sars cov 2 wuhan variant  (ATCC)


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    ATCC sars cov 2 wuhan variant

    Sars Cov 2 Wuhan Variant, 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
    https://www.bioz.com/result/sars cov 2 wuhan variant/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    sars cov 2 wuhan variant - by Bioz Stars, 2024-06
    86/100 stars

    Images

    1) Product Images from "Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater"

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    Journal: bioRxiv

    doi: 10.1101/2024.06.16.599198


    Figure Legend Snippet:

    Techniques Used: Sequencing, Whole Genome Amplification, Variant Assay, Amplification

    Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.
    Figure Legend Snippet: Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.

    Techniques Used: Amplification, Sequencing

    Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.
    Figure Legend Snippet: Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.

    Techniques Used: Sequencing, Variant Assay

    Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.
    Figure Legend Snippet: Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.

    Techniques Used: Sequencing, Variant Assay


    Figure Legend Snippet:

    Techniques Used: Variant Assay, Concentration Assay

    sars cov 2 wuhan variant  (ATCC)


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    ATCC sars cov 2 wuhan variant

    Sars Cov 2 Wuhan Variant, 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
    https://www.bioz.com/result/sars cov 2 wuhan variant/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    sars cov 2 wuhan variant - by Bioz Stars, 2024-06
    86/100 stars

    Images

    1) Product Images from "Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater"

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    Journal: bioRxiv

    doi: 10.1101/2024.06.16.599198


    Figure Legend Snippet:

    Techniques Used: Sequencing, Whole Genome Amplification, Variant Assay, Amplification

    Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.
    Figure Legend Snippet: Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.

    Techniques Used: Amplification, Sequencing

    Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.
    Figure Legend Snippet: Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.

    Techniques Used: Sequencing, Variant Assay

    Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.
    Figure Legend Snippet: Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.

    Techniques Used: Sequencing, Variant Assay


    Figure Legend Snippet:

    Techniques Used: Variant Assay, Concentration Assay

    sars cov 2 delta variant  (ATCC)


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    ATCC sars cov 2 delta variant
    (A-I) CFU counts for biofilm with <t>SARS-CoV-2</t> Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.
    Sars Cov 2 Delta Variant, 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 delta variant - by Bioz Stars, 2024-06
    86/100 stars

    Images

    1) Product Images from "SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants"

    Article Title: SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants

    Journal: PLOS ONE

    doi: 10.1371/journal.pone.0304504

    (A-I) CFU counts for biofilm with SARS-CoV-2 Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.
    Figure Legend Snippet: (A-I) CFU counts for biofilm with SARS-CoV-2 Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.

    Techniques Used: Variant Assay

    (A-C) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant A on stainless steel, PVC and on ceramic tile chips, (D-F) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant B on stainless steel, PVC, and on ceramic tile chips, (G-I) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant C on stainless steel, PVC, and on ceramic tile chips. 1.0 x 10 4 PFU of SARS-CoV-2 Delta variant were added to a stainless steel, PVC, or ceramic tile chip along with a floor drain biofilm sample collected from the cooler of meat packaging plant A, B, or C. The RT-qPCR samples were analyzed in duplicate. Gene copy numbers were calculated from a standard curve of known quantities of SARS-CoV-2 Delta variant RNA in a 25 μL qPCR reaction. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. ns: not significant; **: p < 0.01; ***: p < 0.001.
    Figure Legend Snippet: (A-C) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant A on stainless steel, PVC and on ceramic tile chips, (D-F) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant B on stainless steel, PVC, and on ceramic tile chips, (G-I) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant C on stainless steel, PVC, and on ceramic tile chips. 1.0 x 10 4 PFU of SARS-CoV-2 Delta variant were added to a stainless steel, PVC, or ceramic tile chip along with a floor drain biofilm sample collected from the cooler of meat packaging plant A, B, or C. The RT-qPCR samples were analyzed in duplicate. Gene copy numbers were calculated from a standard curve of known quantities of SARS-CoV-2 Delta variant RNA in a 25 μL qPCR reaction. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. ns: not significant; **: p < 0.01; ***: p < 0.001.

