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2.
Mycoses ; 65(5): 526-540, 2022 May.
Article in English | MEDLINE | ID: covidwho-1741478

ABSTRACT

BACKGROUND: The second COVID-19 wave in India has been associated with an unprecedented increase in cases of COVID-19 associated mucormycosis (CAM), mainly Rhino-orbito-cerebral mucormycosis (ROCM). METHODS: This retrospective cohort study was conducted at Noble hospital and Research Centre (NHRC), Pune, India, between 1 April, 2020, and 1 August, 2021, to identify CAM patients and assess their management outcomes. The primary endpoint was incidence of all-cause mortality due to CAM. RESULTS: 59 patients were diagnosed with CAM. Median duration from the first positive COVID-19 RT PCR test to diagnosis of CAM was 17 (IQR: 12,22) days. 90% patients were diabetic with 89% having uncontrolled sugar level (HbA1c >7%). All patients were prescribed steroids during treatment for COVID-19. 56% patients were prescribed steroids for non-hypoxemic, mild COVID-19 (irrational steroid therapy), while in 9%, steroids were prescribed in inappropriately high dose. Patients were treated with a combination of surgical debridement (94%), intravenous liposomal Amphotericin B (91%) and concomitant oral Posaconazole (95.4%). 74.6% patients were discharged after clinical and radiologic recovery while 25.4% died. On relative risk analysis, COVID-19 CT severity index ≥18 (p = .017), presence of orbital symptoms (p = .002), presence of diabetic ketoacidosis (p = .011) and cerebral involvement (p = .0004) were associated with increased risk of death. CONCLUSIONS: CAM is a rapidly progressive, angio-invasive, opportunistic fungal infection, which is fatal if left untreated. Combination of surgical debridement and antifungal therapy leads to clinical and radiologic improvement in majority of cases.


Subject(s)
COVID-19 , Mucormycosis , Orbital Diseases , Antifungal Agents/therapeutic use , COVID-19/epidemiology , Humans , India/epidemiology , Mucormycosis/diagnosis , Mucormycosis/drug therapy , Mucormycosis/epidemiology , Orbital Diseases/drug therapy , Retrospective Studies , SARS-CoV-2 , Steroids/therapeutic use
3.
Nature ; 602(7897): 487-495, 2022 02.
Article in English | MEDLINE | ID: covidwho-1585830

ABSTRACT

The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.


Subject(s)
COVID-19/immunology , COVID-19/virology , Evolution, Molecular , Immune Evasion , Immunity, Innate/immunology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , COVID-19/transmission , Coronavirus Nucleocapsid Proteins/chemistry , Coronavirus Nucleocapsid Proteins/metabolism , Humans , Immunity, Innate/genetics , Interferons/immunology , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphorylation , Proteomics , RNA, Viral/genetics , RNA-Seq , SARS-CoV-2/classification , SARS-CoV-2/growth & development
4.
Medicine (Baltimore) ; 100(29): e26705, 2021 Jul 23.
Article in English | MEDLINE | ID: covidwho-1475905

ABSTRACT

ABSTRACT: Cytokine release syndrome (CRS) or cytokine storm is thought to be the cause of inflammatory lung damage, worsening pneumonia and death in patients with COVID-19. Steroids (Methylprednislone or Dexamethasone) and Tocilizumab (TCZ), an interleukin-6 receptor antagonist, are approved for treatment of CRS in India. The aim of this study was to evaluate the efficacy and safety of combination therapy of TCZ and steroid in COVID-19 associated CRS.This retrospective cohort study was conducted at Noble hospital and Research Centre (NHRC), Pune, India between April 2 and November 2, 2020. All patients administered TCZ and steroids during this period were included. The primary endpoint was incidence of all cause mortality. Secondary outcomes studied were need for mechanical ventilation and incidence of systemic and infectious complications. Baseline and time dependent risk factors significantly associated with death were identified by Relative risk estimation.Out of 2831 admitted patients, 515 (24.3% females) were administered TCZ and steroids. There were 135 deaths (26.2%), while 380 patients (73.8%) had clinical improvement. Mechanical ventilation was required in 242 (47%) patients. Of these, 44.2% (107/242) recovered and were weaned off the ventilator. Thirty seven percent patients were managed in wards and did not need intensive care unit (ICU) admission. Infectious complications like hospital acquired pneumonia, blood stream bacterial and fungal infections were observed in 2.13%, 2.13% and 0.06% patients respectively. Age ≥ 60 years (P = .014), presence of co-morbidities like hypertension (P = .011), IL-6 ≥ 100 pg/ml (P = .002), D-dimer ≥ 1000 ng/ml (P < .0001), CT severity index ≥ 18 (P < .0001) and systemic complications like lung fibrosis (P = .019), cardiac arrhythmia (P < .0001), hypotension (P < .0001) and encephalopathy (P < .0001) were associated with increased risk of death.Combination therapy of TCZ and steroids is likely to be safe and effective in management of COVID-19 associated cytokine release syndrome. Efficacy of this anti-inflammatory combination therapy needs to be validated in randomized controlled trials.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , COVID-19/drug therapy , Cytokine Release Syndrome/drug therapy , Dexamethasone/therapeutic use , Methylprednisolone/therapeutic use , Antibodies, Monoclonal, Humanized/administration & dosage , COVID-19/complications , COVID-19/mortality , Cytokine Release Syndrome/etiology , Cytokine Release Syndrome/mortality , Dexamethasone/administration & dosage , Drug Therapy, Combination , Female , Humans , India , Intensive Care Units/statistics & numerical data , Length of Stay/statistics & numerical data , Male , Methylprednisolone/administration & dosage , Middle Aged , Retrospective Studies , Treatment Outcome
5.
Cureus ; 13(7): e16598, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1348773

