus are a few that are well-known to be modified. This review discusses various host and virus-mediated PTMs that play a role in the outcome during the infection.


Subject(s)
Protein Processing, Post-Translational , RNA Virus Infections/enzymology , RNA Virus Infections/virology , RNA Viruses/metabolism , RNA Viruses/pathogenicity , Viral Proteins/metabolism , Acetylation , Chikungunya virus/metabolism , Coronavirus/metabolism , Coronavirus/pathogenicity , Cytopathogenic Effect, Viral , Glycosylation , HIV/metabolism , HIV/pathogenicity , Host Microbial Interactions , Humans , Phosphorylation , RNA Virus Infections/immunology , RNA Virus Infections/metabolism , RNA Viruses/immunology , Ubiquitination , Virus Replication/physiology , Zika Virus/metabolism , Zika Virus/pathogenicity
6.
Mol Ther ; 29(3): 1174-1185, 2021 03 03.
Article in English | MEDLINE | ID: covidwho-985497

ABSTRACT

Self-amplifying RNA (saRNA) is a cutting-edge platform for both nucleic acid vaccines and therapeutics. saRNA is self-adjuvanting, as it activates types I and III interferon (IFN), which enhances the immunogenicity of RNA vaccines but can also lead to inhibition of translation. In this study, we screened a library of saRNA constructs with cis-encoded innate inhibiting proteins (IIPs) and determined the effect on protein expression and immunogenicity. We observed that the PIV-5 V and Middle East respiratory syndrome coronavirus (MERS-CoV) ORF4a proteins enhance protein expression 100- to 500-fold in vitro in IFN-competent HeLa and MRC5 cells. We found that the MERS-CoV ORF4a protein partially abates dose nonlinearity in vivo, and that ruxolitinib, a potent Janus kinase (JAK)/signal transducer and activator of transcription (STAT) inhibitor, but not the IIPs, enhances protein expression of saRNA in vivo. Both the PIV-5 V and MERS-CoV ORF4a proteins were found to enhance the percentage of resident cells in human skin explants expressing saRNA and completely rescued dose nonlinearity of saRNA. Finally, we observed that the MERS-CoV ORF4a increased the rabies virus (RABV)-specific immunoglobulin G (IgG) titer and neutralization half-maximal inhibitory concentration (IC50) by ∼10-fold in rabbits, but not in mice or rats. These experiments provide a proof of concept that IIPs can be directly encoded into saRNA vectors and effectively abate the nonlinear dose dependency and enhance immunogenicity.


Subject(s)
Immunity, Innate/drug effects , Immunogenicity, Vaccine , Protein Biosynthesis/drug effects , Vaccines, Synthetic/pharmacology , Viral Envelope Proteins/administration & dosage , Animals , Cell Line , Encephalitis Virus, Venezuelan Equine/drug effects , Encephalitis Virus, Venezuelan Equine/immunology , Encephalitis Virus, Venezuelan Equine/pathogenicity , Fibroblasts , Gene Expression Regulation , HeLa Cells , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Immunoglobulin G/biosynthesis , Interferon Regulatory Factor-3/genetics , Interferon Regulatory Factor-3/immunology , Janus Kinases/antagonists & inhibitors , Janus Kinases/genetics , Janus Kinases/immunology , Mice , Middle East Respiratory Syndrome Coronavirus/drug effects , Middle East Respiratory Syndrome Coronavirus/immunology , Middle East Respiratory Syndrome Coronavirus/pathogenicity , NF-kappa B/genetics , NF-kappa B/immunology , Parainfluenza Virus 5/drug effects , Parainfluenza Virus 5/immunology , Parainfluenza Virus 5/pathogenicity , Pyrazoles/pharmacology , Rabbits , Rabies virus/drug effects , Rabies virus/immunology , Rabies virus/pathogenicity , Rats , STAT Transcription Factors/antagonists & inhibitors , STAT Transcription Factors/genetics , STAT Transcription Factors/immunology , Signal Transduction , Vaccines, Synthetic/biosynthesis , Viral Envelope Proteins/genetics , Viral Envelope Proteins/immunology
7.
Emerg Microbes Infect ; 9(1): 727-732, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1169498

