Journal: Cell Reports

Article Title: Systemic IL-15, IFN-γ, and IP-10/CXCL10 signature associated with effective immune response to SARS-CoV-2 in BNT162b2 mRNA vaccine recipients

doi: 10.1016/j.celrep.2021.109504

Figure Lengend Snippet:

Article Snippet: SpectraMax M3 , Molecular Devices, LLC , N/A.

Techniques: Recombinant, Biomarker Assay, Neutralization, Luciferase, Cell Culture, Lysis, Expressing, Software

Journal: Journal of Virology

Article Title: Anti-Severe Acute Respiratory Syndrome Coronavirus Spike Antibodies Trigger Infection of Human Immune Cells via a pH- and Cysteine Protease-Independent Fc R Pathway

doi: 10.1128/jvi.00671-11

Figure Lengend Snippet: FIG. 2. Anti-Spike antibodies trigger SARS-CoV infection of human Raji B cells. VeroE6 or human Raji cells were infected (MOI 1) with SARS-CoV strain HK39849 (SCoV) in the presence of either control or Anti-Spike serum for 1 h. Samples were fixed with 4% paraformaldehyde at 15 h postinfection. A mouse monoclonal antibody specific for the SCoV nucleocapsid (N) and rabbit polyclonal antibodies specific for SCoV membrane (M) protein were visualized using TRITC-conjugated goat anti-mouse and FITC-conjugated goat anti-rabbit antibodies, respectively. Cell nuclei were labeled with DAPI, and separate channel images were acquired. (A) As expected, SCoV infection of VeroE6 (I) was completely blocked by anti-Spike serum (1/500, II). (B) In contrast, SCoV viral proteins were detected in Raji cells only when they were incubated with anti-Spike (1/500, IV) but never with control serum (III). Quantification of infection (right-hand portions in panels A and B) was done by counting positive cells in 30 randomly chosen fields (630, final magnification), using Metamorph as described in Materials and Methods. The results are shown as means the SD of the number of fields.

Article Snippet: The cells were then washed, and the primary antibody binding was revealed by staining at 4°C for 30 min with FITC-conjugated goat anti-mouse antibodies (Jackson Immunoresearch).

Techniques: Infection, Control, Membrane, Labeling, Incubation

Journal: Journal of Virology

Article Title: Anti-Severe Acute Respiratory Syndrome Coronavirus Spike Antibodies Trigger Infection of Human Immune Cells via a pH- and Cysteine Protease-Independent Fc R Pathway

doi: 10.1128/jvi.00671-11

Figure Lengend Snippet: FIG. 5. Blockade of FcRII abrogates antibody-mediated infection of human immune cell lines. (A) Total RNAs from the indicated cell lines were extracted for RT-PCR amplification as described under Materials and Methods. cDNAs and negative RT controls (RT) were probed for detection of FcεR1-chain, FcRIA (CD64a), FcRIIA (CD32a), FcRIIB (CD32b), FcRIIIA (CD16a), ACE2, and GAPDH. DNA plasmids containing the coding sequence of the human Fc receptors or the human ACE2 (104 and 106 copies) were used as positive controls. Amplicons were visualized by ethidium bromide staining after agarose gel electrophoresis. For reference, a 1-kb molecular-weight standard is also shown. Due to the murine origin of the macrophage-like P388D1 and J774A.1 cell lines and because the primers were designed for the detection of human FcR (Table 2), no FcR transcripts were detected in P388D1 and J774A.1 cells. (B) Hematopoietic cell lines displaying a detectable level of FcR transcript in panel A were subjected to flow cytometry. Cell lines were stained with either isotype-matched control antibody (gray-filled histograms) or FcR-specific mouse monoclonal antibody (open histograms) as indicated, followed by secondary FITC-conjugated goat anti-mouse antibodies. Labeled samples were then read by flow cytometry and post-acquisition analysis was performed using FlowJo software. Insets show the median of fluorescence intensity of the anti-FcR staining. When not visible, the open histograms were superimposed on the gray-filled ones. The data are representative of two independent experiments with similar results. (C) Effect of FcR blockage on susceptibility of the cells to ADE infection. Prior to infection, cells were treated with anti-FcR blocking antibodies. At 3 days postinfection, luciferase substrate reagent was added to wells, and the luminescence was measured. The data were normalized to control conditions, viz., cells infected in the presence of IgG isotype-matched control antibody, and expressed as a percentage of the changes in luminescence. For all conditions, values of background luminescence (never exceeding 3% of control) were subtracted prior to normalization. The results are the means the SD of nine measurements from three independent experiments. ‡, P 0.05; *, P 0.001 (unpaired Student t test).

Article Snippet: The cells were then washed, and the primary antibody binding was revealed by staining at 4°C for 30 min with FITC-conjugated goat anti-mouse antibodies (Jackson Immunoresearch).