ABSTRACT

Background Blood groups are considered to have an impact on the occurrence and severity of coronavirus disease. While among Chinese and Caucasian, blood group O individuals were less and group A were more likely to have severe disease and mortality, data on South Asians aren't available.  Objective This study aimed to find out the association of disease severity with blood group among coronavirus disease 2019 (COVID-19) patients. Materials and methodology Data were collected on a predesigned questionnaire containing details of patient demographics, medical comorbidities, clinical presentation, and laboratory parameters. Multiple logistic regression was used to determine the association of the blood group with the severity of coronavirus disease. Result Among the study participants, blood group B has the highest distribution (39.8%), followed by O (30.0), A (21.9%), and AB (8.1%). About three-fourths (69.9%) had mild to moderate disease while 30.0% had severe disease. Age, gender, hypertension, diabetes mellitus, and hemoglobin level were all associated with disease severity among COVID-19 patients in univariate analysis on P-value for selection (<0.25). The final model showed that the odds of disease severity is 3.62 times higher among males (OR: 3.62, 95% CI: 2.15-6.08) and 2.00 times higher among diabetic patients (OR: 2.00, 95% CI: 1.10-3.01) as compared to female and non-diabetic respectively. However, there was no significant association found between blood group and disease severity. Conclusion Blood groups don't have any role in forecasting the severity of coronavirus disease. However, the male gender and diabetics are prone to have severe disease.

6.
EMBO Mol Med ; 13(8): e14532, 2021 08 09.
Article in English | MEDLINE | ID: covidwho-1310255

ABSTRACT

Since the start of 2020, the world has been upended by the pandemic caused by the severe acute respiratory coronavirus type 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It has not only led to a tragic loss of life and terrible economic costs but has also been met with an unprecedented response of the scientific and medical communities. In an effort to better understand this viral infection, scientists around the world generated the largest surge in research in documented history for any topic (Lever & Altman, 2021). A part of this work has included the need to better understand the impact of the virus on human proteins-the key machinery of the cell-and human physiology. In their recent study, Geyer and colleagues (Geyer et al, 2021) analyzed a total of 720 proteomes from longitudinal serum samples of 31 hospitalized COVID-19 patients and control individuals with COVID-19-like symptoms but not infected with SARS-CoV-2, providing a comprehensive characterization of the plasma proteome changes along the time course of infection.


Subject(s)
COVID-19 , Proteomics , Humans , Pandemics , Proteome , SARS-CoV-2
7.
Science ; 370(6521)2020 12 04.
Article in English | MEDLINE | ID: covidwho-873450

ABSTRACT

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.


Subject(s)
COVID-19/metabolism , Coronavirus Nucleocapsid Proteins/metabolism , Host Microbial Interactions , Mitochondrial Membrane Transport Proteins/metabolism , Protein Interaction Maps , SARS Virus/metabolism , SARS-CoV-2/metabolism , Severe Acute Respiratory Syndrome/metabolism , Conserved Sequence , Coronavirus Nucleocapsid Proteins/genetics , Cryoelectron Microscopy , Humans , Mitochondrial Membrane Transport Proteins/genetics , Phosphoproteins/genetics , Phosphoproteins/metabolism , Protein Conformation
8.
Cell ; 182(3): 685-712.e19, 2020 08 06.
Article in English | MEDLINE | ID: covidwho-624826

ABSTRACT

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/metabolism , Drug Evaluation, Preclinical/methods , Pneumonia, Viral/metabolism , Proteomics/methods , A549 Cells , Angiotensin-Converting Enzyme 2 , Animals , Antiviral Agents/pharmacology , COVID-19 , Caco-2 Cells , Casein Kinase II/antagonists & inhibitors , Casein Kinase II/metabolism , Chlorocebus aethiops , Coronavirus Infections/virology , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/metabolism , HEK293 Cells , Host-Pathogen Interactions , Humans , Pandemics , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Phosphoinositide-3 Kinase Inhibitors/pharmacology , Phosphorylation , Pneumonia, Viral/virology , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins/antagonists & inhibitors , Proto-Oncogene Proteins/metabolism , Receptor Protein-Tyrosine Kinases/antagonists & inhibitors , Receptor Protein-Tyrosine Kinases/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/metabolism , Vero Cells , p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors , p38 Mitogen-Activated Protein Kinases/metabolism
9.
Nature ; 583(7816): 459-468, 2020 07.
Article in English | MEDLINE | ID: covidwho-152254

ABSTRACT

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.


Subject(s)
Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Coronavirus Infections/metabolism , Drug Repositioning , Molecular Targeted Therapy , Pneumonia, Viral/drug therapy , Pneumonia, Viral/metabolism , Protein Interaction Maps , Viral Proteins/metabolism , Animals , Antiviral Agents/classification , Antiviral Agents/pharmacology , Betacoronavirus/genetics , Betacoronavirus/metabolism , Betacoronavirus/pathogenicity , COVID-19 , Chlorocebus aethiops , Cloning, Molecular , Coronavirus Infections/immunology , Coronavirus Infections/virology , Drug Evaluation, Preclinical , HEK293 Cells , Host-Pathogen Interactions/drug effects , Humans , Immunity, Innate , Mass Spectrometry , Pandemics , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Binding , Protein Biosynthesis/drug effects , Protein Domains , Protein Interaction Mapping , Receptors, sigma/metabolism , SARS-CoV-2 , SKP Cullin F-Box Protein Ligases/metabolism , Vero Cells , Viral Proteins/genetics
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