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with droplets and contact as the main means of transmission. Since the first case appeared in Wuhan, China, in December 2019, the outbreak has gradually spread nationwide. Up to now, according to official data released by the Chinese health commission, the number of newly diagnosed patients has been declining, and the epidemic is gradually being controlled. Although most patients have mild symptoms and good prognosis after infection, some patients developed severe and die from multiple organ complications. The pathogenesis of SARS-CoV-2 infection in humans remains unclear. Immune function is a strong defense against invasive pathogens and there is currently no specific antiviral drug against the virus. This article reviews the immunological changes of coronaviruses like SARS, MERS and other viral pneumonia similar to SARS-CoV-2. Combined with the published literature, the potential pathogenesis of COVID-19 is inferred, and the treatment recommendations for giving high-doses intravenous immunoglobulin and low-molecular-weight heparin anticoagulant therapy to severe type patients are proposed.


Subject(s)
Coronavirus Infections/immunology , Pneumonia, Viral/immunology , Severe Acute Respiratory Syndrome/immunology , Animals , Antibodies, Viral/blood , Antibodies, Viral/immunology , Anticoagulants/therapeutic use , B-Lymphocytes/immunology , Betacoronavirus/pathogenicity , Coronavirus Infections/drug therapy , Coronavirus Infections/therapy , Coronavirus Infections/virology , Cytokines/immunology , Cytokines/metabolism , Heparin, Low-Molecular-Weight/therapeutic use , Humans , Immunoglobulins, Intravenous/therapeutic use , Immunologic Factors/therapeutic use , Influenza A Virus, H1N1 Subtype , Influenza, Human/immunology , Mice , Middle East Respiratory Syndrome Coronavirus/immunology , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , SARS Virus/immunology , T-Lymphocytes/immunology
8.
Life Sci Alliance ; 4(6)2021 06.
Article in English | MEDLINE | ID: covidwho-1170604

ABSTRACT

Infection of certain influenza viruses is triggered when its HA is cleaved by host cell proteases such as proprotein convertases and type II transmembrane serine proteases (TTSP). HA with a monobasic motif is cleaved by trypsin-like proteases, including TMPRSS2 and HAT, whereas the multibasic motif found in high pathogenicity avian influenza HA is cleaved by furin, PC5/6, or MSPL. MSPL belongs to the TMPRSS family and preferentially cleaves [R/K]-K-K-R↓ sequences. Here, we solved the crystal structure of the extracellular region of human MSPL in complex with an irreversible substrate-analog inhibitor. The structure revealed three domains clustered around the C-terminal α-helix of the SPD. The inhibitor structure and its putative model show that the P1-Arg inserts into the S1 pocket, whereas the P2-Lys and P4-Arg interacts with the Asp/Glu-rich 99-loop that is unique to MSPL. Based on the structure of MSPL, we also constructed a homology model of TMPRSS2, which is essential for the activation of the SARS-CoV-2 spike protein and infection. The model may provide the structural insight for the drug development for COVID-19.


Subject(s)
Influenza in Birds/virology , Membrane Proteins/chemistry , Orthomyxoviridae/pathogenicity , Serine Endopeptidases/chemistry , Animals , Birds , Crystallography, X-Ray , Humans , Protein Conformation
9.
Clin Sci (Lond) ; 134(22): 2987-3006, 2020 11 27.
Article in English | MEDLINE | ID: covidwho-1152900

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is responsible for the global corona virus disease 2019 (COVID-19) pandemic enters host cells via a mechanism that includes binding to angiotensin converting enzyme (ACE) 2 (ACE2). Membrane-bound ACE2 is depleted as a result of this entry mechanism. The consequence is that the protective renin-angiotensin system (RAS), of which ACE2 is an essential component, is compromised through lack of production of the protective peptides angiotensin-(1-7) and angiotensin-(1-9), and therefore decreased stimulation of Mas (receptor Mas) and angiotensin AT2-receptors (AT2Rs), while angiotensin AT1-receptors (AT1Rs) are overstimulated due to less degradation of angiotensin II (Ang II) by ACE2. The protective RAS has numerous beneficial actions, including anti-inflammatory, anti-coagulative, anti-fibrotic effects along with endothelial and neural protection; opposite to the deleterious effects caused by heightened stimulation of angiotensin AT1R. Given that patients with severe COVID-19 exhibit an excessive immune response, endothelial dysfunction, increased clotting, thromboses and stroke, enhancing the activity of the protective RAS is likely beneficial. In this article, we discuss the evidence for a dysfunctional protective RAS in COVID and develop a rationale that the protective RAS imbalance in COVID-19 may be corrected by using AT2R agonists. We further review preclinical studies with AT2R agonists which suggest that AT2R stimulation may be therapeutically effective to treat COVID-19-induced disorders of various organ systems such as lung, vasculature, or the brain. Finally, we provide information on the design of a clinical trial in which patients with COVID-19 were treated with the AT2R agonist Compound 21 (C21). This trial has been completed, but results have not yet been reported.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/pharmacology , Betacoronavirus/pathogenicity , Coronavirus Infections/virology , Pneumonia, Viral/virology , Receptor, Angiotensin, Type 2/agonists , ras Proteins/metabolism , Coronavirus Infections/drug therapy , Humans , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/drug therapy , Renin-Angiotensin System/drug effects , Renin-Angiotensin System/physiology
10.
mBio ; 12(2)2021 03 23.
Article in English | MEDLINE | ID: covidwho-1148106