Techniques: Infection, Reverse Transcription Polymerase Chain Reaction, Sequencing, Staining, Agarose Gel Electrophoresis, Molecular Weight, Cytometry, Control, Labeling, Software, Blocking Assay, Luciferase

Journal: Journal of Virology

Article Title: Anti-Severe Acute Respiratory Syndrome Coronavirus Spike Antibodies Trigger Infection of Human Immune Cells via a pH- and Cysteine Protease-Independent Fc R Pathway

doi: 10.1128/jvi.00671-11

Figure Lengend Snippet: FIG. 6. Human FcRIIA and B1, but not huFcRIA nor huFcRIIIA, are responsible for ADE of SARS-CoV pseudoparticles (SARS-CoVpp) infection. (A) Human Raji, parental, and monoclonal FcR-transduced human ST486 B cell lines were stained with either isotype-matched control antibody (gray-tinted histogram) or FcR-specific mouse monoclonal antibody (open histogram) as indicated, followed by secondary FITC- conjugated goat anti-mouse antibodies. Labeled samples were then read by flow cytometry and postacquisition analysis was performed using FlowJo software. The inset shows the median of fluorescence intensity of the anti-FcR staining. When not visible, the open histograms were superimposed on the gray-filled ones. (B) Potency of FcR(s) to trigger antibody-mediated entry of SARS-CoVpp was assessed by using ST486 cell lines stably expressing a single FcR. SARS-CoVpp were incubated in the presence or absence of different dilutions (1/1,000, 1/2,000, and 1/4,000) of either control (solid bars) or anti-Spike (hatched bars) serum for 1 h prior to addition to the cells. At 3 days postinfection, luciferase substrate reagent was added to wells, and the luminescence was measured. The data were normalized to control conditions, viz., cells incubated with SARS-CoVpp in the absence of any serum (black bar, taken as unity) and expressed as fold changes in luminescence. Because results for SARS-CoVpp control serum were virtually identical with all cell lines, for the sake of clarity only one dilution (1/4,000) is shown. The results are the means the SD of nine measurements from three independent experiments. Statistical significance was assessed by comparing the appropriate dilutions of mock and anti-Spike serum. ‡, P 0.05; *, P 0.01 (unpaired Student t test).

Article Snippet: The cells were then washed, and the primary antibody binding was revealed by staining at 4°C for 30 min with FITC-conjugated goat anti-mouse antibodies (Jackson Immunoresearch).

Techniques: Infection, Staining, Control, Labeling, Cytometry, Software, Stable Transfection, Expressing, Incubation, Luciferase

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: A schematic 2D LIGPLOT (LIGPLOT software is a program to generate schematic diagrams of protein-ligand interactions) representation showing 3a–f , Remdesivir, and Molnupiravir before and after docking into the binding pocket of 7BQY. The variations in the ligands are highlighted by yellow circles.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques: Software, Binding Assay

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: A schematic 2D LIGPLOT representation of Molnupiravir and 3b against the complex 7BQY showing the hydrogen and hydrophobic interactions.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques:

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Box plot representing the comparison between hydrogen and hydrophobic bonds among the amino acid residues of the COVID-19 M pro substrate-binding pocket produced by docking with the six newly synthesized ligands 3a–f , Remdesivir, and Molnupiravir.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques: Binding Assay, Produced, Synthesized

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Means and SDs of the binding affinities of the nine docking poses for compounds against the COVID-19 main protease 7BQY.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques: Binding Assay

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Acute oral toxicity predicted by the ProTox-II web server for ligands 3a–f and the approved drugs.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques:

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Organ toxicity and toxicological endpoints-predicted activity calculated using the ProTox-II web server for ligands 3a–f , Molnupiravir, and Remdesivir.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques: Activity Assay

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Physicochemical properties and lipophilicity of ligands 3a–f in comparison with the approved drugs Molnupiravir and Remdesivir.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques: Molecular Weight

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: Bioavailability radar for ligands 3a–f and the approved drugs Molnupiravir and Remdesivir.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques:

Journal: Molecules

Article Title: Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

doi: 10.3390/molecules27020488

Figure Lengend Snippet: The pharmacokinetics properties of ligands 3a–f in comparison with those of the approved drugs, Molnupiravir and Remdesivir.

Article Snippet: However, the TSAP of 3b was 144.26 Å 2 closer to that of Molnupiravir (143.14 Å 2 ), whereas Remdesivir showed the most significant value (213.36 Å 2 ).

Techniques:

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Identification and isolation of coronavirus from Oryx leucoryx . (A) Pan-coronavirus nested PCR targeting the RdRp gene by amplifying a final product of 440 bp. RNA was isolated from five oryx fecal samples, ISR1127 samples 1 to 5. c-I, negative control for RNA isolation; c-M, negative control for PCR; C+, positive control, bovine coronavirus RNA. (B) Purified RNA from ISR1127 samples 1 to 5 was used to perform RT-qPCR for BCoV detection. (C) Replication of ISR1127 in HRT-18G cells. Cells were infected with isolate ISR1127 (sample 1) and harvested at different time points, and replication was measured by BCoV RT-qPCR. (D) TEM images showing CoV particles in infected HRT-18G cells at 48 h postinfection. The area of interest outlined in yellow in the left panel is enlarged in the right panel; scale bar, 200 nm.

