wild type sars cov 2 reference rna  (ATCC)


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    ATCC wild type sars cov 2 reference rna
    Wild Type Sars Cov 2 Reference Rna, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    type sars cov 2  (ATCC)


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    ATCC type sars cov 2
    a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of <t>SARS-CoV-2</t> spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.
    Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow"

    Article Title: Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow

    Journal: Nature Communications

    doi: 10.1038/s41467-024-48570-0

    a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of SARS-CoV-2 spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.
    Figure Legend Snippet: a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of SARS-CoV-2 spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.

    Techniques Used: Selection, Mutagenesis, Expressing, Two Tailed Test, MANN-WHITNEY, Clone Assay, Sequencing, Comparison

    a Schematic representation of vaccination, blood collection and sample analysis. Arrows indicate time points when transcriptome and full-length B-cell receptor repertoire sequencing was performed. b UMAP representation of the expression levels of selected genes in 55071 CD27 high CD38 high sorted peripheral blood ASC from 36 healthy individuals after COVID-19 or diphtheria, tetanus, pertussis (DTP) vaccination (see Supplementary Table for information on participants and different vaccination schemes). Colour scale represents the expression level of the indicated genes. c Identification of SARS-CoV-2 spike-specific (red) public clones among analysed ASC. Public clones were defined by displaying >80% CDR3 sequence identity when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). The number of public clones found is shown on the UMAP. d Bubble plot of mutation rates in the framework regions (FR1-3, left) and in the CDR regions (CDR1-3, right) of identified spike-specific public clones per isotype identified in time point after COVID-19 vaccination. Colour scale indicates median mutation rates. Values above the scale limits are shown in red. Bubble sizes correspond to the percentage of spike-specific cells expressing a defined isotype within the indicated group. e Density plots of BMPC significantly enriched in gene signatures from peripheral blood ASC isolated at different time points after vaccination as identified by Gene Set Enrichment Analysis (GSEA). Violin plots of the normalised enrichment score (NES) per BMPC cluster are depicted in Supplementary Fig. . Statistical significance between NES scores is shown in Supplementary Data (two-tailed Mann–Whitney U test). Source data are provided as a Source Data file.
    Figure Legend Snippet: a Schematic representation of vaccination, blood collection and sample analysis. Arrows indicate time points when transcriptome and full-length B-cell receptor repertoire sequencing was performed. b UMAP representation of the expression levels of selected genes in 55071 CD27 high CD38 high sorted peripheral blood ASC from 36 healthy individuals after COVID-19 or diphtheria, tetanus, pertussis (DTP) vaccination (see Supplementary Table for information on participants and different vaccination schemes). Colour scale represents the expression level of the indicated genes. c Identification of SARS-CoV-2 spike-specific (red) public clones among analysed ASC. Public clones were defined by displaying >80% CDR3 sequence identity when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). The number of public clones found is shown on the UMAP. d Bubble plot of mutation rates in the framework regions (FR1-3, left) and in the CDR regions (CDR1-3, right) of identified spike-specific public clones per isotype identified in time point after COVID-19 vaccination. Colour scale indicates median mutation rates. Values above the scale limits are shown in red. Bubble sizes correspond to the percentage of spike-specific cells expressing a defined isotype within the indicated group. e Density plots of BMPC significantly enriched in gene signatures from peripheral blood ASC isolated at different time points after vaccination as identified by Gene Set Enrichment Analysis (GSEA). Violin plots of the normalised enrichment score (NES) per BMPC cluster are depicted in Supplementary Fig. . Statistical significance between NES scores is shown in Supplementary Data (two-tailed Mann–Whitney U test). Source data are provided as a Source Data file.