    Techniques Used: Quantitative RT-PCR, Variant Assay

    (A and B): Experimental set up with Biofilm with SARS-CoV-2 Delta variant, Biofilm without SARS-CoV-2 Delta variant, SARS-CoV-2 Delta variant—Biofilm, and Negative Control in duplicate. The experimental set is incubated at 7°C for 5 days. (C). After 5 days, the biofilm was harvested from SS, PVC, or ceramic tile chips using a cell lifter and forceps and rinsed with 1000 μL of LB-NS. (D) Harvested cells were stored in a screw-cap tube at -80°C until needed.
    Figure Legend Snippet: (A and B): Experimental set up with Biofilm with SARS-CoV-2 Delta variant, Biofilm without SARS-CoV-2 Delta variant, SARS-CoV-2 Delta variant—Biofilm, and Negative Control in duplicate. The experimental set is incubated at 7°C for 5 days. (C). After 5 days, the biofilm was harvested from SS, PVC, or ceramic tile chips using a cell lifter and forceps and rinsed with 1000 μL of LB-NS. (D) Harvested cells were stored in a screw-cap tube at -80°C until needed.

    Techniques Used: Variant Assay, Negative Control, Incubation

    sars cov 2 variants  (ATCC)


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    ATCC sars cov 2 variants
    Sars Cov 2 Variants, 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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    Average 86 stars, based on 1 article reviews
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    sars cov 2 variants - by Bioz Stars, 2024-06
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    sars cov 2 variants  (ATCC)


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    ATCC sars cov 2 variants
    A Western Blot analysis of the FLAG-tagged viral proteins expressed in HEK-293 cells confirm their molecular weight. B Immunofluorescence of anti-FLAG staining of HEK-293 cells show different subcellular localization of the <t>SARS-CoV-2</t> viroporins.
    Sars Cov 2 Variants, 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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    Images

    1) Product Images from "SARS-CoV-2 and its ORF3a, E and M viroporins activate inflammasome in human macrophages and induce of IL-1 α in pulmonary epithelial and endothelial cells"

    Article Title: SARS-CoV-2 and its ORF3a, E and M viroporins activate inflammasome in human macrophages and induce of IL-1 α in pulmonary epithelial and endothelial cells

    Journal: Cell Death Discovery

    doi: 10.1038/s41420-024-01966-9

    A Western Blot analysis of the FLAG-tagged viral proteins expressed in HEK-293 cells confirm their molecular weight. B Immunofluorescence of anti-FLAG staining of HEK-293 cells show different subcellular localization of the SARS-CoV-2 viroporins.
    Figure Legend Snippet: A Western Blot analysis of the FLAG-tagged viral proteins expressed in HEK-293 cells confirm their molecular weight. B Immunofluorescence of anti-FLAG staining of HEK-293 cells show different subcellular localization of the SARS-CoV-2 viroporins.

    Techniques Used: Western Blot, Molecular Weight, Immunofluorescence, Staining

    SARS-CoV-2 proteins ORF3a, E and M were expressed in THP-1-ASC-GFP cell line to trace inflammasome assembly and pyroptosis in the presence of selected inhibitors of the inflammasome: MCC950, colchicine, disulfiram and KCl. A Time-lapse analysis of ASC-speck formation. B Time-lapse analysis of cell death kinetics. C Level of cell death assessed by LDH secretion 24 h after lentiviral infection. D IL-1 β secretion 24 h after lentiviral infection. Graphs represent means ± SEM, n = 3–5, multiple comparisons were performed with Kruskall-Wallis test. p < 0.05 vs control is marked: * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.
    Figure Legend Snippet: SARS-CoV-2 proteins ORF3a, E and M were expressed in THP-1-ASC-GFP cell line to trace inflammasome assembly and pyroptosis in the presence of selected inhibitors of the inflammasome: MCC950, colchicine, disulfiram and KCl. A Time-lapse analysis of ASC-speck formation. B Time-lapse analysis of cell death kinetics. C Level of cell death assessed by LDH secretion 24 h after lentiviral infection. D IL-1 β secretion 24 h after lentiviral infection. Graphs represent means ± SEM, n = 3–5, multiple comparisons were performed with Kruskall-Wallis test. p < 0.05 vs control is marked: * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