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Isolation, Nested PCR, Negative Control, Positive Control, Purification, Quantitative RT-PCR, Infection

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Detection of oryx coronavirus in tissue sections. (A) Identification of coronavirus RNA in FFPE sections from oryx tissues. RNA isolated from oryx tissue section sample ISR1117 was used for BCoV RT-qPCR to determine viral copy number in target tissues. (B to I) IHC analysis for oryx coronavirus in tissue cross sections of sample ISR1117 with an antinucleocapsid antibody. (B) Low magnification of the mucosa of the ileum (small intestine) exhibiting a strong positive cytoplasmic IHC labeling of oryx coronavirus in mucosal epithelial cells. Magnification, ×40; scale bar, 100 μm. (C) Section outlined in panel B; black arrows indicate positive regions. (D) Cross section of the heart exhibiting strong IHC labeling within a bundle of Purkinje fibers (black arrow). (E) Kidney cross section showing IHC labeling of the epithelium of the distal convoluted tubules (black arrow). (F) Abomasum cross section exhibiting a strong positive IHC labeling within epithelial cells. (G) Cross section of the liver exhibiting weak positive IHC labeling within bile duct epithelium (black arrow). (H) Cross section of the spleen exhibiting moderate to strong positive IHC labeling of presumptive histiocytes. (I) Thyroid staining exhibiting negative to very weak IHC labeling of the thyroidal follicular cells. (C to I) Magnification, ×200; scale bar. 50 μm; IHC with hematoxylin counterstain.

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Isolation, Quantitative RT-PCR, Labeling, Staining

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Phylogenetic analysis and amino acid comparison of the newly identified Betacoronavirus from Oryx leucoryx . (A) Phylogenetic tree of the S1 region of local BCoV strains and Oryx leucoryx sample ISR1127 (highlighted in red). A phylogenetic tree was generated based on S1 nucleotide sequences (nucleotides 1 to 2731) using the neighbor-joining method with bootstrap analysis (1,000 replicates, >70%). The scale bar shows the number of substitutions per site. Spike partial sequences were retrieved from GenBank and have been previously published . The accession number for each strain is shown in parentheses. (B) Phylogenetic analysis of the full genome of representative coronaviruses. Oryx leucoryx sample ISR1127 is highlighted in red. A phylogenetic tree was generated based on full genomes using the neighbor-joining method with bootstrap analysis (1,000 replicates, >70%). Full-genome sequences were retrieved from GenBank, and their accession numbers are shown in parentheses. Phylogenetic trees were generated using Geneious Prime software. (C) Amino acid comparison of Embecovirus ORF1ab and structural proteins. Oryx leucoryx sample ISR1127 was used as a reference. Numbers and colors in the heat map represent the percent identities between selected strains and Oryx leucoryx coronavirus. Pairwise identity was generated using Geneious Prime software, and the heat map was generated in Prism software.

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Comparison, Generated, Software

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Pairwise amino acid identity of replicase conserved domains of OrCoV/ISR1127 with representative coronaviruses ^a

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Virus

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Genomic organization of Oryx leucoryx coronavirus. (A) Full-genome organization of OrCoV/ISR1127 (GenBank accession no. OM397541). The scheme shows genome size and major ORF positions. (B) Genomic organization of the region between the S gene and NS5. The scheme shows distinct ORFs in this region of 7.8 kDa and 4.7 kDa. Alignment with DcCoV (accession no. MN514966 ) in this region shows two deletion domains in OrCoV/ISR1127 (black lines). (C) Deduced amino acid comparison of an OrCoV/ISR1127 (accession no. OM397541) ORF encoding a 7.8-kDa protein with a DcCoV (accession no. MN514966 ) ORF encoding an 8.9-kDa protein. Alignments show that deletion in this region resulted in a premature stop codon and a truncated protein of 7.8 kDa in OrCoV/ISR1127 (deletion region highlighted in red). An amino acid comparison was generated using Geneious Prime software.

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Comparison, Generated, Software

Journal: Microbiology Spectrum

Article Title: Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

doi: 10.1128/spectrum.04848-22

Figure Lengend Snippet: Recombination analysis of Oryx leucoryx coronavirus with selected embecoviruses. (A) Recombination events were explored using Bootscan analysis in Simplot software version 3.5.1. OrCoV/ISR 1127 was used as the query. (B) A phylogenetic tree of hemagglutinin esterase (HE) was generated using the neighbor-joining method with bootstrap analysis (1,000 replicates, >70%) in Geneious Prime software. Accession numbers are shown in parentheses. BCoV is highlighted in red, and DcDCoV HKU23 is highlighted in blue.

Article Snippet: Following molecular detection of coronavirus, positive fecal samples were filtered using a 0.45-μm membrane and used for virus isolation by serial passaging on the human rectal tumor cell line HRT-18G (ATCC CRL11663).

Techniques: Software, Generated