Journal: Viruses

Article Title: An ACE2-Based Decoy Inhibitor Effectively Neutralizes SARS-CoV-2 Omicron BA.5 Variant

doi: 10.3390/v14112387

Figure Lengend Snippet: SPR-based characterization of Kansetin’s binding affinity to Spike RBD protein of SARS-CoV-2 Omicron BA.5 strain ( A ) and Spike S1+S2 trimer protein ( B ).

Article Snippet: The His-tagged RBD of the SARS-CoV-2 Omicron BA.5 strain (Sino Biological Inc, Beijing, China) was diluted to a two-fold dilution series (0, 10, 20, 40, 80, and 160 nM), and the Spike S1+S2 trimer of the BA.5 strain (Sino Biological Inc, Beijing, China) was diluted to a two-fold dilution series (0, 2.5, 5, 10, and 20 nM).

Techniques: Binding Assay

Journal: Viruses

Article Title: An ACE2-Based Decoy Inhibitor Effectively Neutralizes SARS-CoV-2 Omicron BA.5 Variant

doi: 10.3390/v14112387

Figure Lengend Snippet: Summarization of data between different SARS-CoV-2 strains 1 .

Article Snippet: The His-tagged RBD of the SARS-CoV-2 Omicron BA.5 strain (Sino Biological Inc, Beijing, China) was diluted to a two-fold dilution series (0, 10, 20, 40, 80, and 160 nM), and the Spike S1+S2 trimer of the BA.5 strain (Sino Biological Inc, Beijing, China) was diluted to a two-fold dilution series (0, 2.5, 5, 10, and 20 nM).

Techniques:

Journal: bioRxiv

Article Title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

doi: 10.1101/2024.07.10.602843

Figure Lengend Snippet: (A) Workflow of this study. (B) Binding affinity (ELISA OD450) and pseudovirus-neutralization activities(Half maximal inhibitory concentration, IC50) of isolated monoclonal antibodies (n = 361) against WT, BA.5, BA.2.75 and XBB. Medians and means are depicted as black circles or short lines in the figure. Pie charts represent the distribution of pseudovirus-neutralization activities of high-affinity antibodies (OD450 > 2) against the corresponding variant. Neutralization potency is categorized as potent (IC 50 ≤ 0.05), medium (0.05 < IC 50 ≤ 1), and weak/non-neutralizing (IC 50 > 1). (C) Categories of the 361 antibodies based on affinity. Define high affinity for OD450 ≥ 2 and low affinity for OD450 < 2. The antibodies are categorized into six groups: Broad-reactive, showing high affinity to WT, BA.2.75, BA.5, and XBB NTDs (247 of 361); WT/BA.5 cross-reactive, showing high affinity to WT and BA.5 NTDs (72 of 361); WT/BA.2.75 cross-reactive, showing high affinity to WT and BA.2.75 NTDs (4 of 361); Omicron-specific, showing high affinity to BA.2.75, BA.5, or XBB NTDs but low affinity to WT NTD (33 of 361); Weak affinity, showing low affinity to WT, BA.2.75, BA.5, and XBB NTDs (3 of 361); and WT-specific, showing high affinity to WT NTD but low affinity to BA.2.75, BA.5, and XBB NTDs (2 of 361). (D) The heavy chain V domain somatic hypermutation (SHM) ratio of broad-reactive, WT/BA.5 cross and Omicron-specific antibodies. Two-tailed Wilcoxon rank-sum tests was used to examine the significant differences of unpaired samples. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; NS, not significant (P > 0.05). (E-G) Pseudovirus-neutralization activities of broad-reactive (E) WT/BA.5 cross (F) and Omicron-specific (G) antibodies. Geometric mean titres (GMTs) are shown.

Article Snippet: B cells were stained with 3 μL FITC anti-human CD20 antibody (BioLegend, 302304, clone: 2H7), 3.5 μL Brilliant Violet 421 anti-human CD27 antibody (BioLegend, 302824, clone: O323), 2 μL PE/Cyanine7 anti-human IgM antibody (BioLegend, 314532, clone: MHM-88), 2 μL PE/Cyanine7 anti-human IgD antibody (BioLegend, 348210, clone: IA6-2), 0.013 μg biotinylated SARS-CoV-2 BA.5/BF.7 NTD protein (Sino Biological, 22BD75-77) conjugated with PE-streptavidin (BioLegend, 405204) or APC-streptavidin (BioLegend, 405207), 0.013 μg biotinylated SARS-CoV-2 WT NTD protein (Sino Biological, 40591-V49H-B) conjugated with APC-streptavidin (S3A Fig), and 0.013 μg biotinylated SARS-CoV-2 BA.5 RBD protein (Sino Biological, 22BD75-73) conjugated with PE-streptavidin.