ABSTRACT

Complement, contact activation, coagulation, and fibrinolysis are serum protein cascades that need strict regulation to maintain human health. Serum glycoprotein, a C1 inhibitor (C1-INH), is a key regulator (inhibitor) of serine proteases of all the above-mentioned pathways. Recently, an autotransporter protein, virulence-associated gene 8 (Vag8), produced by the whooping cough pathogen, Bordetella pertussis, was shown to bind to C1-INH and interfere with its function. Here, we present the structure of the Vag8-C1-INH complex determined using cryo-electron microscopy at a 3.6-Å resolution. The structure shows a unique mechanism of C1-INH inhibition not employed by other pathogens, where Vag8 sequesters the reactive center loop of C1-INH, preventing its interaction with the target proteases.IMPORTANCE The structure of a 10-kDa protein complex is one of the smallest to be determined using cryo-electron microscopy at high resolution. The structure reveals that C1-INH is sequestered in an inactivated state by burial of the reactive center loop in Vag8. By so doing, the bacterium is able to simultaneously perturb the many pathways regulated by C1-INH. Virulence mechanisms such as the one described here assume more importance given the emerging evidence about dysregulation of contact activation, coagulation, and fibrinolysis leading to COVID-19 pneumonia.


Subject(s)
Bacterial Proteins/metabolism , Bordetella pertussis/pathogenicity , Complement C1 Inhibitor Protein/metabolism , Immune Evasion , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites , Blood Coagulation , Bordetella pertussis/chemistry , Bordetella pertussis/metabolism , Complement C1 Inhibitor Protein/chemistry , Complement System Proteins/metabolism , Cryoelectron Microscopy , Fibrinolysis , Models, Molecular , Mutation , Protein Binding , Protein Domains , Type V Secretion Systems/genetics , Type V Secretion Systems/metabolism , Virulence
11.
Cytometry A ; 97(9): 882-886, 2020 09.
Article in English | MEDLINE | ID: covidwho-790373

ABSTRACT

Operating shared resource laboratories (SRLs) in times of pandemic is a challenge for research institutions. In a multiuser, high-turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS-CoV-2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus-free. These recommendations may prove useful for other types of SRLs. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.


Subject(s)
Betacoronavirus/pathogenicity , Biomedical Research/organization & administration , Coronavirus Infections/prevention & control , Infection Control , Laboratories/organization & administration , Microscopy , Occupational Health , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Cooperative Behavior , Coronavirus Infections/transmission , Coronavirus Infections/virology , Decontamination , Equipment Contamination/prevention & control , Germany , Humans , Occupational Exposure/prevention & control , Personal Protective Equipment , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Protective Factors , Research Personnel/organization & administration , Risk Assessment , Risk Factors , Workflow
15.
Sci Rep ; 10(1): 3963, 2020 03 03.
Article in English | MEDLINE | ID: covidwho-659769

ABSTRACT

The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing ("meta-transcriptomics") to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. Samples were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species diversity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease.


