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1.
Bioorganic Chemistry ; : 105799, 2022.
Article in English | ScienceDirect | ID: covidwho-1797131

ABSTRACT

The emerging COVID-19 pandemic generated by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has severely threatened human health. The main protease (Mpro) of SARS-CoV-2 is promising target for antiviral drugs, which plays a vital role for viral duplication. Development of the inhibitor against Mpro is an ideal strategy to combat COVID-19. In this work, twenty-three hydroxamates 1a-i and thiosemicarbazones 2a-n were identified by FRET screening to be the potent inhibitors of Mpro, which exhibited more than 94% (except 1c) and more than 69% inhibition, and an IC50 value in the range of 0.12-31.51 and 2.43-34.22 μM, respectively. 1a and 2b were found to be the most effective inhibitors in the hydroxamates and thiosemicarbazones, with an IC50 of 0.12 and 2.43 μM, respectively. Enzyme kinetics, jump dilution and thermal shift assays revealed that 2b is a competitive inhibitor of Mpro, while 1a is a time-dependently inhibitor;2b reversibly but 1a irreversibly bound to the target;the binding of 2b increased but 1a decreased stability of the target, and DTT assays indicate that 1a is the promiscuous cysteine protease inhibitor. Cytotoxicity assays showed that 1a has low, but 2b has certain cytotoxicity on the mouse fibroblast cells (L929). Docking studies revealed that the benzyloxycarbonyl carbon of 1a formed thioester with Cys145, while the phenolic hydroxyl oxygen of 2b formed H-bonds with Cys145 and Asn142. This work provided two promising scaffolds for the development of Mpro inhibitors to combat COVID-19.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-312208

ABSTRACT

SARS-CoV-2 survives and remains viable on surfaces for several days under different environments as reported in recent studies. However, it is unclear how the viruses survive for such a long time and why their survivability varies across different surfaces. To address these questions, we conduct systematic experiments investigating the evaporation of droplets produced by a nebulizer and human-exhaled gas on surfaces. We found that these droplets do not disappear with evaporation, but instead shrink to a size of a few micrometers (referred to as residues), persist for more than 24 hours, and are highly durable against changes of environmental conditions. The characteristics of these residues change significantly across surface types. Specifically, surfaces with high thermal conductivity like copper do not leave any resolvable residues, while stainless steel, plastic, and glass surfaces form residues from a varying fraction of all deposited droplets at 40% relative humidity. Lowering humidity level suppresses the formation of residues while increasing humidity level enhances it. Our results suggest that these microscale residues can potentially insulate the virus against environmental changes, allowing them to survive inhospitable environments and remain infectious for prolonged durations after deposition. Our findings can also be extended to other viruses transmitted through respiratory droplets (e.g., SARS-CoV, flu viruses, etc.), and can thus lead to practical guidelines for disinfecting surfaces and other prevention measures (e.g., humidity control) for limiting viral transmission.

3.
Microbiol Spectr ; 9(2): e0135221, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1526454

ABSTRACT

The emerging new lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have marked a new phase of coronavirus disease 2019 (COVID-19). Understanding the recognition mechanisms of potent neutralizing monoclonal antibodies (NAbs) against the spike protein is pivotal for developing new vaccines and antibody drugs. Here, we isolated several monoclonal antibodies (MAbs) against the SARS-CoV-2 spike protein receptor-binding domain (S-RBD) from the B cell receptor repertoires of a SARS-CoV-2 convalescent. Among these MAbs, the antibody nCoV617 demonstrates the most potent neutralizing activity against authentic SARS-CoV-2 infection, as well as prophylactic and therapeutic efficacies against the human angiotensin-converting enzyme 2 (ACE2) transgenic mouse model in vivo. The crystal structure of S-RBD in complex with nCoV617 reveals that nCoV617 mainly binds to the back of the "ridge" of RBD and shares limited binding residues with ACE2. Under the background of the S-trimer model, it potentially binds to both "up" and "down" conformations of S-RBD. In vitro mutagenesis assays show that mutant residues found in the emerging new lineage B.1.1.7 of SARS-CoV-2 do not affect nCoV617 binding to the S-RBD. These results provide a new human-sourced neutralizing antibody against the S-RBD and assist vaccine development. IMPORTANCE COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic has posed a serious threat to global health and the economy, so it is necessary to find safe and effective antibody drugs and treatments. The receptor-binding domain (RBD) in the SARS-CoV-2 spike protein is responsible for binding to the angiotensin-converting enzyme 2 (ACE2) receptor. It contains a variety of dominant neutralizing epitopes and is an important antigen for the development of new coronavirus antibodies. The significance of our research lies in the determination of new epitopes, the discovery of antibodies against RBD, and the evaluation of the antibodies' neutralizing effect. The identified antibodies here may be drug candidates for the development of clinical interventions for SARS-CoV-2.


