Journal: Cell reports. Medicine

Article Title: Safety and immunogenicity of SARS-CoV-2 self-amplifying RNA vaccine expressing an anchored RBD: A randomized, observer-blind phase 1 study.

doi: 10.1016/j.xcrm.2023.101134

Figure Lengend Snippet: Figure 3. SARS-CoV-2 IgG and neutralizing antibody responses (A and B) Serum IgG titers against wild-type SARS- CoV-2 RBD protein (A) and pseudovirus neutralizing antibody titers (ID50) against SARS-CoV-2 variants (B) for non-elderly (left side) and elderly (right side) participants (n = 10 per dose group, and n = 6 for the placebo group). Participants received one injection of VLPCOV-01 (0.3, 1.0, or 3.0 mg), 30 mg BNT162b2, or placebo on day 1 (week 0). Logarithmic values are reported as geometric mean titers for serum IgG and neutralizing antibody against pseudovirus. Bars indicate 95% CIs. (C) The correlation between serum neutralizing antibody titers against pseudovirus Wuhan (wild type) and IgG antibody titers against SARS-CoV-2 RBD protein following booster vaccination. Pearson’s product-moment correlation coefficient and p value were calculated following log trans- formation of source data (r = 0.950, p < 0.001).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD154-FITC (clone: TRAP1) BD Biosciences cat# 555699; RRID: AB_396049 Mouse anti-human CD3-BUV615 (clone: SP34-2) BD Biosciences cat# 751249; RRID: AB_2875266 Mouse anti-human CD4-PE-Cy5.5 (clone: S3.5) Thermo Ficher Scientific cat# MHCD0418; RRID: AB_10376013 Mouse anti-human CD8-BUV563 (clone: RPA-T8) BD Biosciences cat# 612914; RRID: AB_2870200 Mouse anti-human CD27-PE-Cy5 (clone: 1A4CD27) Beckman coulter cat# 6607107 Mouse anti-human CD45RO-BUV805 (clone: UCHL1) BD Biosciences cat# 748367; RRID: AB_2872786 Mouse anti-human IFN-g-BV786 (clone: 4S.B3) BioLegend cat# 502542; RRID: AB_2563882 Mouse anti-human TNF-BV650 (clone: MAb11) BioLegend cat# 502938; RRID: AB_2562741 Rat anti-human IL-13-BV421 (clone: JES10-5A2) BD Biosciences cat# 563580; RRID: AB_2738290 Mouse anti-human IL-21-Ax647 (clone: 3A3-N21) BD Biosciences cat# 560493; RRID: AB_1645421 Mouse anti-human IL-4-PE-Cy7 (clone:8D4-8) BD Biosciences cat# 560672; RRID: AB_1727547 Mouse anti-human IL-17A-BV605 (clone: BL168) BioLegend cat# 512326; RRID: AB_2563887 Rat anti-human IL-2-BUV737 (clone: MQ117H12) BD Biosciences cat# 612836 Mouse anti-human CD107A-BV711 (clone: H4A3) BioLegend cat# 328640; RRID: AB_2565840 Mouse anti-human MIP1b-Alexa700 (clone: D21-1351) BD Biosciences cat# 561278; RRID: AB_10612008 Anti-SARS-CoV-2 Spike RBD Neutralizing Antibody, Human IgG1 (AS35) ACROBiosystems cat# SAD-S35 Anti-SARS-CoV-2 Spike RBD Neutralizing Antibody, Human IgG2 (AS35) ACROBiosystems cat# SAD-S66 Anti-SARS-CoV-2 Spike RBD Neutralizing Antibody, Human IgG3 (AS35) ACROBiosystems cat# SAD-S67 Anti-SARS-CoV-2 Spike RBD Neutralizing Antibody, Human IgG4 (AS35) ACROBiosystems cat# SAD-S68 Mouse anti-Human IgG1 Fc Secondary Antibody, HRP Thermo Fisher Scientific cat# MH1715; RRID: AB_2539710 Mouse Anti-Human IgG2 Fc-BIOT HP6002 SouthernBiotech cat# 9070-08; RRID: AB_2796638 Mouse Anti-Human IgG3 Hinge-BIOT HP6050 SouthernBiotech cat# 9210-08; RRID: AB_2796700 Mouse Anti-Human IgG4 Fc-BIOT HP6025 SouthernBiotech cat# 9200-08; RRID: AB_2796692 Biological samples Human PBMCs This study This study Chemicals, peptides, and recombinant proteins Benzonase Nuclease, Purity >90% MERCK Millipore cat# 70746 (Continued on next page) Cell Reports Medicine 4, 101134, August 15, 2023 e1