Subject(s)
Metagenome/genetics , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , Bacteria/classification , Bacteria/genetics , Bacteria/pathogenicity , DNA Viruses/classification , DNA Viruses/genetics , DNA Viruses/pathogenicity , Drug Resistance, Microbial/genetics , Female , Fungi/classification , Fungi/genetics , Fungi/pathogenicity , Humans , Male , Phylogeny , RNA Viruses/classification , RNA Viruses/genetics , RNA Viruses/pathogenicity , Viruses/classification , Viruses/genetics , Viruses/pathogenicity
16.
PLoS One ; 15(4): e0232188, 2020.
Article in English | MEDLINE | ID: covidwho-659620

ABSTRACT

OBJECTIVE: The World Health Organization created the Severe Acute Respiratory Infection (SARI) criteria in 2011 to monitor influenza (flu)-related hospitalization. Many studies have since used the SARI case definition as inclusion criteria for surveillance studies. We sought to determine the sensitivity, specificity, positive predictive value, and negative predictive value of the SARI criteria for detecting ten different respiratory viruses in a Middle Eastern pediatric cohort. MATERIALS AND METHODS: The data for this study comes from a prospective acute respiratory surveillance study of hospitalized children <2 years in Amman, Jordan from March 16, 2010 to March 31, 2013. Participants were recruited if they had a fever and/or respiratory symptoms. Nasal and throat swabs were obtained and tested by real-time RT-PCR for eleven viruses. Subjects meeting SARI criteria were determined post-hoc. Sensitivity, specificity, positive predictive value, and negative predictive value of the SARI case definition for detecting ten different viruses were calculated and results were stratified by age. RESULTS: Of the 3,175 patients enrolled, 3,164 were eligible for this study, with a median age of 3.5 months, 60.4% male, and 82% virus-positive (44% RSV and 3.8% flu). The sensitivity and specificity of the SARI criteria for detecting virus-positive patients were 44% and 77.9%, respectively. Sensitivity of SARI criteria for any virus was lowest in children <3 months at 22.4%. Removing fever as a criterion improved the sensitivity by 65.3% for detecting RSV in children <3 months; whereas when cough was removed, the sensitivity improved by 45.5% for detecting flu in same age group. CONCLUSIONS: The SARI criteria have poor sensitivity for detecting RSV, flu, and other respiratory viruses-particularly in children <3 months. Researchers and policy makers should use caution if using the criteria to estimate burden of disease in children.


Subject(s)
Respiratory Syncytial Virus Infections/diagnosis , Cough/virology , Female , Fever/virology , Hospitalization , Humans , Infant , Influenza, Human/diagnosis , Influenza, Human/virology , Jordan , Male , Prospective Studies , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Viruses/pathogenicity , Seasons , Sensitivity and Specificity , World Health Organization
17.
Int J Antimicrob Agents ; 56(4): 106129, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-1121213

ABSTRACT

INTRODUCTION: The effect of anti-infective agents in COVID-19 is unclear. The impact of changes in practice on prognosis over time has not been evaluated. METHODS: Single center, retrospective study in adults hospitalized in a medicine ward for COVID-19 from March 5th to April 25th 2020. Patient characteristics were compared between two periods (before/after March 19th) considering French guidelines. The aim of the study was to evaluate how medical care impacted unfavorable outcome, namely admission to intensive care unit (ICU) and/or death. RESULTS: A total of 132 patients were admitted: mean age 59.0±16.3 years; mean C-reactive protein (CRP) level 84.0±71.1 mg/L; 46% had a lymphocyte count <1000/mm3. Prescribed anti-infective agents were lopinavir-ritonavir (n=12), azithromycin (AZI) (n=28) and AZI combined with hydroxychloroquine (HCQ) (n=52). There was a significant decrease in ICU admission, from 43% to 12%, between the two periods (P<0.0001). Delays until transfer to ICU were similar between periods (P=0.86). Pulmonary computerized tomography (CT)-scans were performed significantly more often with time (from 50% to 90%, P<0.0001), and oxygen-dependency (53% vs 80%, P=0.001) and prescription of AZI±HCQ (from 25% to 76%, P<0.0001) were also greater over time. Multivariate analyses showed a reduction of unfavorable outcome in patients receiving AZI±HCQ (hazard ratio [HR]=0.45, 95% confidence interval [CI: 0.21-0.97], P=0.04), particularly among an identified category of individuals (lymphocyte ≥1000/mm3 or CRP ≥100 mg/L). CONCLUSION: The present study showed a significant decrease in admission to ICU over time, which was probably related to multiple factors, including a better indication of pulmonary CT-scan, oxygen therapy, and a suitable prescription of anti-infective agents.