Subject(s)
Antibodies, Neutralizing/therapeutic use , Antibodies, Viral/therapeutic use , COVID-19/therapy , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/immunology , Animals , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/therapeutic use , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/metabolism , Antibodies, Viral/immunology , Antibodies, Viral/metabolism , Binding Sites/immunology , COVID-19 Vaccines/immunology , Crystallography, X-Ray , Disease Models, Animal , Female , Humans , Immunization, Passive/methods , Immunoglobulin G/blood , Mice , Mice, Inbred C57BL , Mice, Transgenic , Protein Interaction Domains and Motifs/immunology , Viral Load/drug effects
4.
Non-conventional in English | [Unspecified Source], Grey literature | ID: grc-750354

ABSTRACT

The lack of quantitative risk assessment of airborne transmission of COVID-19 under practical settings leads to large uncertainties and inconsistencies in our preventive measures. Combining in situ measurements and numerical simulations, we quantify the exhaled aerosols from normal respiratory behaviors and their transport under elevator, small classroom and supermarket settings to evaluate the risk of inhaling potentially virus-containing aerosols. Our results show that the design of ventilation is critical for reducing the risk of aerosol encounters. Inappropriate design can significantly limit the efficiency of aerosol removal, create local hot spots with orders of magnitude higher risks, and enhance aerosol deposition causing surface contamination. Additionally, our measurements reveal the presence of substantial fraction of crystalline aerosols from normal breathing and its strong correlation with breathing depth.

6.
Int J Biol Macromol ; 193(Pt B): 1124-1129, 2021 Dec 15.
Article in English | MEDLINE | ID: covidwho-1487744

ABSTRACT

Thrombotic complication has been an important symptom in critically ill patients with COVID-19. It has not been clear whether the virus spike (S) protein can directly induce blood coagulation in addition to inflammation. Heparan sulfate (HS)/heparin, a key factor in coagulation process, was found to bind SARS-CoV-2 S protein with high affinity. Herein, we found that the S protein can competitively inhibit the bindings of antithrombin and heparin cofactor II to heparin/HS, causing abnormal increase in thrombin activity. SARS-CoV-2 S protein at a similar concentration (~10 µg/mL) as the viral load in critically ill patients can cause directly blood coagulation and thrombosis in zebrafish model. Furthermore, exogenous heparin/HS can significantly reduce coagulation caused by S protein, pointing to a potential new direction to elucidate the etiology of the virus and provide fundamental support for anticoagulant therapy especially for the COVID-19 critically ill patients.


Subject(s)
Blood Coagulation , Heparitin Sulfate , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Thrombosis/metabolism , Animals , Heparitin Sulfate/chemistry , Heparitin Sulfate/metabolism , Humans , Mice , Protein Binding , SARS-CoV-2/chemistry , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
7.
Signal Transduct Target Ther ; 6(1): 369, 2021 10 25.
Article in English | MEDLINE | ID: covidwho-1483125

