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2.
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
3.
J Am Board Fam Med ; 34(6): 1189-1202, 2021.
Article in English | MEDLINE | ID: covidwho-1581435

ABSTRACT

BACKGROUND: Primary care is crucial to the health of individuals and communities, but it faces numerous structural and systemic challenges. Our study assessed the state of primary care in Virginia to prepare for Medicaid expansion. It also provides insight into the frontline of health care prior to an unprecedented global COVID-19 pandemic. METHODS: We surveyed 1622 primary care practices to understand organizational characteristics, scope of care, capacity, and organizational stress. RESULTS: Practices (484) varied in type, ownership, location, and care for medically underserved and diverse patient populations. Most practices accepted uninsured and Medicaid patients. Practices reported a broad scope of care, including offering behavioral health and medication-assisted therapy for opioid addiction. Over half addressed social needs like transportation and unstable housing. One in three practices experienced a significant stress in 2019, prepandemic, and only 18.8% of practices anticipated a stress in 2020. CONCLUSIONS: Primary care serves as the foundation of our health care system and is an essential service, but it is severely stressed, under-resourced, and overburdened in the best of times. Primary care needs strategic workforce planning, adequate access to resources, and financial investment to sustain its value and innovation.


Subject(s)
COVID-19 , Pandemics , Health Services Accessibility , Humans , Medicaid , Primary Health Care , SARS-CoV-2 , United States , Virginia
4.
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
5.
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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