Subject(s)
Anti-Infective Agents/therapeutic use , Azithromycin/therapeutic use , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Hydroxychloroquine/therapeutic use , Lopinavir/therapeutic use , Pneumonia, Viral/drug therapy , Ritonavir/therapeutic use , Adult , Aged , Betacoronavirus/pathogenicity , C-Reactive Protein/metabolism , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/mortality , Coronavirus Infections/pathology , Disease Progression , Drug Combinations , Female , Humans , Intensive Care Units , Male , Middle Aged , Multivariate Analysis , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/mortality , Pneumonia, Viral/pathology , Prognosis , Retrospective Studies , Survival Analysis , T-Lymphocytes/pathology , T-Lymphocytes/virology , Tomography, X-Ray Computed , Treatment Outcome
18.
Viruses ; 12(9)2020 09 22.
Article in English | MEDLINE | ID: covidwho-1120904

ABSTRACT

The relationship between parasite virulence and transmission is a pillar of evolutionary theory that has implications for public health. Part of this canon involves the idea that virulence and free-living survival (a key component of transmission) may have different relationships in different host-parasite systems. Most examinations of the evolution of virulence-transmission relationships-Theoretical or empirical in nature-Tend to focus on the evolution of virulence, with transmission being a secondary consideration. Even within transmission studies, the focus on free-living survival is a smaller subset, though recent studies have examined its importance in the ecology of infectious diseases. Few studies have examined the epidemic-scale consequences of variation in survival across different virulence-survival relationships. In this study, we utilize a mathematical model motivated by aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) natural history to investigate how evolutionary changes in survival may influence several aspects of disease dynamics at the epidemiological scale. Across virulence-survival relationships (where these traits are either positively or negatively correlated), we found that small changes (5% above and below the nominal value) in survival can have a meaningful effect on certain outbreak features, including R0, and on the size of the infectious peak in the population. These results highlight the importance of properly understanding the mechanistic relationship between virulence and parasite survival, as the evolution of increased survival across different relationships with virulence may have considerably different epidemiological signatures.


Subject(s)
Betacoronavirus/physiology , Betacoronavirus/pathogenicity , Coronavirus Infections/transmission , Pneumonia, Viral/transmission , Basic Reproduction Number , Biological Evolution , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Host-Pathogen Interactions , Humans , Microbial Viability , Models, Biological , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Prevalence , Virulence
19.
Clin Microbiol Rev ; 34(2)2021 03 17.
Article in English | MEDLINE | ID: covidwho-1119279

ABSTRACT

To date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to severe disease with accompanying lung injury, multiorgan failure, and death. Although the lungs are believed to be the site at which SARS-CoV-2 replicates, infected patients often report other symptoms, suggesting the involvement of the gastrointestinal tract, heart, cardiovascular system, kidneys, and other organs; therefore, the following question arises: is COVID-19 a respiratory or systemic disease? This review aims to summarize existing data on the replication of SARS-CoV-2 in different tissues in both patients and ex vivo models.


Subject(s)
/epidemiology , Middle East Respiratory Syndrome Coronavirus/pathogenicity , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/physiopathology , /pathogenicity , China/epidemiology , Humans , Pandemics
20.
Viruses ; 13(3)2021 02 26.
Article in English | MEDLINE | ID: covidwho-1115433

ABSTRACT

Ubiquitination of proteins is a post-translational modification process with many different cellular functions, including protein stability, immune signaling, antiviral functions and virus replication. While ubiquitination of viral proteins can be used by the host as a defense mechanism by destroying the incoming pathogen, viruses have adapted to take advantage of this cellular process. The ubiquitin system can be hijacked by viruses to enhance various steps of the replication cycle and increase pathogenesis. Emerging viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), flaviviruses like Zika and dengue, as well as highly pathogenic viruses like Ebola and Nipah, have the ability to directly use the ubiquitination process to enhance their viral-replication cycle, and evade immune responses. Some of these mechanisms are conserved among different virus families, especially early during virus entry, providing an opportunity to develop broad-spectrum antivirals. Here, we discuss the mechanisms used by emergent viruses to exploit the host ubiquitin system, with the main focus on the role of ubiquitin in enhancing virus replication.


Subject(s)
Ubiquitin/metabolism , Virus Diseases/metabolism , Virus Replication , Viruses/metabolism , Immune Evasion , Ubiquitination , Viral Proteins/metabolism , Virus Assembly , Virus Diseases/immunology , Virus Diseases/virology , Virus Internalization , Virus Release , Viruses/classification , Viruses/immunology , Viruses/pathogenicity
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