ABSTRACT

The lung is the prophylaxis target against SARS-CoV-2 infection, and neutralizing antibodies are a leading class of biological products against various infectious viral pathogen. In this study, we develop a safe and cost-effective platform to express neutralizing antibody in the lung with replicating mRNA basing on alphavirus replicon particle (VRP) delivery system, to prevent SARS-CoV-2 infections. First, a modified VEEV replicon with two subgenomic (sg) promoters was engineered to translate the light and heavy chains of antibody simultaneously, for expression and assembly of neutralizing anti-SARS-CoV-2 antibody CB6. Second, the feasibility and protective efficacy of replicating mRNA against SARS-CoV-2 infection were demonstrated through both in vitro and in vivo assays. The lung target delivery with the help of VRP system resulted in efficiently block SARS-CoV-2 infection with reducing viral titer and less tissue damage in the lung of mice. Overall, our data suggests that expressing neutralizing antibodies in the lungs with the help of self-replicating mRNA could potentially be a promising prophylaxis approach against SARS-CoV-2 infection.


Subject(s)
Alphavirus , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/therapy , Replicon , SARS-CoV-2/metabolism , Animals , Antibodies, Neutralizing/biosynthesis , Antibodies, Neutralizing/genetics , Antibodies, Viral/biosynthesis , Antibodies, Viral/genetics , COVID-19/genetics , COVID-19/metabolism , Chlorocebus aethiops , Cricetinae , Female , Mice , Mice, Inbred BALB C , RNA, Messenger/genetics , RNA, Messenger/metabolism , SARS-CoV-2/genetics , Vero Cells
8.
Health Services Research ; 56(S2):52-52, 2021.
Article in English | Wiley | ID: covidwho-1409256

ABSTRACT

Research Objective In 2020 COVID-19 became the leading cause of death in the United States,[1] with nursing home (NH) residents accounting for approximately 40% of all COVID-19 deaths.[2] To help NHs combat COVID-19, the Centers for Medicare and Medicaid Services (CMS) directed targeted response (TR) interventions through its twelve Quality Improvement Network ? Quality Improvement Organization (QIN-QIOs) contractors. TR involves focused onsite and/or virtual one-on-one technical assistance to nursing homes. For COVID-19 TR, the most common QIN-QIO-reported activities include: assistance with developing and implementing policies and improved processes for hand hygiene, ensuring availability and proper use of personal protective equipment, and general infection control. CMS? criteria to refer NHs for QIN-QIO assistance varied over the entire study period as the program evolved. At various times, these criteria included: infection control-related health inspection deficiencies, NHs located in counties designated as geographic hot spots, having 30 or more new COVID-19 cases in the past week. NH participation in TR is voluntary and free-of-charge. The objective of this study was to assess TR impact on COVID-19 incidence in NHs. Study Design We used a quasi-experimental observational design. NHs may have started receiving TR any time between April 24, and October 28, 2020. COVID-19 incidence data were obtained for May 31 through November 29, 2020 from the National Healthcare Safety Network. Each program NH was matched at the time of first QIN-QIO interaction with a similar non-TR NH. Matching characteristics were: overall NH star rating, health inspections star rating, bed size, state, area deprivation index, and county-level COVID incidence in the month of and the month prior to first receipt of TR. We used longitudinal regression models in the period following first QIN-QIO interaction to compare COVID-19 incidence between NHs that received TR to matched controls that did not. Generalized estimating equations with a Poisson distribution and log-link were used to model COVID-19 incidence, TR status and a full set of covariates. Population Studied CMS-certified NHs providing short-stay, long-stay, or both types of care. Principal Findings Among the 2474 NHs that received TR in the study period, 2013 were matched to 2013 similar NHs that did not. Depending on the month, COVID-19 incidence after matching was similar or higher in the TR group at baseline, but all other covariates were balanced. In this preliminary analysis, NHs receiving TR had 27.7% (p-value <0.0001, 95% CI: 17.2%?36.9%) lowered COVID-19 incidence compared to similar NHs that did not receive TR. Effect estimates withstood early sensitivity analyses. Conclusions The TR intervention was associated with a decline in COVID-19 incidence in TR NHs relative to non-TR NHs. Future analyses will explore which aspects of TR and QIN-QIOs may have been most effective and the attributes of nursing homes that demonstrated improvement. Implications for Policy or Practice Deploying TR for quality improvement in NHs in real-time demonstrated a relative improvement in infection control. CMS should consider expanding TR to a broader range of outcomes. In addition, we must continue to conduct real-time evaluation of the QIN-QIO program as the tools and technologies evolve to prevent infections and other negative outcomes in facilities. Primary Funding Source Centers for Medicare and Medicaid Services.