Techniques: Injection

Journal: Bioactive Materials

Article Title: Sulfated liposome-based artificial cell membrane glycocalyx nanodecoys for coronavirus inactivation by membrane fusion

doi: 10.1016/j.bioactmat.2023.10.021

Figure Lengend Snippet: Nanodecoy membrane fusion causes virus block. The cryo-TEM image of (A) SARS-CoV-2 or (B) SARS-CoV-2 incubated with 40S_Lip. The arrow pointing the spike protein. Scale bar: 50 nm. (C) The membrane fusion profile of the FRET lipid labeled nanodecoy 40S_Lip(FRET) incubated with no FRET lipid labeled nanodecoy 40S_Lip, SARS-CoV-2 pseudovirus, or 40S_Lip and SARS-CoV-2 pseudovirus. (D) The MD simulation result of the spike protein incubated with 40S_Lip for 0, 0.12, and 2 ns. (E) The potential of mean force curves for 40S_Lip and S protein. (F) The CD spectrum of the native spike protein or when incubated with 40S_Lip. (G) The percentage of the detected free spike protein after incubation with heparin, 40S_Lip(Large), or 40S_Lip. (H) The percentage of the detected spike protein on the SARS-CoV-2 pseudovirus after incubation with heparin, 40S_Lip(Large), or 40S_Lip.

Article Snippet: The SARS-CoV-2 spike protein S1 RBD ELISA kit was purchased from Elabscience Biotechnology Co., Ltd. (Wuhan, China).

Techniques: Membrane, Virus, Blocking Assay, Incubation, Labeling

Journal: medRxiv

Article Title: SARS-CoV-2 specific immune-signature in direct contacts of COVID-19 cases protect them from contracting disease: A Retrospective Study

doi: 10.1101/2021.03.11.21253367

Figure Lengend Snippet: A , Box plots showing the anti-SARS-CoV-2 IgA, IgM and IgG antibody proportions in serum samples from control, infected and contact along with B , Serum cytokine levels in pg/ml (Eotaxin, G-CSF, IL-7, MIF and MIP 1-□) determined by bio plex. C , The area under the receiver-operating characteristic (ROC) curve of the cytokines having more than 0.8 AUC. D , Box plot depicting the percent inhibition of neutralizing antibodies in an in -vitro spike RBD-ACE2 interaction based Surrogate Virus Neutralization assay. Statistical comparisons were performed using unpaired Wilcoxon test, p-values are written against respective comparisons. Where, n = number of individuals, IgA-Immunoglobulin A, IgM-Immunoglobulin M and IgG-Immunoglobulin G, control (n-14), infected (n-23, Symptomatic n-10 and Asymptomatic n-13) and contact (n-24).

Article Snippet: For IgA and IgM quantification, RBD (SARS-CoV-2 spike RBD recombinant protein, mFc-Tag, CST # 41701S) antigen at a concentration of 200ng/well was coated in a 96-well high binding micro titre plate (HIMEDIA-EP1) in 1x TBS pH-7.4 for 2h at 37□.

