sars cov 2 spike neutralizing antibody Search Results


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Figure 3. SARS-CoV-2 <t>IgG</t> 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).
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(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 <t>neutralizing</t> 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.
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(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 <t>neutralizing</t> 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.
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(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 <t>neutralizing</t> 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.
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(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 <t>neutralizing</t> 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.
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(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 <t>neutralizing</t> 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.
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Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of <t>SARS-CoV-2</t> WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .
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Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of <t>SARS-CoV-2</t> WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .
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Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of <t>SARS-CoV-2</t> WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .
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Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of <t>SARS-CoV-2</t> WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .
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Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of <t>SARS-CoV-2</t> WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .
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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).

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

(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.

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

Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of SARS-CoV-2 WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .

Journal: bioRxiv

Article Title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

doi: 10.1101/2024.03.08.583965

Figure Lengend Snippet: Fetal lung xenografts (fLX) of BLT-L mice were infected with 1×10 6 PFU of SARS-CoV-2 WA-1 isolate via subcutaneous intra-graft injection. (A) BLT-L mice were monitored for weight change over the course of 12-days post infection (dpi). (B) Immunohistochemistry for SARS-CoV-2 S protein (a-d) and hematoxylin and eosin staining (e-f) were performed on naïve fLX (a,e) and fLX at 2 dpi (b,f) , 6 dpi (c,g), and 12 dpi (d,h) . Scale bar = 100 μM (C) Viral titer (log(PFU/mg)) in fLX at 2, 6, and 12 dpi as determined by plaque assay. (D) Histopathological scoring of naïve fLX and fLX at 2, 6, and 12 dpi. Data are representative of two or three independent experiments. n = 6 -10 per timepoint. Error bars represent mean ± standard error of the mean (SEM). One-way ANOVA analysis was performed. p-values are indicated on graphs and only significant comparisons are shown .

Article Snippet: After a 24 h incubation at 37 °C with 5% CO2 media was removed and cells were fixed with 10% formalin for 1 h. A SARS-CoV-2 spike neutralizing antibody (Sino Biological Inc., Beijing, China; 2 μg/μL; Clone #57) was used as a positive control.

Techniques: Infection, Injection, Immunohistochemistry, Staining, Plaque Assay

Single cell RNA sequencing analysis was performed on single cell suspensions of naïve fLX and fLX at 2 and 12 dpi. Naïve n=3 fLX (9,605 cells), 2 dpi n=2 fLX (4,405 cells), and 12 dpi n = 2 fLX (5,857 cells). (A) UMAP plot clustering of the human cell compartment of naïve fLX and fLX at 2 and 12 dpi. (B) Temporal annotation of the human clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). Clusters unique to 2 dpi are annotated by A (T cell compartment), B (mesenchymal compartment), or C (myeloid compartment). (C) Frequency of each cell compartment determined by single cell RNA-sequencing. (D) Dot plots displaying the expression of SARS-CoV-2 viral RNA transcripts identified in scRNA-seq. (E) UMAP plot showing the distribution of SARS-CoV-2 viral RNA transcripts across all human cell clusters and time points. (F) UMAP plot sub-clustering of the human epithelial compartment of fLX across all time points. (G) Temporal annotation of the human epithelial sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). The inset graph indicates the change in frequency of each compartment (AT2; black, Basal; pink, Secretory; teal, and AT1; purple) within the epithelial compartment. Red line indicates the change in the AT2 compartment over time. (H) Heatmap displaying the relative expression (from -1 to 1) of the top differentially regulated genes over the course of infection within the AT2 compartment.

Journal: bioRxiv

Article Title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

doi: 10.1101/2024.03.08.583965

Figure Lengend Snippet: Single cell RNA sequencing analysis was performed on single cell suspensions of naïve fLX and fLX at 2 and 12 dpi. Naïve n=3 fLX (9,605 cells), 2 dpi n=2 fLX (4,405 cells), and 12 dpi n = 2 fLX (5,857 cells). (A) UMAP plot clustering of the human cell compartment of naïve fLX and fLX at 2 and 12 dpi. (B) Temporal annotation of the human clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). Clusters unique to 2 dpi are annotated by A (T cell compartment), B (mesenchymal compartment), or C (myeloid compartment). (C) Frequency of each cell compartment determined by single cell RNA-sequencing. (D) Dot plots displaying the expression of SARS-CoV-2 viral RNA transcripts identified in scRNA-seq. (E) UMAP plot showing the distribution of SARS-CoV-2 viral RNA transcripts across all human cell clusters and time points. (F) UMAP plot sub-clustering of the human epithelial compartment of fLX across all time points. (G) Temporal annotation of the human epithelial sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). The inset graph indicates the change in frequency of each compartment (AT2; black, Basal; pink, Secretory; teal, and AT1; purple) within the epithelial compartment. Red line indicates the change in the AT2 compartment over time. (H) Heatmap displaying the relative expression (from -1 to 1) of the top differentially regulated genes over the course of infection within the AT2 compartment.