12.
J Gen Virol ; 102(5)2021 05.
Article in English | MEDLINE | ID: covidwho-1218063

ABSTRACT

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, which is highly pathogenic and classified as a biosafety level 3 (BSL-3) agent, has greatly threatened global health and efficacious antivirals are urgently needed. The high requirement of facilities to manipulate the live virus has limited the development of antiviral study. Here, we constructed a reporter replicon of SARS-CoV-2, which can be handled in a BSL-2 laboratory. The Renilla luciferase activity effectively reflected the transcription and replication levels of the replicon genome. We identified the suitability of the replicon in antiviral screening using the known inhibitors, and thus established the replicon-based high-throughput screening (HTS) assay for SARS-CoV-2. The application of the HTS assay was further validated using a few hit natural compounds, which were screened out in a SARS-CoV-2 induced cytopathic-effect-based HTS assay in our previous study. This replicon-based HTS assay will be a safe platform for SARS-CoV-2 antiviral screening in a BSL-2 laboratory without the live virus.


Subject(s)
Antiviral Agents/pharmacology , Drug Evaluation, Preclinical/methods , Replicon/drug effects , SARS-CoV-2/drug effects , Animals , COVID-19/drug therapy , Chlorocebus aethiops , Drug Discovery , High-Throughput Screening Assays/methods , Humans , Replicon/genetics , SARS-CoV-2/genetics , Vero Cells , Virus Replication/drug effects
13.
Bioconjug Chem ; 32(5): 1034-1046, 2021 05 19.
Article in English | MEDLINE | ID: covidwho-1217668

ABSTRACT

SARS-CoV-2 caused the COVID-19 pandemic that lasted for more than a year. Globally, there is an urgent need to use safe and effective vaccines for immunization to achieve comprehensive protection against SARS-CoV-2 infection. Focusing on developing a rapid vaccine platform with significant immunogenicity as well as broad and high protection efficiency, we designed a SARS-CoV-2 spike protein receptor-binding domain (RBD) displayed on self-assembled ferritin nanoparticles. In a 293i cells eukaryotic expression system, this candidate vaccine was prepared and purified. After rhesus monkeys are immunized with 20 µg of RBD-ferritin nanoparticles three times, the vaccine can elicit specific humoral immunity and T cell immune response, and the neutralizing antibodies can cross-neutralize four SARS-CoV-2 strains from different sources. In the challenge protection test, after nasal infection with 2 × 105 CCID50 SARS-CoV-2 virus, compared with unimmunized control animals, virus replication in the vaccine-immunized rhesus monkeys was significantly inhibited, and respiratory pathology observations also showed only slight pathological damage. These analyses will benefit the immunization program of the RBD-ferritin nanoparticle vaccine in the clinical trial design and the platform construction to present a specific antigen domain in the self-assembling nanoparticle in a short time to harvest stable, safe, and effective vaccine candidates for new SARS-CoV-2 isolates.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19/prevention & control , Nanoparticles/chemistry , Spike Glycoprotein, Coronavirus/metabolism , T-Lymphocytes/immunology , Animals , Antibodies, Neutralizing/immunology , Binding Sites , CD8-Positive T-Lymphocytes/immunology , COVID-19/immunology , Ferritins/chemistry , Ferritins/metabolism , Immunity, Humoral , Macaca mulatta , Male , Nanoparticles/metabolism , SARS-CoV-2/isolation & purification , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , T-Lymphocytes/metabolism , Ultracentrifugation
14.
Phys Fluids (1994) ; 33(1): 013309, 2021 Jan 01.
Article in English | MEDLINE | ID: covidwho-1060635