    Techniques Used: Sequencing, Expressing, Clone Assay, Mutagenesis, Isolation, Two Tailed Test, MANN-WHITNEY

    a Representative pseudocolour plots of intracellular double-positive SARS-CoV-2 RBD (left) or tetanus toxoid (TT, right) staining in CD38 high CD138 + CD14 − CD3 − live singlet BMPC (gating strategy in Supplementary Fig. ). b – e Each symbol represents one donor/sample (see Supplementary Table ). Filled symbols represent BMPC samples which were also analysed by single-cell sequencing (Fig. ). b Frequencies of RBD-specific and TT-specific BMPC within total BMPC. Horizontal lines indicate the median. Statistics were performed using the one-tailed Mann–Whitney U test. n = 20 BM samples. c Frequencies of CD19 low cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. d Frequencies of IgG+ (left) and IgA+ (right) cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. e Correlation between the frequency of CD19 low RBD-specific BMPC and days after 3rd vaccination against SARS-CoV-2. Statistics were performed using one-tailed Spearman’s correlations. n = 11 BM samples. Source data are provided as a Source Data file.
    Figure Legend Snippet: a Representative pseudocolour plots of intracellular double-positive SARS-CoV-2 RBD (left) or tetanus toxoid (TT, right) staining in CD38 high CD138 + CD14 − CD3 − live singlet BMPC (gating strategy in Supplementary Fig. ). b – e Each symbol represents one donor/sample (see Supplementary Table ). Filled symbols represent BMPC samples which were also analysed by single-cell sequencing (Fig. ). b Frequencies of RBD-specific and TT-specific BMPC within total BMPC. Horizontal lines indicate the median. Statistics were performed using the one-tailed Mann–Whitney U test. n = 20 BM samples. c Frequencies of CD19 low cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. d Frequencies of IgG+ (left) and IgA+ (right) cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. e Correlation between the frequency of CD19 low RBD-specific BMPC and days after 3rd vaccination against SARS-CoV-2. Statistics were performed using one-tailed Spearman’s correlations. n = 11 BM samples. Source data are provided as a Source Data file.

    Techniques Used: Staining, Sequencing, One-tailed Test, MANN-WHITNEY

    wild type sars cov 2  (ATCC)


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    ATCC wild type sars cov 2
    Wild Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    wild type sars cov 2  (ATCC)


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    ATCC wild type sars cov 2
    IFN-γ level after two doses of COVID-19 vaccines in individuals with or without prior <t>SARS-CoV-2</t> infections. (a) The level of IFN-γ in response to the AG1 epitope. (b) The level of IFN-γ in response to the AG2 epitope. The dotted line indicates the cutoff value (0.2 IU/mL).
    Wild Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Kinetics of adaptive immune responses after administering mRNA-Based COVID-19 vaccination in individuals with and without prior SARS-CoV-2 infections"

    Article Title: Kinetics of adaptive immune responses after administering mRNA-Based COVID-19 vaccination in individuals with and without prior SARS-CoV-2 infections

    Journal: BMC Infectious Diseases

    doi: 10.1186/s12879-023-08728-5

    IFN-γ level after two doses of COVID-19 vaccines in individuals with or without prior SARS-CoV-2 infections. (a) The level of IFN-γ in response to the AG1 epitope. (b) The level of IFN-γ in response to the AG2 epitope. The dotted line indicates the cutoff value (0.2 IU/mL).
    Figure Legend Snippet: IFN-γ level after two doses of COVID-19 vaccines in individuals with or without prior SARS-CoV-2 infections. (a) The level of IFN-γ in response to the AG1 epitope. (b) The level of IFN-γ in response to the AG2 epitope. The dotted line indicates the cutoff value (0.2 IU/mL).

    Techniques Used: Vaccines

    Neutralizing activity in individuals with or without prior SARS-CoV-2 infections. ( a ) representing neutralizing activity against the Wuhan strain, ( b ) against the Delta variant, and ( c ) against the Omicron variant. The upper panel represents the plaque reduction from each serum dilution. The lower panel demonstrates the PRNT 50 titer
    Figure Legend Snippet: Neutralizing activity in individuals with or without prior SARS-CoV-2 infections. ( a ) representing neutralizing activity against the Wuhan strain, ( b ) against the Delta variant, and ( c ) against the Omicron variant. The upper panel represents the plaque reduction from each serum dilution. The lower panel demonstrates the PRNT 50 titer

    Techniques Used: Activity Assay, Variant Assay

    type wuhan hu 1 sars cov 2 virus  (ATCC)


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    ATCC type wuhan hu 1 sars cov 2 virus
    PWH had lower <t>SARS-CoV-2</t> nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and . " width="250" height="auto" />
    Type Wuhan Hu 1 Sars Cov 2 Virus, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Immunogenicity of COVID-19 vaccines and their effect on HIV reservoir in older people with HIV"

    Article Title: Immunogenicity of COVID-19 vaccines and their effect on HIV reservoir in older people with HIV

    Journal: iScience

    doi: 10.1016/j.isci.2023.107915

    PWH had lower SARS-CoV-2 nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and . " title="PWH had lower SARS-CoV-2 nAb titers after two vaccine doses than HIV ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: PWH had lower SARS-CoV-2 nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and .