Article Snippet: After a 24 h incubation at 37 °C with 5% CO2 media was removed and cells were fixed with 10% formalin for 1 h. A SARS-CoV-2 spike neutralizing antibody (Sino Biological Inc., Beijing, China; 2 μg/μL; Clone #57) was used as a positive control.

Techniques: RNA Sequencing Assay, Expressing, Infection

(A) UMAP plot showing sub-clustering of the human myeloid compartment of fLX across all time points. (B) Temporal annotation of the myeloid sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). iMO cluster is indicated with a blue circle. (C) UMAP plot (all time points) showing the distribution of SARS-CoV-2 viral RNA transcripts in the myeloid compartment. (D-F) UMAP plot showing the expression of CD 163 (D), CD4 (E) , and MRC1 (F) across myeloid sub-sets. (G) Frequency of each myeloid sub-cluster by timepoint. (H) Relative expression of highly upregulated ISGs and inflammatory markers in each of the myeloid sub-clusters. (I) Multiplex fluorescent immunohistochemistry of naïve fLX and fLX at 2 and 12 dpi. CD163: teal, CD4: yellow, CD3: orange, PPARγ: green, Dapi: gray. Two representative images. Scale bar = 100 μM (J) Violin plots showing expression level of differentially expressed genes between SARS-CoV-2 positive and negative iMo (cluster 3).

Journal: bioRxiv

Article Title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

doi: 10.1101/2024.03.08.583965

Figure Lengend Snippet: (A) UMAP plot showing sub-clustering of the human myeloid compartment of fLX across all time points. (B) Temporal annotation of the myeloid sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). iMO cluster is indicated with a blue circle. (C) UMAP plot (all time points) showing the distribution of SARS-CoV-2 viral RNA transcripts in the myeloid compartment. (D-F) UMAP plot showing the expression of CD 163 (D), CD4 (E) , and MRC1 (F) across myeloid sub-sets. (G) Frequency of each myeloid sub-cluster by timepoint. (H) Relative expression of highly upregulated ISGs and inflammatory markers in each of the myeloid sub-clusters. (I) Multiplex fluorescent immunohistochemistry of naïve fLX and fLX at 2 and 12 dpi. CD163: teal, CD4: yellow, CD3: orange, PPARγ: green, Dapi: gray. Two representative images. Scale bar = 100 μM (J) Violin plots showing expression level of differentially expressed genes between SARS-CoV-2 positive and negative iMo (cluster 3).

Article Snippet: After a 24 h incubation at 37 °C with 5% CO2 media was removed and cells were fixed with 10% formalin for 1 h. A SARS-CoV-2 spike neutralizing antibody (Sino Biological Inc., Beijing, China; 2 μg/μL; Clone #57) was used as a positive control.

Techniques: Expressing, Multiplex Assay, Immunohistochemistry

(A) UMAP plot showing the sub-clustering of the human T-cell compartment of fLX across all time points. (B) Temporal annotation of the human T-cell sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). (C) UMAP plot (all time points) showing the distribution of SARS-CoV-2 viral RNA transcripts in the T-cell compartment. (D) Go-term analysis showing the most highly upregulated signaling pathways in the macrophage-like T-cell cluster (cluster 6). (E) Relative expression of T-cells, macrophage, mesenchymal and antiviral markers within each of the T-cell sub-clusters (From 0 to 8; as labeled in panel A.).

Journal: bioRxiv

Article Title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

doi: 10.1101/2024.03.08.583965

Figure Lengend Snippet: (A) UMAP plot showing the sub-clustering of the human T-cell compartment of fLX across all time points. (B) Temporal annotation of the human T-cell sub-clusters on the UMAP plot: naïve (black), 2 dpi (red), 12 dpi (blue). (C) UMAP plot (all time points) showing the distribution of SARS-CoV-2 viral RNA transcripts in the T-cell compartment. (D) Go-term analysis showing the most highly upregulated signaling pathways in the macrophage-like T-cell cluster (cluster 6). (E) Relative expression of T-cells, macrophage, mesenchymal and antiviral markers within each of the T-cell sub-clusters (From 0 to 8; as labeled in panel A.).

Article Snippet: After a 24 h incubation at 37 °C with 5% CO2 media was removed and cells were fixed with 10% formalin for 1 h. A SARS-CoV-2 spike neutralizing antibody (Sino Biological Inc., Beijing, China; 2 μg/μL; Clone #57) was used as a positive control.

Techniques: Expressing, Labeling

Immunological events defining the successful resolution of SARS-CoV-2 infection in human lung tissues.

Journal: bioRxiv

Article Title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

doi: 10.1101/2024.03.08.583965

Figure Lengend Snippet: Immunological events defining the successful resolution of SARS-CoV-2 infection in human lung tissues.

Article Snippet: After a 24 h incubation at 37 °C with 5% CO2 media was removed and cells were fixed with 10% formalin for 1 h. A SARS-CoV-2 spike neutralizing antibody (Sino Biological Inc., Beijing, China; 2 μg/μL; Clone #57) was used as a positive control.

Techniques: Infection