    Techniques Used: Infection

    Immortalized human bronchial epithelial cells and human umbilical vein endothelial cells expressing the ASC::GFP fusion protein (HBEK-3KT-ASC-GFP, HUVEC-ASC-GFP, respectively) were infected with lentiviral particles to express the SARS-CoV-2 proteins ORF3a, E and M. Green fluorescence represents ASC::GFP and red represents DRAQ7-incorporating dead cells. Representative pictures, comparison of kinetics of cell death upon expression of different viroporins and the effects of MCC950 on cell death are shown for: A – C . HBEC-3KT-ASC-GFP. D – F . HUVEC-ASC-GFP. Graphs represent means ± SEM, n = 3. Multiple comparisons were performed with two-way ANOVA or Kruskall-Wallis test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.
    Figure Legend Snippet: Immortalized human bronchial epithelial cells and human umbilical vein endothelial cells expressing the ASC::GFP fusion protein (HBEK-3KT-ASC-GFP, HUVEC-ASC-GFP, respectively) were infected with lentiviral particles to express the SARS-CoV-2 proteins ORF3a, E and M. Green fluorescence represents ASC::GFP and red represents DRAQ7-incorporating dead cells. Representative pictures, comparison of kinetics of cell death upon expression of different viroporins and the effects of MCC950 on cell death are shown for: A – C . HBEC-3KT-ASC-GFP. D – F . HUVEC-ASC-GFP. Graphs represent means ± SEM, n = 3. Multiple comparisons were performed with two-way ANOVA or Kruskall-Wallis test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

    Techniques Used: Expressing, Infection, Fluorescence, Comparison

    Human monocyte-derived macrophages were infected with SARS-CoV-2 at MOI 1 for 8 h. A Confocal microscopy analysis of the presence of SARS-CoV-2 dsRNA in CD68 + macrophages. B Western blot analysis of the expression of NLRP3, IL-1 β (pro and cleaved p17), GSDMD-N and β -actin as loading control (left) upon infection with wild type, α and δ SARS-CoV-2 strains, M1, M2 – mock; densitometric analysis (right). C Concentration of LDH, IL-1 β , IL-18, and IL-33 was analyzed in the supernatant from the infected macrophages. Graphs represent means ± SEM, n = 3. Two groups comparisons were analyzed with t-test. * p < 0.05.
    Figure Legend Snippet: Human monocyte-derived macrophages were infected with SARS-CoV-2 at MOI 1 for 8 h. A Confocal microscopy analysis of the presence of SARS-CoV-2 dsRNA in CD68 + macrophages. B Western blot analysis of the expression of NLRP3, IL-1 β (pro and cleaved p17), GSDMD-N and β -actin as loading control (left) upon infection with wild type, α and δ SARS-CoV-2 strains, M1, M2 – mock; densitometric analysis (right). C Concentration of LDH, IL-1 β , IL-18, and IL-33 was analyzed in the supernatant from the infected macrophages. Graphs represent means ± SEM, n = 3. Two groups comparisons were analyzed with t-test. * p < 0.05.

    Techniques Used: Derivative Assay, Infection, Confocal Microscopy, Western Blot, Expressing, Concentration Assay

    A Immunolocalization of spike protein in SAECs after 1 h of infection. B Western blot analysis of the expression of NLRP3, IL-1 α (pro and cleaved p17), GSDMD, GSDMD-N and β -actin as loading control (left) in SAECs upon infection with wilde type, α and δ SARS-CoV-2 strains; respective densitometric analysis (right column). C Concentration of LDH, IL-18, IL-1 α and IL-33 was analyzed in the SAECs supernatant 1- and 3-day post infection. D Immunolocalization of spike protein in HPMECs after 1 h of infection. E Western blot analysis of the expression of NLRP3, IL-1 α (pro and cleaved p17), GSDMD, GSDMD-N and β -actin as loading control in HPMECs (left) upon infection with Wilde type, α and δ SARS-CoV-2 strains; respective densitometric analysis (right column). F Concentration of LDH, IL-18, IL-1 α and IL-33 was analyzed in the HPMECs supernatant 1- and 3-day post infection. Graphs represent means ± SEM, n = 3. Two groups comparisons were analyzed with t-test. * p < 0.05.
    Figure Legend Snippet: A Immunolocalization of spike protein in SAECs after 1 h of infection. B Western blot analysis of the expression of NLRP3, IL-1 α (pro and cleaved p17), GSDMD, GSDMD-N and β -actin as loading control (left) in SAECs upon infection with wilde type, α and δ SARS-CoV-2 strains; respective densitometric analysis (right column). C Concentration of LDH, IL-18, IL-1 α and IL-33 was analyzed in the SAECs supernatant 1- and 3-day post infection. D Immunolocalization of spike protein in HPMECs after 1 h of infection. E Western blot analysis of the expression of NLRP3, IL-1 α (pro and cleaved p17), GSDMD, GSDMD-N and β -actin as loading control in HPMECs (left) upon infection with Wilde type, α and δ SARS-CoV-2 strains; respective densitometric analysis (right column). F Concentration of LDH, IL-18, IL-1 α and IL-33 was analyzed in the HPMECs supernatant 1- and 3-day post infection. Graphs represent means ± SEM, n = 3. Two groups comparisons were analyzed with t-test. * p < 0.05.