    Techniques Used: Neutralization, Flow Cytometry

    IRs mount strong T cell responses to two and three vaccine doses, outperforming HIV – individuals, while INRs show modest responses Changes in anti-spike T cell responses in HIV − participants (blue), total PWH (green), IRs (cyan), and INRs (purple) following COVID-19 vaccination are determined with ELISpot as frequencies of cells secreting IFN-γ (top), IL-2 (middle) or both (‘Dual’, bottom) in response to stimulation with SARS-CoV-2 spike peptide pool and expressed as spot-forming cells (SFC) per 10 6 PBMC. The horizontal bars show median frequencies. p values for differences between PWH and HIV − participants, and those between IRs and INRs, are based on Wilcoxon rank-sum test and are shown below their respective violin plots or above each IR/INR pair: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top of each panel and are color-coded accordingly (based on quantile regression). LLV participants are shown as red dots. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Tables S19 and . " title="... both (‘Dual’, bottom) in response to stimulation with SARS-CoV-2 spike peptide pool and expressed as spot-forming cells ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: IRs mount strong T cell responses to two and three vaccine doses, outperforming HIV – individuals, while INRs show modest responses Changes in anti-spike T cell responses in HIV − participants (blue), total PWH (green), IRs (cyan), and INRs (purple) following COVID-19 vaccination are determined with ELISpot as frequencies of cells secreting IFN-γ (top), IL-2 (middle) or both (‘Dual’, bottom) in response to stimulation with SARS-CoV-2 spike peptide pool and expressed as spot-forming cells (SFC) per 10 6 PBMC. The horizontal bars show median frequencies. p values for differences between PWH and HIV − participants, and those between IRs and INRs, are based on Wilcoxon rank-sum test and are shown below their respective violin plots or above each IR/INR pair: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top of each panel and are color-coded accordingly (based on quantile regression). LLV participants are shown as red dots. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Tables S19 and .

    Techniques Used: Enzyme-linked Immunospot

    wild type sars cov 2  (ATCC)


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    ATCC wild type sars cov 2
    Wild Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    wild type sars cov 2  (ATCC)


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    ATCC wild type sars cov 2
    Wild Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    wild type sars cov 2  (ATCC)


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    ATCC wild type sars cov 2
    Figure shows dot plot of antibody responses against <t>SARS-CoV-2</t> in samples collected from patients with MERS-CoV before and after COVID-19 vaccination. Patients who had SARS-CoV-2 infection and individuals with COVID-19 vaccination (with no history of previous infections) served as controls. A, immunoglobin M (IgM) antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. B, IgG antibodies against S and N proteins. C, IgA antibodies against the receptor-binding domain (RBD). D, Neutralizing antibodies (NAbs) against the RBD. E, Total antibodies against the RBD. F, IgG antibodies against the RBD. P values were calculated using a 1-way analysis of variance test. AU indicates arbitrary units; BAU, binding antibody units; COI, cutoff index; S/CO, signal/cutoff.
    Wild Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Assessment of Broadly Reactive Responses in Patients With MERS-CoV Infection and SARS-CoV-2 Vaccination"

    Article Title: Assessment of Broadly Reactive Responses in Patients With MERS-CoV Infection and SARS-CoV-2 Vaccination