Techniques: Infection, Inhibition, In Vitro, Neutralization

Journal: Nature communications

Article Title: A high-throughput screen for TMPRSS2 expression identifies FDA-approved compounds that can limit SARS-CoV-2 entry.

doi: 10.1038/s41467-021-24156-y

Figure Lengend Snippet: Fig. 7 Agents that reduce TMPRSS2 expression markedly inhibit SARS-CoV-2 pseudoviral infection. A Schematic of pseudoviral construction and assay. The S protein of SARS-CoV-2 was C-terminally tagged with HiBiT. B Level of viral transduction in various cell lines plotted on a logarithmic scale. Calu-3 and Caco-2 cells had the highest observed rates of infection. Data are mean ± SEM (n = 4–6 biologically independent samples). C Effects of HHT or HFG on pseudoviral-mediated GFP expression, determined by immunostaining, scale bar = 500 µm. D, E Effects of increasing concentrations of homoharringtonine (HHT) (D) or halofuginone (HFG) (E) on SARS-CoV-2 pseudoviral infection. Data are mean ± SEM (n = 3–6 biologically independent samples). F, G SARS- CoV-2 pseudoviral infection of primary human bronchial epithelial cells in the presence of increasing concentrations of HHT (F) and HFG (G). Data are mean ± SEM (n = 3 biologically independent samples). H SARS-CoV-2 pseudoviral infection of Caco-2 cells transfected with DCAF1 siRNA along with HFG treatment (100 nM). Data are mean ± SEM (n = 6 biologically independent samples). I SARS-CoV-2 pseudoviral infection of Caco-2 cells transfected with TMPRSS2 WT or lysine mutant prior to HFG treatment (100 nM). All SARS-CoV-2 pseudoviral data is corrected to cell number as determined by CellTiter- Glo. Data are mean ± SEM (n = 6 biologically independent samples). P-values are shown for comparisons to 0 time point or control, or as indicated by one- way ANOVA with Dunnett’s test of multiple comparisons (F, G), or a two-way ANOVA with Tukey’s test of multiple comparisons (B, H, I).

Article Snippet: Pseudovirus with SARS-CoV-2 spike protein with a Cterminal HiBiT tag was generated by co-transfection of 293 T cells with psPAX2 (Addgene, MA), pLenti-c-mGFP (Origene, MD), and PFC37K-HIBIT-SARS-CoV-2-S (Backbone was from Promega, WI) by using lipofectamine 3000 (Invitrogen, CA).

Techniques: Expressing, Infection, Transduction, Immunostaining, Transfection, Mutagenesis, Control

Journal: Nature Communications

Article Title: A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples

doi: 10.1038/s41467-022-32371-4

Figure Lengend Snippet: a Schematic illustration of the workflow of the UCAD assay. b Sequence design of the dsDNA template for triggering the collateral cleavage activity of CRISPR-Cas12a, as well as the strategy to split the dsDNA template into TS and NTS probes for UCAD. c Proximity binding of the two UCAD probes to the same anti-RBD antibody through affinity motifs enhances the T m of the duplex domain from 10 to 46 °C and thus enables the stable binding between TS and NTS probes. d , e Kinetic curves for the detection of anti-RBD IgG ( d ) and IgM ( e ) in commercially purchased certified anti-SARS-CoV-2 IgG/IgM positive and negative serum samples using UCAD. f A calibration curve for the detection of anti-SARS-CoV-2 spike protein RBD human mAb (clone: OTIH401) in the range of 1 aM to 1 pM was established by plotting fluorescence intensity at 40 min of the CRISPR-Cas12a reaction as a function of target concentrations, which was also compared with UCAD without RPA amplification. Each concentration has replicated measurements ( n = 2). g , h Detection of anti-RBD IgG ( g ) and IgM ( h ) in certified anti-SARS-CoV-2 IgG/IgM positive serum diluted in negative human serum with dilution factors from 1 to 100,000 using both UCAD and commercial ELISA kits. Each concentration has replicated measurements ( n = 2). Source data are available in the Source Data file.

