Journal: PeerJ

Article Title: Nationwide wastewater sequencing surveillance of SARS-CoV-2 lineages: validation against clinical data across 28 U.S. states

doi: 10.7717/peerj.20941

Figure Lengend Snippet: Spearman rank correlation coefficient between wastewater abundances and clinical abundances of SARS-CoV-2 lineages. All correlations were positive and significant after a Bonferroni correction, indicating clear agreement. Lower correlation coefficients are thought to be a result of either limited data points (BA) or ongoing epidemiological dynamics (LF, KP) for more recent lineages.

Article Snippet: For all sequencing runs, SARS-CoV-2 gRNA (ATCC VR-1986D), an early isolate of the original SARS-CoV-2 virus from March of 2020 in Washington, is used as a positive control (GenBank: MT246667.1 ).

Techniques:

Journal: PeerJ

Article Title: Nationwide wastewater sequencing surveillance of SARS-CoV-2 lineages: validation against clinical data across 28 U.S. states

doi: 10.7717/peerj.20941

Figure Lengend Snippet: Box and whisker plot of days from average emergence (defined as the date in which a lineage represented over 10% of the total abundance of lineages in at least 5 of our sites) for each SARS-CoV-2 lineage lineage. Each dot represents an individual WWTP. A larger spread indicates a slower spread across the country. Negative values represent an earlier emergence. Each of these dates is calculated with respect to each lineage’s average emergence across all sites.

Article Snippet: For all sequencing runs, SARS-CoV-2 gRNA (ATCC VR-1986D), an early isolate of the original SARS-CoV-2 virus from March of 2020 in Washington, is used as a positive control (GenBank: MT246667.1 ).

Techniques: Whisker Assay

Journal: Biosensors

Article Title: Point-of-Care Diagnostic Biosensors to Monitor Anti-SARS-CoV-2 Neutralizing IgG/sIgA Antibodies and Antioxidant Activity in Saliva

doi: 10.3390/bios13020167

Figure Lengend Snippet: Current-potential profiles ( a , c ) and calibration curves ( b , d ) of neutralizing antibodies sIgA and IgG were obtained using the GLEIA−based electrochemical immunosensor. Current−potential responses were tested under different concentrations of ( a ) sIgA 100 ng/mL (blue), 20 ng/mL (grey), 5 ng/mL (orange), 1 ng/mL (red), and 0 ng/mL (black) and ( c ) IgG 62.5 U/mL (blue), 25 U/mL (grey), 6.25 U/mL (orange), 2.5 U/mL (red), and 0 U/mL (black). Calibration curves were indicated for sIgA ( b ) and IgG ( d ) as Michaelis–Menten-type functions by a non-linear curve fitted in the graphing software Origin2022 (OriginLab).

Article Snippet: As positive controls for neutralizing antibodies, the sIgA antibody (E-AB-V1027, Elabscience, Houston, TX, USA), IgG antibody (SPD-M180, Acro Biosystems, Tokyo, Japan), and IgG standard in the IgG ELISA kit (290-84201, FUJIFILM Wako, Osaka, Japan) were used.

Techniques: Software

Journal: Biosensors

Article Title: Point-of-Care Diagnostic Biosensors to Monitor Anti-SARS-CoV-2 Neutralizing IgG/sIgA Antibodies and Antioxidant Activity in Saliva

doi: 10.3390/bios13020167

Figure Lengend Snippet: Comparisons of concentrations of neutralizing antibody IgG ( a ) and sIgA ( b ), antioxidant activity (indicated by luminescence inhibition rate) ( c ), and protein concentration ( d ) using saliva samples from 10 individuals are presented together. All 10 saliva samples were collected 3 weeks after the second dose of the vaccine.

Article Snippet: As positive controls for neutralizing antibodies, the sIgA antibody (E-AB-V1027, Elabscience, Houston, TX, USA), IgG antibody (SPD-M180, Acro Biosystems, Tokyo, Japan), and IgG standard in the IgG ELISA kit (290-84201, FUJIFILM Wako, Osaka, Japan) were used.