    Journal: JAMA Network Open

    doi: 10.1001/jamanetworkopen.2023.19222

    Figure shows dot plot of antibody responses against SARS-CoV-2 in samples collected from patients with MERS-CoV before and after COVID-19 vaccination. Patients who had SARS-CoV-2 infection and individuals with COVID-19 vaccination (with no history of previous infections) served as controls. A, immunoglobin M (IgM) antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. B, IgG antibodies against S and N proteins. C, IgA antibodies against the receptor-binding domain (RBD). D, Neutralizing antibodies (NAbs) against the RBD. E, Total antibodies against the RBD. F, IgG antibodies against the RBD. P values were calculated using a 1-way analysis of variance test. AU indicates arbitrary units; BAU, binding antibody units; COI, cutoff index; S/CO, signal/cutoff.
    Figure Legend Snippet: Figure shows dot plot of antibody responses against SARS-CoV-2 in samples collected from patients with MERS-CoV before and after COVID-19 vaccination. Patients who had SARS-CoV-2 infection and individuals with COVID-19 vaccination (with no history of previous infections) served as controls. A, immunoglobin M (IgM) antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. B, IgG antibodies against S and N proteins. C, IgA antibodies against the receptor-binding domain (RBD). D, Neutralizing antibodies (NAbs) against the RBD. E, Total antibodies against the RBD. F, IgG antibodies against the RBD. P values were calculated using a 1-way analysis of variance test. AU indicates arbitrary units; BAU, binding antibody units; COI, cutoff index; S/CO, signal/cutoff.

    Techniques Used: Infection, Binding Assay

    A, Neutralization of pseudoviruses expressing MERS-CoV and SARS-CoV-2 spike (S) protein in prevaccination and postvaccination samples. B, ADCC activity against SARS-CoV-2 nucleocapsid protein (NP) and full S. The figure also compares the assessed groups with controls of patients with SARS-CoV infection and COVID-19–vaccinated individuals with mRNA vaccines. C and D, Neutralization of pseudoviruses expressing MERS-CoV (C) and SARS-CoV-2 (D) S protein in patients with follow-up samples collected before and after COVID-19 vaccination. E and F, ADCC activity against SARS-CoV-2 NP (E) and full S (F) in patients with follow-up samples collected before and after COVID-19 vaccination. P values were calculated using paired t test or 1-way analysis of variance test. PV indicates pseudovirus; PVNT, pseudovirus neutralization test.
    Figure Legend Snippet: A, Neutralization of pseudoviruses expressing MERS-CoV and SARS-CoV-2 spike (S) protein in prevaccination and postvaccination samples. B, ADCC activity against SARS-CoV-2 nucleocapsid protein (NP) and full S. The figure also compares the assessed groups with controls of patients with SARS-CoV infection and COVID-19–vaccinated individuals with mRNA vaccines. C and D, Neutralization of pseudoviruses expressing MERS-CoV (C) and SARS-CoV-2 (D) S protein in patients with follow-up samples collected before and after COVID-19 vaccination. E and F, ADCC activity against SARS-CoV-2 NP (E) and full S (F) in patients with follow-up samples collected before and after COVID-19 vaccination. P values were calculated using paired t test or 1-way analysis of variance test. PV indicates pseudovirus; PVNT, pseudovirus neutralization test.

    Techniques Used: Neutralization, Expressing, Activity Assay, Infection

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    ATCC type sars cov 2
    Type Sars Cov 2, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    sars cov 2 pseudo types  (ATCC)


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    ATCC sars cov 2 pseudo types
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    ATCC wild type sars cov 2 reference rna
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    ATCC type sars cov 2
    a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of <t>SARS-CoV-2</t> spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.
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    ATCC wild type sars cov 2
    a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of <t>SARS-CoV-2</t> spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.
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    PWH had lower <t>SARS-CoV-2</t> nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and . " width="250" height="auto" />
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    ATCC sars cov 2 pseudo types
    PWH had lower <t>SARS-CoV-2</t> nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and . " width="250" height="auto" />
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    a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of SARS-CoV-2 spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow

    doi: 10.1038/s41467-024-48570-0

    Figure Lengend Snippet: a Number of clonal families of BCRs found within the different BMPC clusters (diversity) and probability of finding different clonal families by random selection of cells (Simpson diversity index). A clonal family was defined by V and J gene composition and a CDR3 region with <20% Hamming distance in both the heavy and light chains originating from one donor. b Mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of the heavy and light chain rearrangements across BMPC clusters. c Bubble plot of the mutation rates in the framework regions FR1-3 (left) and in the CDR1-3 regions (right) of BCRs per isotype and cluster. Colour scale indicates median mutation rates. Values below or above the scale limits are shown in blue or red, respectively. Bubble sizes correspond to the percentage of cells expressing a defined isotype within the indicated cluster. d Violin plot depicting the mutation rates in the V gene of the BCRs of BMPC per cluster. Statistical significance between clusters is shown in Supplementary Data (two-tailed Mann–Whitney U test). Horizontal lines represent the median mutation rate. Violins are coloured by the z score of CD19 gene expression in each cluster. e Identification of SARS-CoV-2 spike-specific and tetanus toxoid-specific public clones (in black) among analysed BMPC. Public clones were defined by exhibiting over 80% CDR3 sequence identity in both heavy and light chains when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). f Relative distribution of spike-specific (red) and tetanus-specific (blue) BMPC (depicted in e ) per cluster. g Comparison of mutation rates within the framework regions FR1-3 (left) and the CDR1-3 regions (right) of spike-specific (red) and tetanus-specific (blue) BMPC per isotype. Horizontal lines represent the median mutation rate. Statistics were performed using a two-tailed Mann–Whitney U test. Source data are provided as a Source Data file.

    Article Snippet: HEK293T cells (ATCC CRL-3216) were transfected with a plasmid expressing wild-type SARS-CoV-2 S protein.

    Techniques: Selection, Mutagenesis, Expressing, Two Tailed Test, MANN-WHITNEY, Clone Assay, Sequencing, Comparison

    a Schematic representation of vaccination, blood collection and sample analysis. Arrows indicate time points when transcriptome and full-length B-cell receptor repertoire sequencing was performed. b UMAP representation of the expression levels of selected genes in 55071 CD27 high CD38 high sorted peripheral blood ASC from 36 healthy individuals after COVID-19 or diphtheria, tetanus, pertussis (DTP) vaccination (see Supplementary Table for information on participants and different vaccination schemes). Colour scale represents the expression level of the indicated genes. c Identification of SARS-CoV-2 spike-specific (red) public clones among analysed ASC. Public clones were defined by displaying >80% CDR3 sequence identity when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). The number of public clones found is shown on the UMAP. d Bubble plot of mutation rates in the framework regions (FR1-3, left) and in the CDR regions (CDR1-3, right) of identified spike-specific public clones per isotype identified in time point after COVID-19 vaccination. Colour scale indicates median mutation rates. Values above the scale limits are shown in red. Bubble sizes correspond to the percentage of spike-specific cells expressing a defined isotype within the indicated group. e Density plots of BMPC significantly enriched in gene signatures from peripheral blood ASC isolated at different time points after vaccination as identified by Gene Set Enrichment Analysis (GSEA). Violin plots of the normalised enrichment score (NES) per BMPC cluster are depicted in Supplementary Fig. . Statistical significance between NES scores is shown in Supplementary Data (two-tailed Mann–Whitney U test). Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow

    doi: 10.1038/s41467-024-48570-0

    Figure Lengend Snippet: a Schematic representation of vaccination, blood collection and sample analysis. Arrows indicate time points when transcriptome and full-length B-cell receptor repertoire sequencing was performed. b UMAP representation of the expression levels of selected genes in 55071 CD27 high CD38 high sorted peripheral blood ASC from 36 healthy individuals after COVID-19 or diphtheria, tetanus, pertussis (DTP) vaccination (see Supplementary Table for information on participants and different vaccination schemes). Colour scale represents the expression level of the indicated genes. c Identification of SARS-CoV-2 spike-specific (red) public clones among analysed ASC. Public clones were defined by displaying >80% CDR3 sequence identity when compared to the BCR of sequenced peripheral blood and bone marrow spike- and tetanus-specific cells from vaccinated individuals (see Supplementary Fig. and Supplementary Data ). The number of public clones found is shown on the UMAP. d Bubble plot of mutation rates in the framework regions (FR1-3, left) and in the CDR regions (CDR1-3, right) of identified spike-specific public clones per isotype identified in time point after COVID-19 vaccination. Colour scale indicates median mutation rates. Values above the scale limits are shown in red. Bubble sizes correspond to the percentage of spike-specific cells expressing a defined isotype within the indicated group. e Density plots of BMPC significantly enriched in gene signatures from peripheral blood ASC isolated at different time points after vaccination as identified by Gene Set Enrichment Analysis (GSEA). Violin plots of the normalised enrichment score (NES) per BMPC cluster are depicted in Supplementary Fig. . Statistical significance between NES scores is shown in Supplementary Data (two-tailed Mann–Whitney U test). Source data are provided as a Source Data file.