Article Snippet: SARS-CoV-2 Spike RBD human monoclonal antibody (Cat #: TA190325, clone name: OTIH401) and SARS-CoV-2 N protein human monoclonal antibody (Cat #: TA190323, clone name: OTIH1G5) were purchased from Origene, Beijing, China.

Techniques: Sequencing, Activity Assay, CRISPR, Binding Assay, Fluorescence, Amplification, Concentration Assay, Enzyme-linked Immunosorbent Assay

Journal: Nature Communications

Article Title: A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples

doi: 10.1038/s41467-022-32371-4

Figure Lengend Snippet: a Detection of the target anti-human RBD and closely related nontargeted anti-MERS-CoV spike protein RBD human mAb (clone: m336), anti-SARS-CoV-2 nucleocapsid (N) protein human mAb, and anti-SARS-CoV-2 spike protein RBD rabbit pAb at a concentration of 10 fM using UCAD. Each sample was measured twice in two independent experiments. b , c Evaluation of the specificity of UCAD for anti-RBD IgG ( b ) and IgM ( c ) against anti-SARS-CoV in clinical sera from three SARS patients in 2003. Each serum sample was measured twice in two independent experiments. The UCAD signals of anti-SARS-CoV positive sera were significantly lower than the anti-SARS-CoV-2 positive serum ( p = 0.0004 for IgG, p = 0.0025 for IgM). Ordinary one-way ANOVA were used to compare the difference between multiple groups. d Schematic illustration of the modularity of UCAD for varying mutants of RBD and the N protein of SARS-CoV-2 by switching the recognition motif on the TS probe. e Heatmap of the detection of 10 fM wild-type (WT), Delta specific, and Omicron specific anti-RBD human mAb by using WT RBD, Delta RBD, and Omicron RBD (B.1.1.529) modified TS probes. f Heatmap of the detection of 10 fM WT RBD human mAb and anti-N protein human mAb with WT RBD and N protein modified TS probes. Source data are available in the Source Data file. ns: p > 0.05, *** p ≤ 0.001.

Article Snippet: SARS-CoV-2 Spike RBD human monoclonal antibody (Cat #: TA190325, clone name: OTIH401) and SARS-CoV-2 N protein human monoclonal antibody (Cat #: TA190323, clone name: OTIH1G5) were purchased from Origene, Beijing, China.

Techniques: Concentration Assay, Modification

Journal: Nature Communications

Article Title: A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples

doi: 10.1038/s41467-022-32371-4

Figure Lengend Snippet: a Schematic illustration of lateral flow readout for UCAD for the detection of anti-SARS-CoV-2 IgG and IgM. b The design of the lateral flow strip that captured all anti-FAM labeled AuNPs at C-line in the absence of the target antibody. In the presence of ant-SARS-CoV-2 IgG or IgM, the FAM-Dig dual-labeled reporters were cleaved by Cas12a-crRNA so that AuNPs could escape the capture at C-line and accumulated at T-line through the immobilized secondary antibody. c Visual detection of 15 positive clinical sera and 15 pre-pandemic sera by UCAD integrated with lateral flow strips.

Article Snippet: SARS-CoV-2 Spike RBD human monoclonal antibody (Cat #: TA190325, clone name: OTIH401) and SARS-CoV-2 N protein human monoclonal antibody (Cat #: TA190323, clone name: OTIH1G5) were purchased from Origene, Beijing, China.

Techniques: Stripping Membranes, Labeling

Journal: Biosensors

Article Title: Comparison of Three Lateral Flow Immunoassay Formats for the Detection of Antibodies against the SARS-CoV-2 Antigen

doi: 10.3390/bios13070750

Figure Lengend Snippet: Comparison of conditions for Scheme A of SARS-CoV-2 serodiagnosis: ( a ) choice of OD 520 for protein A–GNPs conjugate at RBD concentration applied to AZ of 0.5 mg/mL; and ( b ) choice of RBD concentration loaded to AZ at OD 520 of protein A–GNPs conjugate of 5.0. The red bars in ( a , b ) correspond to the 30-fold diluted pooled negative serum, and the black bars correspond to the same diluted serum with added AB RBD 5324 antibody at a concentration of 5 µg/mL.