    Techniques Used: Infection, Western Blot, Expressing, Concentration Assay

    sars cov 2 virus original variant b 1  (ATCC)


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    ATCC sars cov 2 virus original variant b 1
    Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 <t>(SARS‐CoV‐2)</t> in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.
    Sars Cov 2 Virus Original Variant B 1, 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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    Average 86 stars, based on 1 article reviews
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    sars cov 2 virus original variant b 1 - by Bioz Stars, 2024-06
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    1) Product Images from "Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID‐19: An early phase 1 descriptive study"

    Article Title: Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID‐19: An early phase 1 descriptive study

    Journal: Health Science Reports

    doi: 10.1002/hsr2.1949

    Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.
    Figure Legend Snippet: Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.

    Techniques Used: Neutralization, Plaque Reduction Neutralization Test

    sars cov 2 variant b 1 1 7  (ATCC)


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    ATCC sars cov 2 variant b 1 1 7
    A schematic layout of the QPsor system to monitor <t>SARS-CoV-2</t> viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.
    Sars Cov 2 Variant B 1 1 7, 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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    Images

    1) Product Images from "Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies"

    Article Title: Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies

    Journal: Biosensors

    doi: 10.3390/bios14030115

    A schematic layout of the QPsor system to monitor SARS-CoV-2 viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.
    Figure Legend Snippet: A schematic layout of the QPsor system to monitor SARS-CoV-2 viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.

    Techniques Used:

    Evaluation of the specificity of RNA-specific amplification of SARS-CoV-2 virus and PMMoV.
    Figure Legend Snippet: Evaluation of the specificity of RNA-specific amplification of SARS-CoV-2 virus and PMMoV.

    Techniques Used: Amplification, Virus

    Lab-free detection of SARS-CoV-2 by concentrated lysate/RNA elute-to-RICCA’s RNA amplification-to-LF assay for wastewater samples. Test line results are highlighted by red box.
    Figure Legend Snippet: Lab-free detection of SARS-CoV-2 by concentrated lysate/RNA elute-to-RICCA’s RNA amplification-to-LF assay for wastewater samples. Test line results are highlighted by red box.

    Techniques Used: Amplification

    length sars cov 2 spike protein variants  (ATCC)


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    ATCC length sars cov 2 spike protein variants
    Length Sars Cov 2 Spike Protein Variants, 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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    length sars cov 2 spike protein variants  (ATCC)


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    ATCC length sars cov 2 spike protein variants
    a Nine PLCs emerge from analysis of 100,450 previously published paired VH-VL sequences. b Screening with VHs (H-CDR3 depicted) identified by IgSeq and YSD against the panel of nine PLCs to determine productive VH-VL pairings. IgG mAbs ELISA EC 50 s revealed that partnering VHs with PLCs can create low nM affinity binders. Grey boxes indicate that binding was detected but at an affinity too low to determine an EC 50 in the concentration range tested. White boxes, no binding was detected. c 17 VH-PLC pairs from ( b ) neutralize <t>SARS-CoV-2</t> WA1 virus, fit to two biological replicates.
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    1) Product Images from "SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode"