Techniques: Antioxidant Activity Assay, Inhibition, Protein Concentration

Journal: Biosensors

Article Title: Point-of-Care Diagnostic Biosensors to Monitor Anti-SARS-CoV-2 Neutralizing IgG/sIgA Antibodies and Antioxidant Activity in Saliva

doi: 10.3390/bios13020167

Figure Lengend Snippet: The four datasets of neutralizing antibodies—IgG and sIgA, antioxidant activity, and protein concentration—measured in 10 samples are depicted individually in a radar chart for each individual. The numbers T1–T10 correspond to the sample numbers 1–10 in . The data are shown as a ratio of the maximum concentration of each measured item.

Article Snippet: As positive controls for neutralizing antibodies, the sIgA antibody (E-AB-V1027, Elabscience, Houston, TX, USA), IgG antibody (SPD-M180, Acro Biosystems, Tokyo, Japan), and IgG standard in the IgG ELISA kit (290-84201, FUJIFILM Wako, Osaka, Japan) were used.

Techniques: Antioxidant Activity Assay, Protein Concentration, Concentration Assay

Journal: Biosensors

Article Title: Point-of-Care Diagnostic Biosensors to Monitor Anti-SARS-CoV-2 Neutralizing IgG/sIgA Antibodies and Antioxidant Activity in Saliva

doi: 10.3390/bios13020167

Figure Lengend Snippet: The results of continuous monitoring of the concentration of neutralizing IgG ( B ) and sIgA ( C ) antibodies, antioxidant activity ( D ), and protein concentration ( E ) in saliva and neutralizing IgG concentration in serum ( A ) before and after 1st, 2nd, and 3rd vaccinations in the same individual over time were compared vertically. The abscissa represents the date and time of sampling. 0: at first vaccination; 1a: 4 days later, 1b: 1 week later, 1c: 2 weeks later, and 1d: 3 weeks later; 2a: 4 days after second vaccination; 2b: 1 week later, 2c: 2 weeks later, 2d: 3 weeks later, 2e: 1 month later, 2f: 2 months later, 2g: 3 months later, 2h: 4 months later, 2i: 5 months later, 2j: 6 months later, and 2k: 8 months later; 3a: 3 days after the third vaccination, 3b: 2 weeks later, and 3c: 1 month later. The units on the vertical axis are as follows: ( A , B ) U/mL, ( C ) ng/mL, ( D ) %, and ( E ) mg/mL.

Article Snippet: As positive controls for neutralizing antibodies, the sIgA antibody (E-AB-V1027, Elabscience, Houston, TX, USA), IgG antibody (SPD-M180, Acro Biosystems, Tokyo, Japan), and IgG standard in the IgG ELISA kit (290-84201, FUJIFILM Wako, Osaka, Japan) were used.

Techniques: Concentration Assay, Antioxidant Activity Assay, Protein Concentration, Sampling

Journal: bioRxiv

Article Title: SARS-CoV-2 Defective Viral Genomes from Distinct Genomic Regions Drive Divergent Interferon Responses