    Article Snippet: HEK293T cells (ATCC CRL-3216) were transfected with a plasmid expressing wild-type SARS-CoV-2 S protein.

    Techniques: Sequencing, Expressing, Clone Assay, Mutagenesis, Isolation, Two Tailed Test, MANN-WHITNEY

    a Representative pseudocolour plots of intracellular double-positive SARS-CoV-2 RBD (left) or tetanus toxoid (TT, right) staining in CD38 high CD138 + CD14 − CD3 − live singlet BMPC (gating strategy in Supplementary Fig. ). b – e Each symbol represents one donor/sample (see Supplementary Table ). Filled symbols represent BMPC samples which were also analysed by single-cell sequencing (Fig. ). b Frequencies of RBD-specific and TT-specific BMPC within total BMPC. Horizontal lines indicate the median. Statistics were performed using the one-tailed Mann–Whitney U test. n = 20 BM samples. c Frequencies of CD19 low cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. d Frequencies of IgG+ (left) and IgA+ (right) cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. e Correlation between the frequency of CD19 low RBD-specific BMPC and days after 3rd vaccination against SARS-CoV-2. Statistics were performed using one-tailed Spearman’s correlations. n = 11 BM samples. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Recruitment of plasma cells from IL-21-dependent and IL-21-independent immune reactions to the bone marrow

    doi: 10.1038/s41467-024-48570-0

    Figure Lengend Snippet: a Representative pseudocolour plots of intracellular double-positive SARS-CoV-2 RBD (left) or tetanus toxoid (TT, right) staining in CD38 high CD138 + CD14 − CD3 − live singlet BMPC (gating strategy in Supplementary Fig. ). b – e Each symbol represents one donor/sample (see Supplementary Table ). Filled symbols represent BMPC samples which were also analysed by single-cell sequencing (Fig. ). b Frequencies of RBD-specific and TT-specific BMPC within total BMPC. Horizontal lines indicate the median. Statistics were performed using the one-tailed Mann–Whitney U test. n = 20 BM samples. c Frequencies of CD19 low cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. d Frequencies of IgG+ (left) and IgA+ (right) cells within RBD-specific BMPC (red), TT-specific BMPC (blue) and total BMPC (black). Horizontal lines indicate the median. Statistics were performed using the Kruskal–Wallis tests with Dunn’s correction for multiple comparisons. n = 20 BM samples. e Correlation between the frequency of CD19 low RBD-specific BMPC and days after 3rd vaccination against SARS-CoV-2. Statistics were performed using one-tailed Spearman’s correlations. n = 11 BM samples. Source data are provided as a Source Data file.

    Article Snippet: HEK293T cells (ATCC CRL-3216) were transfected with a plasmid expressing wild-type SARS-CoV-2 S protein.

    Techniques: Staining, Sequencing, One-tailed Test, MANN-WHITNEY

    PWH had lower SARS-CoV-2 nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and . " width="100%" height="100%">

    Journal: iScience

    Article Title: Immunogenicity of COVID-19 vaccines and their effect on HIV reservoir in older people with HIV