    Article Title: SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode

    Journal: Communications Biology

    doi: 10.1038/s42003-023-05649-6

    a Nine PLCs emerge from analysis of 100,450 previously published paired VH-VL sequences. b Screening with VHs (H-CDR3 depicted) identified by IgSeq and YSD against the panel of nine PLCs to determine productive VH-VL pairings. IgG mAbs ELISA EC 50 s revealed that partnering VHs with PLCs can create low nM affinity binders. Grey boxes indicate that binding was detected but at an affinity too low to determine an EC 50 in the concentration range tested. White boxes, no binding was detected. c 17 VH-PLC pairs from ( b ) neutralize SARS-CoV-2 WA1 virus, fit to two biological replicates.
    Figure Legend Snippet: a Nine PLCs emerge from analysis of 100,450 previously published paired VH-VL sequences. b Screening with VHs (H-CDR3 depicted) identified by IgSeq and YSD against the panel of nine PLCs to determine productive VH-VL pairings. IgG mAbs ELISA EC 50 s revealed that partnering VHs with PLCs can create low nM affinity binders. Grey boxes indicate that binding was detected but at an affinity too low to determine an EC 50 in the concentration range tested. White boxes, no binding was detected. c 17 VH-PLC pairs from ( b ) neutralize SARS-CoV-2 WA1 virus, fit to two biological replicates.

    Techniques Used: Enzyme-linked Immunosorbent Assay, Binding Assay, Concentration Assay

    a Composite cryo-EM map of N3-1-bound SARS-CoV-2 Wuhan-Hu-1 spike. Each protomer is depicted in steel blue, royal blue and sky blue. The heavy chain of N3-1 is colored firebrick, and the light chain is colored coral. A lower resolution contour is shown to help visualize the Fabs and the RBDs. b Focused refinement map of N3-1 bound to RBDs in the up and down conformations. c One face of H-CDR3 contacts a conserved hydrophobic pocket (transparent royal blue surface) on RBD-up. The other face of H-CDR3 contacts the ACE2-binding site on RBD-down. H-CDR1 contacts the epitopes on RBD-up, but it is omitted for clarity. d Focused refinement map of N3-1 bound to RBD in the up conformation. e The epitope on RBD-down is centered on Phe486, which fits into a hydrophobic surface formed by Trp96, Tyr58, Tyr52, Arg100e and Val100g (clockwise). f Superimposed crystal structure of RBD-ACE2 complex (PDB ID: 6M0J) with N3-1 bound RBDs. The molecular surface of ACE2 is shown in transparent pale green. The light chain of N3-1 heavily clashes with ACE2. The ACE2-binding site on RBD-down is completely blocked by H-CDR2, H-CDR3 and L-CDR3 ( e ).
    Figure Legend Snippet: a Composite cryo-EM map of N3-1-bound SARS-CoV-2 Wuhan-Hu-1 spike. Each protomer is depicted in steel blue, royal blue and sky blue. The heavy chain of N3-1 is colored firebrick, and the light chain is colored coral. A lower resolution contour is shown to help visualize the Fabs and the RBDs. b Focused refinement map of N3-1 bound to RBDs in the up and down conformations. c One face of H-CDR3 contacts a conserved hydrophobic pocket (transparent royal blue surface) on RBD-up. The other face of H-CDR3 contacts the ACE2-binding site on RBD-down. H-CDR1 contacts the epitopes on RBD-up, but it is omitted for clarity. d Focused refinement map of N3-1 bound to RBD in the up conformation. e The epitope on RBD-down is centered on Phe486, which fits into a hydrophobic surface formed by Trp96, Tyr58, Tyr52, Arg100e and Val100g (clockwise). f Superimposed crystal structure of RBD-ACE2 complex (PDB ID: 6M0J) with N3-1 bound RBDs. The molecular surface of ACE2 is shown in transparent pale green. The light chain of N3-1 heavily clashes with ACE2. The ACE2-binding site on RBD-down is completely blocked by H-CDR2, H-CDR3 and L-CDR3 ( e ).