ABSTRACT

We conducted a systematic investigation of droplet evaporation on different surfaces. We found that droplets formed even with distilled water do not disappear with evaporation but instead shrink to a residue of a few micrometers lasting over 24 h. The residue formation process differs across surfaces and humidity levels. Specifically, under 40% relative humidity, 80% of droplets form residues on plastic and uncoated and coated glass, while less than 20% form on stainless steel and none on copper. The formation of residues and their variability are explained by modeling the evaporation process considering the presence of nonvolatile solutes on substrates and substrate thermal conductivity. Such variability is consistent with the survivability of SARS-CoV-2 measured on these surfaces. We hypothesize that these long-lasting microscale residues can potentially insulate the virus against environmental changes, allowing them to survive and remain infectious for extended durations.

15.
J Aerosol Sci ; 151: 105661, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-997082

ABSTRACT

The lack of quantitative risk assessment of airborne transmission of COVID-19 under practical settings leads to large uncertainties and inconsistencies in our preventive measures. Combining in situ measurements and computational fluid dynamics simulations, we quantify the exhaled particles from normal respiratory behaviors and their transport under elevator, small classroom, and supermarket settings to evaluate the risk of inhaling potentially virus-containing particles. Our results show that the design of ventilation is critical for reducing the risk of particle encounters. Inappropriate design can significantly limit the efficiency of particle removal, create local hot spots with orders of magnitude higher risks, and enhance particle deposition causing surface contamination. Additionally, our measurements reveal the presence of a substantial fraction of faceted particles from normal breathing and its strong correlation with breathing depth.

17.
Kidney Dis (Basel) ; 6(4): 258-270, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-751441

ABSTRACT

BACKGROUND: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. Meanwhile, the presence of B0AT1 (SLC6A19) may prevent TMPRSS2 from accessing the cutting position on ACE2. Identifying the expression of these cell receptor-related genes of SARS-CoV-2 is critical for understanding the pathogenesis of SARS-CoV-2 in various tissues, especially in the kidney. METHODS: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. RESULTS: ACE2 was significantly expressed in the S1, S2, and S3 segments of proximal tubule (PT) cells. TMPRSS2 was widely expressed in several renal tubule populations extending from the PT cells to the collection system cell type, of which intercalated cells and the distal convoluted tubule cells showed more significant expression than PT cells. Unexpectedly, although expressed on various renal tubule populations, SLC6A19 was mainly enriched in PT cells, in line with ACE2 expression. Although alveolar-type (AT) 2 cells of the lung and intestinal epithelial cells expressed ACE2 as well as PT cells, AT 2 cells significantly expressed TMPRSS2 but not SLC6A19, while all 3 genes were significantly expressed in intestinal epithelial cells. CONCLUSIONS: ACE2 was widely expressed in specific cell subgroups of various human tissues, especially in intestinal epithelial cells, kidney PT cells, and also AT 2 cells of the lung. These 3 types of cells demonstrated significant differences in the distribution of the cell receptor-related genes of SARS-CoV-2, which may indicate the diversity of cell surface structures and differences in the affinity between SARS-CoV-2 and cells.

19.
Non-conventional in English | WHO COVID | ID: covidwho-665461

ABSTRACT

The lack of quantitative risk assessment of airborne transmission of COVID-19 under practical settings leads to large uncertainties and inconsistencies in our preventive measures. Combining in situ measurements and numerical simulations, we quantify the exhaled aerosols from normal respiratory behaviors and their transport under elevator, small classroom and supermarket settings to evaluate the risk of inhaling potentially virus-containing aerosols. Our results show that the design of ventilation is critical for reducing the risk of aerosol encounters. Inappropriate design can significantly limit the efficiency of aerosol removal, create local hot spots with orders of magnitude higher risks, and enhance aerosol deposition causing surface contamination. Additionally, our measurements reveal the presence of substantial fraction of crystalline aerosols from normal breathing and its strong correlation with breathing depth.

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