doi: 10.64898/2026.03.19.712870

Figure Lengend Snippet: (A-B) A549:EV and A549:N cells were infected with WT (MOI 1) or DVG-B (MOI 1), respectively, and cells were collected 24-hours post-inoculation for confocal microscopy. (A-B) Maximum intensity projections of merged dsRNA ( A-B , red) staining with the N protein ( A , white) or Nsp6 ( B , white) in A549-EV and A549:N cells. Nuclei were Hoechst stained (blue). Note that DVG-B encoded GFP is depicted (green). Scale bar indicates 20μm. Insets depict magnified cell regions indicated by the white boxes of dsRNA and N protein co-staining ( A ) or dsRNA and Nsp6 co-staining ( B ). Scale bar indicates 5μm. Graphs indicate the Pearson’s correlation coefficient ( R) values for the co-localization of dsRNA and N ( C, above) or dsRNA and Nsp6 ( C, below ) in A549:EV and A549:N cells, respectively. Individual values are shown. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 by one-way ANOVA with Turkey’s multiple comparisons test. Mean±SD. ( D ) A549:EV (left) and A549:N cells (right) were infected with WT (MOI 1) or DVG-B (MOI 50 to maximize the DVG-B infected cell number), respectively, and cells were collected 24-hours post-inoculation for fixation and processing for transmission electron microscopy. Scale bars indicate 2μm. Insets depict magnified cell regions indicated by the white boxes. Scale bars indicate 500nm. Black asterisks indicate single membrane vesicles, red asterisks indicate lysosome-like structures. ( E ) Due to significant more cell death in WT infected A549:EV and A549:N cells, we reduced MOI of WT virus to 0.1 for this experiment. A549:EV and A549:N cells were infected with WT (MOI 0.1) or DVG-B (MOI 1), respectively, and cells were collected 24-hours post-inoculation for RT-qPCR. Expression of host genes and viral genes/DVG-B were calculated relative to GAPDH. IFNB1, IL-29 and ISG54 relative copy number values were normalized to mock for A549:EV and A549:N, respectively. Because the A549:N cell line expresses codon-optimized N, the qPCR primers specifically detect virus-derived N transcripts. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 by two-way ANOVA with Turkey’s multiple comparisons test. N=2 biological repeats, mean±SD. ( F ) A549:EV and A549:N cells were inoculated as in ( E ). Immediately following 2-hours of inoculation, 10μg/mL of a neutralizing SARS-CoV-2 spike antibody or 10μg/mL of an IgG isotype control antibody were added to the infected cell cultures. 24-hours post inoculation cell supernatants were collected for virus titer determination by TCID 50 /mL quantification. Cells were collected for RT-qPCR. Expression of host genes and viral genes/DVG-B were calculated relative to GAPDH. IL-29 relative copy number values were normalized to mock for A549:EV and A549:N, respectively. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 by two-way ANOVA with Turkey’s multiple comparisons test. N=3 biological repeats, mean±SD.

Article Snippet: Post inoculation, cells were washed three times with PBS and cultured in 5% TCM with 10μg/mL of Spike neutralizing antibody (40592-R001, Sino Biological, obtained from BEI resources).

Techniques: Infection, Confocal Microscopy, Staining, Transmission Assay, Electron Microscopy, Membrane, Virus, Quantitative RT-PCR, Expressing, Derivative Assay, Control

Journal: Nature communications

Article Title: SuPAR mediates viral response proteinuria by rapidly changing podocyte function.

doi: 10.1038/s41467-023-40165-5

Figure Lengend Snippet: Fig. 4 | Omicron S1 protein distinguished from its 2019-nCov counterpart both biophysically and functionally. a–d S1 protein binding affinity as indicated by surface plasmon resonance assays. As shown, S1 protein was immobilized onto a CM5 sensor chip, while αvβ3 integrin or ACE2 was applied as an analyte in a series of increasing concentrations. Calculation of KD value indicates that 2019-nCov S1 protein bound more tightly to ACE2 (a) and αvβ3 integrin (c), as compared to Omicron S1 protein (b, d). e, f The effects of S1 protein on cultured human podo- cytes. Fully differentiated humanpodocytes were treated for 16 h before harvest for

Article Snippet: To establish the SARS-CoV-2 spike protein inoculation model, 10–12-week-old male C57BL/6j, Plaur−/−, and suPAR-Tg mice (n = 8 in each group) were inoculated intranasally (I/N) with recombinant 2019- nCov spike S1 (Abeomics, 32-190005) at 2.5 ng/g body weight, once a day for 10days.

Techniques: Protein Binding, SPR Assay, Cell Culture