Techniques: Binding Assay, Enzyme-linked Immunosorbent Assay, Neutralization, Concentration Assay, Isolation, Variant Assay, Two Tailed Test

Journal: bioRxiv

Article Title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

doi: 10.1101/2024.07.10.602843

Figure Lengend Snippet: (A) Pseudovirus-neutralizing IC 50 of 5 ultra-potent NTD-targeting NAbs against SARS-CoV-2 D614G, BA.1, BA.2, BA.2.75, BA.5, BQ.1.1, BQ.1.1+Y144del, XBB, XBB.1, XBB.1.5, EG.5.1 and HK.3.1, and their usage of heavy chain V (VH), heavy chain J (VJ), light chain V (VL) and light chain J (VJ) genes. (B) Heatmap for pair-wised SPR competition scores of 5 ultra-potent NTD-targeting NAbs and BD57-0617, BD57-0740, BD57-0536, BD57-0569, C1717 and C1520 on XBB.1.5 spike. (C) Calculation of immune pressure on each NTD site (residues 13-304 in WT index) and mutation of BD58-0730 escape mutation profiles weighted by BA.5. (D) Average DMS site escape scores of BD58-0730 are indicated on the structure model of the SARS-CoV-2 BA.5 NTD (PDB: 7XNQ). Hotspot residues are indicated by arrows. (E) SPR competition scores of 5 ultra-potent NTD-targeting NAbs, BD57-3253 and BD55-1205 as first antibody against ACE2. (F) Pseudovirus-neutralization curve of full-length IgG, Fab and F(ab’)2 forms of BD58-0730. Data for each form were obtained from a representative neutralization experiment.

Article Snippet: B cells were stained with 3 μL FITC anti-human CD20 antibody (BioLegend, 302304, clone: 2H7), 3.5 μL Brilliant Violet 421 anti-human CD27 antibody (BioLegend, 302824, clone: O323), 2 μL PE/Cyanine7 anti-human IgM antibody (BioLegend, 314532, clone: MHM-88), 2 μL PE/Cyanine7 anti-human IgD antibody (BioLegend, 348210, clone: IA6-2), 0.013 μg biotinylated SARS-CoV-2 BA.5/BF.7 NTD protein (Sino Biological, 22BD75-77) conjugated with PE-streptavidin (BioLegend, 405204) or APC-streptavidin (BioLegend, 405207), 0.013 μg biotinylated SARS-CoV-2 WT NTD protein (Sino Biological, 40591-V49H-B) conjugated with APC-streptavidin (S3A Fig), and 0.013 μg biotinylated SARS-CoV-2 BA.5 RBD protein (Sino Biological, 22BD75-73) conjugated with PE-streptavidin.

Techniques: Mutagenesis, Neutralization

Journal: bioRxiv

Article Title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

doi: 10.1101/2024.07.10.602843

Figure Lengend Snippet: (A) NTD mutations carried by SARS-CoV-2 variants. N1-N5 loops are shown as green, purple, orange, yellow and blue. (B) Pseudovirus-neutralizing IC 50 of 5 ultra-potent NTD-targeting NAbs against XBB.1.5, BA.2.86, XBB.1.5 + MPLFins, BA.2.86 + MPLFdel, BA.2.87.1 and XBB.1.5 + 15-23del. (C) 50% neutralization titers (NT 50 ) against XBB.1.5, XBB.1.5 + MPLFins, BA.2.86 and BA.2.86 + MPLFdel of plasma samples from convalescents infected by XBB after 3 doses of CoronaVac (n = 54).

Article Snippet: B cells were stained with 3 μL FITC anti-human CD20 antibody (BioLegend, 302304, clone: 2H7), 3.5 μL Brilliant Violet 421 anti-human CD27 antibody (BioLegend, 302824, clone: O323), 2 μL PE/Cyanine7 anti-human IgM antibody (BioLegend, 314532, clone: MHM-88), 2 μL PE/Cyanine7 anti-human IgD antibody (BioLegend, 348210, clone: IA6-2), 0.013 μg biotinylated SARS-CoV-2 BA.5/BF.7 NTD protein (Sino Biological, 22BD75-77) conjugated with PE-streptavidin (BioLegend, 405204) or APC-streptavidin (BioLegend, 405207), 0.013 μg biotinylated SARS-CoV-2 WT NTD protein (Sino Biological, 40591-V49H-B) conjugated with APC-streptavidin (S3A Fig), and 0.013 μg biotinylated SARS-CoV-2 BA.5 RBD protein (Sino Biological, 22BD75-73) conjugated with PE-streptavidin.

Techniques: Neutralization, Infection