    Techniques Used: Cryo-EM Sample Prep, Binding Assay

    sars cov 2 variants  (ATCC)


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    ATCC sars cov 2 variants
    Sars Cov 2 Variants, 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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    ATCC sars cov 2 wuhan variant

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    ATCC sars cov 2 delta variant
    (A-I) CFU counts for biofilm with <t>SARS-CoV-2</t> Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.
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    ATCC sars cov 2 variants
    (A-I) CFU counts for biofilm with <t>SARS-CoV-2</t> Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.
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    ATCC sars cov 2 virus original variant b 1
    Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 <t>(SARS‐CoV‐2)</t> in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.
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    ATCC sars cov 2 variant b 1 1 7
    A schematic layout of the QPsor system to monitor <t>SARS-CoV-2</t> viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.
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    ATCC length sars cov 2 spike protein variants
    A schematic layout of the QPsor system to monitor <t>SARS-CoV-2</t> viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.
    Length Sars Cov 2 Spike Protein Variants, 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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    Image Search Results


    Journal: bioRxiv

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    doi: 10.1101/2024.06.16.599198

    Figure Lengend Snippet:

    Article Snippet: Positive extraction controls included a heat- inactivated strain of the SARS-CoV-2 Wuhan variant carried in 1X phosphate buffered saline (PBS) and a heat-inactivated strain of the SARS-CoV-2 Wuhan variant, carried in wastewater (ATCC VR-1986HK).

    Techniques: Sequencing, Whole Genome Amplification, Variant Assay, Amplification

    Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.

    Journal: bioRxiv

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    doi: 10.1101/2024.06.16.599198

    Figure Lengend Snippet: Fifteen wastewater mock communities, spiked with synthetic SARS-CoV-2 genomic RNA, were prepared as tiled amplicon libraries using Freed/Midnight, ARTIC V4, and NEB VarSkip primer schemes. Libraries were sequenced with PE250 and PE150 reads, with approximately 10 3 and 10 4 reads, respectively. (A) Genomic coverage from each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage for the given level of sequencing effort. (B) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected sequencing depth for the given level of sequencing effort. (C) Sequencing depth of each library, as a function of sequencing effort (N = 105). The reference line represents the expected genomic coverage with >20X sequencing depth for the given level of sequencing effort.

    Article Snippet: Positive extraction controls included a heat- inactivated strain of the SARS-CoV-2 Wuhan variant carried in 1X phosphate buffered saline (PBS) and a heat-inactivated strain of the SARS-CoV-2 Wuhan variant, carried in wastewater (ATCC VR-1986HK).

    Techniques: Amplification, Sequencing

    Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.

    Journal: bioRxiv

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    doi: 10.1101/2024.06.16.599198

    Figure Lengend Snippet: Fifteen individual wastewater mock communities were enriched as Freed/Midnight, ARTIC V4, and NEB VarSkip libraries and sequenced with Illumina PE250 and PE150 chemistry. Sequencing reads were assessed using the kallisto workflow to estimate abundance of SARS- CoV-2 variants (Wuhan, Alpha, Beta, Delta), which were spiked into mock communities at known proportions (3%, 14%, 25%, 28%, or 55%). Reads assigned to off-target variants (Epsilon, Eta, Gamma, Iota, Kappa, Mu, Omicron and Zeta) were binned together as “Other” with an expected abundance of 0%. (A) The expected abundance of each variant was compared to observed abundance, as reported by kallisto. Accuracy of the abundance prediction was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, represented by the dashed line. (B) The prediction error associated with each SARS-CoV-2 variant expressed in RMSE. The prediction error is equivalent to the difference between the abundance reported by kallisto and the abundance expected for each variant.

    Article Snippet: Positive extraction controls included a heat- inactivated strain of the SARS-CoV-2 Wuhan variant carried in 1X phosphate buffered saline (PBS) and a heat-inactivated strain of the SARS-CoV-2 Wuhan variant, carried in wastewater (ATCC VR-1986HK).

    Techniques: Sequencing, Variant Assay

    Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.

    Journal: bioRxiv

    Article Title: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

    doi: 10.1101/2024.06.16.599198

    Figure Lengend Snippet: Filtered reads were subset from libraries sequenced with PE150 reads and PE300, across a range of expected sequencing depths. Subset reads were analyzed by kallisto to estimate variant abundance. The accuracy of these estimates was assessed as the R 2 value of the one-to-one model between expected abundance and observed abundance of the SARS-CoV-2 variants in each sample, and as the root-mean-squared error (RMSE) between expected and observed abundance. The median R 2 and RMSE values are presented for each subset, along with the observed range of values.

    Article Snippet: Positive extraction controls included a heat- inactivated strain of the SARS-CoV-2 Wuhan variant carried in 1X phosphate buffered saline (PBS) and a heat-inactivated strain of the SARS-CoV-2 Wuhan variant, carried in wastewater (ATCC VR-1986HK).

    Techniques: Sequencing, Variant Assay

    (A-I) CFU counts for biofilm with SARS-CoV-2 Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.

    Journal: PLOS ONE

    Article Title: SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants

    doi: 10.1371/journal.pone.0304504

    Figure Lengend Snippet: (A-I) CFU counts for biofilm with SARS-CoV-2 Delta variant and biofilm without SARS-CoV-2 Delta variant samples on stainless steel, PVC, and tile chips (A-C) from Plant A, (D-F) from Plant B, and (G-I) from Plant C. Each sample was plated in duplicate. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001.

    Article Snippet: SARS-CoV-2 Delta variant was used for all of the experiments in this study and was acquired from the ATCC (ATCC NR-55672, hCoV-19/USA/MD-HP05647/2021 Delta, batch number: 70046635).

    Techniques: Variant Assay

    (A-C) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant A on stainless steel, PVC and on ceramic tile chips, (D-F) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant B on stainless steel, PVC, and on ceramic tile chips, (G-I) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant C on stainless steel, PVC, and on ceramic tile chips. 1.0 x 10 4 PFU of SARS-CoV-2 Delta variant were added to a stainless steel, PVC, or ceramic tile chip along with a floor drain biofilm sample collected from the cooler of meat packaging plant A, B, or C. The RT-qPCR samples were analyzed in duplicate. Gene copy numbers were calculated from a standard curve of known quantities of SARS-CoV-2 Delta variant RNA in a 25 μL qPCR reaction. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. ns: not significant; **: p < 0.01; ***: p < 0.001.

    Journal: PLOS ONE

    Article Title: SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants

    doi: 10.1371/journal.pone.0304504

    Figure Lengend Snippet: (A-C) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant A on stainless steel, PVC and on ceramic tile chips, (D-F) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant B on stainless steel, PVC, and on ceramic tile chips, (G-I) RT-qPCR analysis of SARS-CoV-2 Delta variant mixed with environmental biofilm organisms from Plant C on stainless steel, PVC, and on ceramic tile chips. 1.0 x 10 4 PFU of SARS-CoV-2 Delta variant were added to a stainless steel, PVC, or ceramic tile chip along with a floor drain biofilm sample collected from the cooler of meat packaging plant A, B, or C. The RT-qPCR samples were analyzed in duplicate. Gene copy numbers were calculated from a standard curve of known quantities of SARS-CoV-2 Delta variant RNA in a 25 μL qPCR reaction. Results in this figure are the mean values and standard deviations (error bars) from three independent experiments. Statistical significance was analyzed by unpaired t-test. ns: not significant; **: p < 0.01; ***: p < 0.001.

    Article Snippet: SARS-CoV-2 Delta variant was used for all of the experiments in this study and was acquired from the ATCC (ATCC NR-55672, hCoV-19/USA/MD-HP05647/2021 Delta, batch number: 70046635).

    Techniques: Quantitative RT-PCR, Variant Assay

    (A and B): Experimental set up with Biofilm with SARS-CoV-2 Delta variant, Biofilm without SARS-CoV-2 Delta variant, SARS-CoV-2 Delta variant—Biofilm, and Negative Control in duplicate. The experimental set is incubated at 7°C for 5 days. (C). After 5 days, the biofilm was harvested from SS, PVC, or ceramic tile chips using a cell lifter and forceps and rinsed with 1000 μL of LB-NS. (D) Harvested cells were stored in a screw-cap tube at -80°C until needed.

    Journal: PLOS ONE

    Article Title: SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants

    doi: 10.1371/journal.pone.0304504

    Figure Lengend Snippet: (A and B): Experimental set up with Biofilm with SARS-CoV-2 Delta variant, Biofilm without SARS-CoV-2 Delta variant, SARS-CoV-2 Delta variant—Biofilm, and Negative Control in duplicate. The experimental set is incubated at 7°C for 5 days. (C). After 5 days, the biofilm was harvested from SS, PVC, or ceramic tile chips using a cell lifter and forceps and rinsed with 1000 μL of LB-NS. (D) Harvested cells were stored in a screw-cap tube at -80°C until needed.

    Article Snippet: SARS-CoV-2 Delta variant was used for all of the experiments in this study and was acquired from the ATCC (ATCC NR-55672, hCoV-19/USA/MD-HP05647/2021 Delta, batch number: 70046635).

    Techniques: Variant Assay, Negative Control, Incubation

    Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.

    Journal: Health Science Reports

    Article Title: Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID‐19: An early phase 1 descriptive study

    doi: 10.1002/hsr2.1949

    Figure Lengend Snippet: Detection of total immunoglobulin G (IgG) and neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in donors and recipients for each transfusion. The titers were measured every 2 days before each of the five transfusions (D0, transfusion 1; D2, transfusion 2; D4, transfusion 3; D6, transfusion 4; D8, transfusion 5). Thus, antibodies were measured in the recipients over time. Owing to a limited supply of plasma units from each donor, the donors were not always the same, and there was no longitudinal tracking of the initial donors' antibody responses. Instead, we independently measured the state of the antibodies in the convalescent plasma (CCP) units from various donors for each donation. (A) Levels of total anti‐SARS‐CoV‐2 IgG in donor CCP units and in recipients (*O.D., optical density; Pos, O.D*. > 6.0; Neg, O.D. < 6.0; nd, no data); Dx, donor; Px, recipient. (B) Levels of neutralization antibodies against SARS‐CoV‐2 in in donor CCP units and in recipients. Plaque‐reduction neutralization test (PRNT) titers results are divided as follows: negative, 0; low positive, <1:160; high positive, ≥1:160; nd, no data.

    Article Snippet: To detect neutralizing antibodies against SARS‐CoV‐2 and to determine their titer in the plasma of donors and recipients, all samples were tested retrospectively by performing a plaque reduction neutralization test (PRNT) using 800 plaque‐forming units (PFU) of the SARS‐CoV‐2 virus original variant B.1. in Vero cells (ATCC‐C1008), with a 1/2 serial dilution of the plasma, starting with 1/10 dilution.

    Techniques: Neutralization, Plaque Reduction Neutralization Test

    A schematic layout of the QPsor system to monitor SARS-CoV-2 viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.

    Journal: Biosensors

    Article Title: Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies

    doi: 10.3390/bios14030115

    Figure Lengend Snippet: A schematic layout of the QPsor system to monitor SARS-CoV-2 viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.

    Article Snippet: In the context of the positive control, three different concentrations of normal saline and wastewater samples inoculated with the heat-inactivated SARS-CoV-2 variant B.1.1.7 (ATCC ® VR-3326HK TM , San Diego, CA, USA) were standardized.

    Techniques:

    Evaluation of the specificity of RNA-specific amplification of SARS-CoV-2 virus and PMMoV.

    Journal: Biosensors

    Article Title: Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies

    doi: 10.3390/bios14030115

    Figure Lengend Snippet: Evaluation of the specificity of RNA-specific amplification of SARS-CoV-2 virus and PMMoV.

    Article Snippet: In the context of the positive control, three different concentrations of normal saline and wastewater samples inoculated with the heat-inactivated SARS-CoV-2 variant B.1.1.7 (ATCC ® VR-3326HK TM , San Diego, CA, USA) were standardized.

    Techniques: Amplification, Virus

    Lab-free detection of SARS-CoV-2 by concentrated lysate/RNA elute-to-RICCA’s RNA amplification-to-LF assay for wastewater samples. Test line results are highlighted by red box.

    Journal: Biosensors

    Article Title: Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies

    doi: 10.3390/bios14030115

    Figure Lengend Snippet: Lab-free detection of SARS-CoV-2 by concentrated lysate/RNA elute-to-RICCA’s RNA amplification-to-LF assay for wastewater samples. Test line results are highlighted by red box.

    Article Snippet: In the context of the positive control, three different concentrations of normal saline and wastewater samples inoculated with the heat-inactivated SARS-CoV-2 variant B.1.1.7 (ATCC ® VR-3326HK TM , San Diego, CA, USA) were standardized.

    Techniques: Amplification