    doi: 10.1016/j.isci.2023.107915

    Figure Lengend Snippet: PWH had lower SARS-CoV-2 nAb titers after two vaccine doses than HIV – individuals, with responses ‘rescued’ by the booster (A) Live SARS-CoV-2 50% neutralization titers (NT 50 ) in HIV − individuals (blue), total PWH (green), IRs (cyan), INRs (purple); the horizontal bars show median titers. The bottom panel shows adjusted median differences between PWH and HIV − participants at each timepoint (based on quantile regression), with p values shown at the top: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from V8 to V9 are shown at the top of the top panel and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 , Tables S9–S11 . (A–C) LLV participants are shown as red dots. (B) Changes in frequency of RBD/NTD-specific B cells in selected PWH (n = 17) following COVID-19 vaccination expressed as the number of RBD + S1 + and NTD + S1 + B cells per 10 6 total B cells, based on spectral flow cytometry data. The horizontal bars show median frequencies. p values are based on quantile regression. See also Figures S2 A and S2B, Table S12 . (C) Changes in concentrations of anti-RBD nAbs in sera (IU/mL) following COVID-19 vaccination: in HIV − participants (blue), total PWH (green), IRs (cyan), INRs (purple). The responses are measured with snELISA based on the ability of sera to displace rACE2 and analyzed by adjusted quantile regression. The horizontal bars show median concentrations; the neutralization cut-off (54.8 IU/mL) and ULOQ (1,520 IU/mL) are shown as dashed horizontal lines. p values for differences between PWH and HIV − participants at each time point are shown at the bottom. p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top and are color-coded accordingly. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Figure S2 C, Tables S13 and .

    Article Snippet: Briefly, heat-inactivated sera were serially diluted and incubated with 100 TCID 50 of the wild type Wuhan-Hu-1 SARS-CoV-2 virus (a gift from Samira Mubareka, Sunnybrook Health Science Centre) in serum-free DMEM, then added onto the VeroE6 cells (a clone of a cell line derived from a kidney tissue of the African green monkey, ATCC Cat#CRL-1586) in 96-well plates.

    Techniques: Neutralization, Flow Cytometry

    IRs mount strong T cell responses to two and three vaccine doses, outperforming HIV – individuals, while INRs show modest responses Changes in anti-spike T cell responses in HIV − participants (blue), total PWH (green), IRs (cyan), and INRs (purple) following COVID-19 vaccination are determined with ELISpot as frequencies of cells secreting IFN-γ (top), IL-2 (middle) or both (‘Dual’, bottom) in response to stimulation with SARS-CoV-2 spike peptide pool and expressed as spot-forming cells (SFC) per 10 6 PBMC. The horizontal bars show median frequencies. p values for differences between PWH and HIV − participants, and those between IRs and INRs, are based on Wilcoxon rank-sum test and are shown below their respective violin plots or above each IR/INR pair: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top of each panel and are color-coded accordingly (based on quantile regression). LLV participants are shown as red dots. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also <xref ref-type=Tables S19 and . " width="100%" height="100%">

    Journal: iScience

    Article Title: Immunogenicity of COVID-19 vaccines and their effect on HIV reservoir in older people with HIV

    doi: 10.1016/j.isci.2023.107915

    Figure Lengend Snippet: IRs mount strong T cell responses to two and three vaccine doses, outperforming HIV – individuals, while INRs show modest responses Changes in anti-spike T cell responses in HIV − participants (blue), total PWH (green), IRs (cyan), and INRs (purple) following COVID-19 vaccination are determined with ELISpot as frequencies of cells secreting IFN-γ (top), IL-2 (middle) or both (‘Dual’, bottom) in response to stimulation with SARS-CoV-2 spike peptide pool and expressed as spot-forming cells (SFC) per 10 6 PBMC. The horizontal bars show median frequencies. p values for differences between PWH and HIV − participants, and those between IRs and INRs, are based on Wilcoxon rank-sum test and are shown below their respective violin plots or above each IR/INR pair: p < 0.001 (∗∗∗), p < 0.01 (∗∗), p < 0.05 (∗), p ≥ 0.05 (ns). p values for within-group/subgroup changes from the preceding timepoint for each pair of adjacent timepoints are shown at the top of each panel and are color-coded accordingly (based on quantile regression). LLV participants are shown as red dots. Vaccination timepoints (D1-2, D3) are indicated with red arrowheads. See also Tables S19 and .

    Article Snippet: Briefly, heat-inactivated sera were serially diluted and incubated with 100 TCID 50 of the wild type Wuhan-Hu-1 SARS-CoV-2 virus (a gift from Samira Mubareka, Sunnybrook Health Science Centre) in serum-free DMEM, then added onto the VeroE6 cells (a clone of a cell line derived from a kidney tissue of the African green monkey, ATCC Cat#CRL-1586) in 96-well plates.

    Techniques: Enzyme-linked Immunospot