Article Snippet: The recombinant RBD of SARS-CoV-2 spike protein and the monoclonal antibodies to it, clone 5324 (AB RBD 5324), were from HyTest (Moscow, Russia).

Techniques: Concentration Assay

Journal: Biosensors

Article Title: Comparison of Three Lateral Flow Immunoassay Formats for the Detection of Antibodies against the SARS-CoV-2 Antigen

doi: 10.3390/bios13070750

Figure Lengend Snippet: Comparison of conditions for Scheme B of SARS-CoV-2 serodiagnosis: ( a ) choice of OD 520 for RBD–GNPs conjugate at RBD concentration applied to AZ of 0.5 mg/mL; and ( b ) choice of RBD concentration loaded to AZ at OD 520 of RBD–GNPs conjugate of 5.0. The red bars in ( a , b ) correspond to the 30-fold diluted pooled negative serum, and the black bars correspond to the same diluted serum with added AB RBD 5324 antibody at a concentration of 5 µg/mL.

Article Snippet: The recombinant RBD of SARS-CoV-2 spike protein and the monoclonal antibodies to it, clone 5324 (AB RBD 5324), were from HyTest (Moscow, Russia).

Techniques: Concentration Assay

Journal: Biosensors

Article Title: Comparison of Three Lateral Flow Immunoassay Formats for the Detection of Antibodies against the SARS-CoV-2 Antigen

doi: 10.3390/bios13070750

Figure Lengend Snippet: Comparison of conditions for Scheme C of SARS-CoV-2 serodiagnosis: ( a ) choice of OD 520 for RBD–GNPs conjugate at protein A concentration applied to AZ of 0.5 mg/mL; and ( b ) choice of protein A concentration loaded to AZ at OD 520 of RBD–GNPs conjugate of 5.0. The red bars in ( a , b ) correspond to the 30-fold diluted pooled negative serum, and the black bars correspond to the same diluted serum with added AB RBD 5324 antibody at a concentration of 5 µg/mL.

Article Snippet: The recombinant RBD of SARS-CoV-2 spike protein and the monoclonal antibodies to it, clone 5324 (AB RBD 5324), were from HyTest (Moscow, Russia).

Techniques: Concentration Assay

Journal: Biosensors

Article Title: Comparison of Three Lateral Flow Immunoassay Formats for the Detection of Antibodies against the SARS-CoV-2 Antigen

doi: 10.3390/bios13070750

Figure Lengend Snippet: LFIAs of the AB RBD 5324 antibodies added to the 30-fold diluted pooled negative serum. ( a ) The appearance of test strips after analysis. The AB RBD 5324 concentrations are 20 (1), 10 (2), 5.0 (3), 2.5 (4), 1.25 (5), 0.62 (6), 0.31 (7), 0.155 (8), 0.078 (9), 0.04 (10), 0.02 (11), 0.01 (12), 0.005 (13) and 0 (14) µg/mL. ( b – d ) Calibration curves of Schemes A, B and C, respectively (with added zooms of their working ranges and the indicated slope α).

Article Snippet: The recombinant RBD of SARS-CoV-2 spike protein and the monoclonal antibodies to it, clone 5324 (AB RBD 5324), were from HyTest (Moscow, Russia).

Techniques:

Journal: Biosensors

Article Title: Comparison of Three Lateral Flow Immunoassay Formats for the Detection of Antibodies against the SARS-CoV-2 Antigen

doi: 10.3390/bios13070750

Figure Lengend Snippet: Comparison of SARS-CoV-2 serodiagnostic schemes for anti-RBD antibody detection.

Article Snippet: The recombinant RBD of SARS-CoV-2 spike protein and the monoclonal antibodies to it, clone 5324 (AB RBD 5324), were from HyTest (Moscow, Russia).

Techniques: