genomic sars cov 2 rna positive control  (ATCC)

Journal: bioRxiv

Article Title: Proximity proteomics reveals a role for IFI16 during human coronavirus infection

doi: 10.64898/2026.04.22.720112

Figure Lengend Snippet: IFI16 promotes coronavirus infection. ( a) CRISPR-Cas9 technology was used to knock out IFI16 in A549 cells and single cell clones were screened for loss of IFI16 expression using qRT-PCR. Data is representative of two independent experiments. ( b) Immunoblot showing the loss of IFI16 expression in IFI16-KO cell line. ( c) Immunofluorescence assay showing reduced number of HCoV-OC43 N-positive cells upon loss of IFI16. Cells were infected at an MOI of 0.1 and incubated for the indicated length of time before fixation and staining for HCoV-OC43 N protein. Scale bar is 10 um. ( d ) Representative flow cytometry analysis of wildtype (WT) A549 cells and IFI16-KO cells infected (in quadruplicate) with HCoV-OC43 at an MOI of 0.01 and 0.1 for 12, 24 and 48 h. Data is representative of 3 independent experiments. (e) and (f) Quantification of flow cytometry data in . ( g) Representative flow cytometry analysis of CRISPRi cell lines infected (in quadruplicate) with HCoV-OC43 at an MOI of 0.01 for 12, 24 and 48 h. data in figure. (h) Quantification of flow cytometry data in . Data is representative of two independent experiments. Statistical significance was assessed by ANOVA. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, and **** P ≤ 0.0001.

Article Snippet: Cells were washed twice with a permeabilization/wash buffer (0.1% saponin and 0.5% BSA in 1X PBS) and stained with a 1:10000 dilution of anti-HCoV-OC43-N rabbit polyclonal antibody (catalogue no. 40643-T62; Sino Biological) for 30 min at 4°C.

Techniques: Infection, CRISPR, Knock-Out, Single Cell, Clone Assay, Expressing, Quantitative RT-PCR, Western Blot, Immunofluorescence, Incubation, Staining, Flow Cytometry

Journal: bioRxiv

Article Title: Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

doi: 10.64898/2026.04.17.719293

Figure Lengend Snippet: A) Experimental protocol with sample collection at 24 and 48 hours post infection (hpi) for two duplicate experiments (A and B). For scRNA-seq, this resulted in transcriptomes from 13,913 cells across all samples, including 4,192 mock-infected and 2,724 virus-infected cells at 24 hpi and 3,593 mock-infected and 3,404 virus-infected cells at 48 hpi. B) The viral load across samples after quality control. The median log1p(viral reads) detected in 24 hpi sample A is 7.0 (SD 1.0), in 24 hpi sample B is 7.1 (SD 0.9), and across samples A and B is 7.1 (SD 1.0). The median log1p(viral reads) detected in 48 hpi sample A is 6.6 (SD 1.0), in 48 hpi sample B is 6.4 (SD 1.0), and across samples A and B is 6.5 (SD 1.0). C) Venn diagram representing the number of differentially expressed genes in a cell-level, time-matched 229E-infected versus mock-control differential expression test at a threshold of adjusted p-value < 0.001 and |log ₂ FC| > 2.

Article Snippet: Human coronavirus strain 229E (HCoV-229E) from ATCC ((#VR-740, Lot #70053995) was used for in-house virus batch propagation.

Techniques: Infection, Virus, Control, Quantitative Proteomics

Journal: bioRxiv

Article Title: Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

doi: 10.64898/2026.04.17.719293

Figure Lengend Snippet: A) The median aggregated accessibility profiles centered on the transcription start sites (TSS; ±3kb) for mock and 229E-infected samples at 24 and 48 hpi. The bold lines show median and mean profiles computed over mean profiles across all samples, while lower opacity profiles show variability across replicates. B) The mean aggregated accessibility profiles centered on the transcription start sites (TSS; ±3kb) for mock and 229E-infected samples at 24 and 48 hpi. The bold lines show median and mean profiles computed over mean profiles across all samples, while lower opacity profiles show variability across replicates. C) Principal component analysis (PCA) of accessibility profiles separates mock-control and 229E infected samples at 24 and 48 hpi. Axes indicate the variance explained by each principal component, marker shapes indicate time point, and marker colors indicate infection status. D) Volcano plots of differential accessibility (infected versus mock-control) at 24 (left) and 48 (right) hpi. Each point is an open chromatin region, and blue points indicate significantly increased accessibility, while orange points indicate significantly decreased accessibility. Gray points are not significant. At 24 hpi, 6% of open chromatin regions (OCRs) show increased chromatin accessibility (blue) and 5% show decreased chromatin accessibility (orange). At 48 hpi, 20% of OCRs show increased chromatin accessibility (blue), and 13% show decreased chromatin accessibility (orange).

Article Snippet: Human coronavirus strain 229E (HCoV-229E) from ATCC ((#VR-740, Lot #70053995) was used for in-house virus batch propagation.

Techniques: Infection, Control, Marker

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: SARS-CoV-2 vaccination boosts pre-existing antibody reactivity to human coronaviruses (HCoVs) (A) Timeline of vaccine administration and peripheral blood sampling in the first (healthcare workers) cohort. (B) IgG responses to the spike protein of SARS-CoV-2 and HCoVs (OC43, HKU1, NL63, and 229E) expressed as arbitrary units per milliliter (AU/mL), shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. (C) Relative IgG avidity profiles against SARS-CoV-2 and HCoV spike, across time points, with LOESS-smoothed trend lines, showing all data points and 95% confidence intervals (gray shade). (D) Corresponding avidity ranges for SARS-CoV-2 and HCoV spike antigen, shown as box-and-whisker plots (similarly defined as in [B]), with all data points. Paired comparisons were conducted between baseline and 14 days after the first vaccine dose, and between 28 days after the first dose and 14 days after the second dose, using a mixed-effects model (∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001). Sample sizes: baseline ( n = 48), 14 days post-first dose ( n = 46), 28 days post-first dose ( n = 35), 14 days post-second dose ( n = 15), and 28 days post-second dose ( n = 11).

Article Snippet: Ten μL of yellow-green fluorescent NeutrAvidin-labeled microspheres (Thermo Fisher Scientific, Waltham, MA, USA; cat# F8776) were washed with PBS containing 0.1% BSA, resuspended in 10 μL of biotinylated SARS-CoV-2 S1, S2 (ACROBiosystems, cat# S1N-C82E8 and S2N-C52E8), HKU1 (Sino Biological, cat# 40606-V08B-B), and NL63 (Sino Biological, cat# 40604-V08B-B) spike proteins (0.1 μg/μL), and incubated at 36 °C for 2 h. Microspheres were washed twice, resuspended in 1 mL PBS, and aliquoted (10 μL) into a 96-well plate.

Techniques: Sampling, Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: Recalled HKU1 spike antibody responses display enhanced ADCP function (A) Antibody-dependent cellular phagocytosis (ADCP) responses against HCoV spike and SARS-CoV-2 S1- and S2-domains across vaccine doses and time points. ADCP scores were compared between baseline and 14 days post-first dose, and between 28 days post-first dose and 14 days post-second dose, using a mixed-effects model. Data are shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. (B) Spearman correlations between HKU1 and NL63 spike, and SARS-CoV-2 S1- and S2-domain-specific ADCP responses, adjusted for multiple comparisons with the Benjamini-Hochberg method. Spearman correlations are shown as a heatmap for each time point. (only significant results are shown; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001). Sample sizes: baseline ( n = 48), 14 days post-first dose ( n = 46), 28 days post-first dose ( n = 35), 14 days post-second dose ( n = 15), and 28 days post-second dose ( n = 11).

Article Snippet: Ten μL of yellow-green fluorescent NeutrAvidin-labeled microspheres (Thermo Fisher Scientific, Waltham, MA, USA; cat# F8776) were washed with PBS containing 0.1% BSA, resuspended in 10 μL of biotinylated SARS-CoV-2 S1, S2 (ACROBiosystems, cat# S1N-C82E8 and S2N-C52E8), HKU1 (Sino Biological, cat# 40606-V08B-B), and NL63 (Sino Biological, cat# 40604-V08B-B) spike proteins (0.1 μg/μL), and incubated at 36 °C for 2 h. Microspheres were washed twice, resuspended in 1 mL PBS, and aliquoted (10 μL) into a 96-well plate.

Techniques: Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: HKU1 antibody reactivity was protective against SARS-CoV-2 infection but increased the risk of post-COVID symptoms in vaccinated, infection-naive individuals (A) Comparison of HCoV spike IgG levels (HKU1, OC43, NL63, and 229E; log-transformed data) at baseline, between individuals infected and those who were not at the one-year follow-up. Comparisons were performed using a Wilcoxon rank-sum test ( n = 700, infected = 509, uninfected = 191). (B) Effects of HCoV spike IgG levels, time interval between the first and second vaccine dose (days), use of mRNA vaccines only, sex, and age at baseline, on the risk of SARS-CoV-2 infection at the one-year follow-up. (C) Comparison of HCoV spike IgG levels at baseline, between individuals who developed post-COVID symptoms versus those who did not, by the one-year follow-up visit. Comparisons were performed using a Wilcoxon rank-sum test ( n = 509, post-COVID symptoms = 165, no post-COVID symptoms = 335; missing data = 9). (D) Effects of HCoV spike IgG levels, time interval between the first and second dose (days), use of mRNA vaccines only, sex, and age at baseline, on the risk of post-COVID symptoms at the one-year follow-up. (B and D) Show adjusted odds ratios with 95% confidence intervals on a logarithmic scale (in blue) where the dashed horizontal line indicates no effect (OR = 1), with corresponding p -values (in red). (E–G) Antibody-dependent complement deposition (ADCD) between individuals with the highest (78 th centile, n = 88) and lowest (22 nd centile, n = 88) HKU1 spike (E), SARS-CoV-2 S1 (F) and S2 (G) IgG levels. Comparisons were performed using a Wilcoxon rank-sum test. For (A, C, E–G) data are shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. For (B, D): Odds Ratios (OR) with 95% confidence intervals (blue line) and p value (in red), on a log scale. (∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001).

Article Snippet: Ten μL of yellow-green fluorescent NeutrAvidin-labeled microspheres (Thermo Fisher Scientific, Waltham, MA, USA; cat# F8776) were washed with PBS containing 0.1% BSA, resuspended in 10 μL of biotinylated SARS-CoV-2 S1, S2 (ACROBiosystems, cat# S1N-C82E8 and S2N-C52E8), HKU1 (Sino Biological, cat# 40606-V08B-B), and NL63 (Sino Biological, cat# 40604-V08B-B) spike proteins (0.1 μg/μL), and incubated at 36 °C for 2 h. Microspheres were washed twice, resuspended in 1 mL PBS, and aliquoted (10 μL) into a 96-well plate.

Techniques: Infection, Comparison, Transformation Assay, Vaccines, Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: SARS-CoV-2 vaccination boosts pre-existing antibody reactivity to human coronaviruses (HCoVs) (A) Timeline of vaccine administration and peripheral blood sampling in the first (healthcare workers) cohort. (B) IgG responses to the spike protein of SARS-CoV-2 and HCoVs (OC43, HKU1, NL63, and 229E) expressed as arbitrary units per milliliter (AU/mL), shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. (C) Relative IgG avidity profiles against SARS-CoV-2 and HCoV spike, across time points, with LOESS-smoothed trend lines, showing all data points and 95% confidence intervals (gray shade). (D) Corresponding avidity ranges for SARS-CoV-2 and HCoV spike antigen, shown as box-and-whisker plots (similarly defined as in [B]), with all data points. Paired comparisons were conducted between baseline and 14 days after the first vaccine dose, and between 28 days after the first dose and 14 days after the second dose, using a mixed-effects model (∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001). Sample sizes: baseline ( n = 48), 14 days post-first dose ( n = 46), 28 days post-first dose ( n = 35), 14 days post-second dose ( n = 15), and 28 days post-second dose ( n = 11).

Article Snippet: For HKU1-specific B cells, biotinylated HKU1 spike proteins were purchased from Sino Biological, Beijing, China (cat# 40606-V08B-B).

Techniques: Sampling, Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: HKU1 immune imprinting predominantly targets the SARS-CoV-2 S2 domain Percentages of antigen-specific memory B cells, IgG + B cells, or plasmablasts calculated as the number of antigen-specific cells within each subset divided by total B cells, IgG + B cells, or plasmablasts, respectively, across time points (flow cytometry). Log10-transformed data are shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points, and LOESS-smoothed trend lines with 95% confidence intervals (gray shade). (A–C) Percentage of S1 and S2-specific cells within memory and IgG+ memory B cells, and plasmablasts. Comparisons were performed between S1 and S2 groups using a Wilcoxon signed-rank test. (D–F) Percentages of HKU1-specific B cells within total and IgG+ memory B cells, and plasmablasts. Comparisons assessed between sequential vaccine time point pairs, using mixed-effects models (only significant results are shown; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001). Sample sizes: baseline ( n = 20); 14 days ( n = 30) and 28 days post-first dose ( n = 19); and 14 days ( n = 22) and 28 days post-second dose ( n = 18).

Article Snippet: For HKU1-specific B cells, biotinylated HKU1 spike proteins were purchased from Sino Biological, Beijing, China (cat# 40606-V08B-B).

Techniques: Flow Cytometry, Transformation Assay, Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: Recalled HKU1 spike antibody responses display enhanced ADCP function (A) Antibody-dependent cellular phagocytosis (ADCP) responses against HCoV spike and SARS-CoV-2 S1- and S2-domains across vaccine doses and time points. ADCP scores were compared between baseline and 14 days post-first dose, and between 28 days post-first dose and 14 days post-second dose, using a mixed-effects model. Data are shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. (B) Spearman correlations between HKU1 and NL63 spike, and SARS-CoV-2 S1- and S2-domain-specific ADCP responses, adjusted for multiple comparisons with the Benjamini-Hochberg method. Spearman correlations are shown as a heatmap for each time point. (only significant results are shown; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001). Sample sizes: baseline ( n = 48), 14 days post-first dose ( n = 46), 28 days post-first dose ( n = 35), 14 days post-second dose ( n = 15), and 28 days post-second dose ( n = 11).

Article Snippet: For HKU1-specific B cells, biotinylated HKU1 spike proteins were purchased from Sino Biological, Beijing, China (cat# 40606-V08B-B).

Techniques: Whisker Assay

Journal: iScience

Article Title: HKU1 immune imprinting is associated with post-COVID symptoms after SARS-CoV-2 infection

doi: 10.1016/j.isci.2026.115175

Figure Lengend Snippet: HKU1 antibody reactivity was protective against SARS-CoV-2 infection but increased the risk of post-COVID symptoms in vaccinated, infection-naive individuals (A) Comparison of HCoV spike IgG levels (HKU1, OC43, NL63, and 229E; log-transformed data) at baseline, between individuals infected and those who were not at the one-year follow-up. Comparisons were performed using a Wilcoxon rank-sum test ( n = 700, infected = 509, uninfected = 191). (B) Effects of HCoV spike IgG levels, time interval between the first and second vaccine dose (days), use of mRNA vaccines only, sex, and age at baseline, on the risk of SARS-CoV-2 infection at the one-year follow-up. (C) Comparison of HCoV spike IgG levels at baseline, between individuals who developed post-COVID symptoms versus those who did not, by the one-year follow-up visit. Comparisons were performed using a Wilcoxon rank-sum test ( n = 509, post-COVID symptoms = 165, no post-COVID symptoms = 335; missing data = 9). (D) Effects of HCoV spike IgG levels, time interval between the first and second dose (days), use of mRNA vaccines only, sex, and age at baseline, on the risk of post-COVID symptoms at the one-year follow-up. (B and D) Show adjusted odds ratios with 95% confidence intervals on a logarithmic scale (in blue) where the dashed horizontal line indicates no effect (OR = 1), with corresponding p -values (in red). (E–G) Antibody-dependent complement deposition (ADCD) between individuals with the highest (78 th centile, n = 88) and lowest (22 nd centile, n = 88) HKU1 spike (E), SARS-CoV-2 S1 (F) and S2 (G) IgG levels. Comparisons were performed using a Wilcoxon rank-sum test. For (A, C, E–G) data are shown as box (median, with lower/higher quartiles)-and-whiskers (upper whisker: Q3+1.5xIQR, lower whisker: Q1-1.5xIQR) plots, with all data points. For (B, D): Odds Ratios (OR) with 95% confidence intervals (blue line) and p value (in red), on a log scale. (∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001).

Article Snippet: For HKU1-specific B cells, biotinylated HKU1 spike proteins were purchased from Sino Biological, Beijing, China (cat# 40606-V08B-B).

Techniques: Infection, Comparison, Transformation Assay, Vaccines, Whisker Assay