mm10 oc43 cov np antibody sino biological cas  (Sino Biological)

Journal: bioRxiv

Article Title: Comparative profiling of SARS-CoV-2 variant infections reveals diverse impacts on host cell RNA and RNA binding protein distribution and regulation

doi: 10.64898/2026.01.22.701202

Figure Lengend Snippet: A) Architecture of the SARS-CoV-2 genome, with black lines indicating canonical junctions yielding subgenomic RNAs. Mutations in pre-VOC, Alpha, Delta and Omicron BA.1 isolates are shown relative to the SARS-CoV-2 reference sequence (NC_045512.2). Non-coding, synonymous and non-synonymous mutations are highlighted in grey, black and red, respectively. B) Representative flow-cytometry plots showing nucleocapsid intensity at 48 hpi. C) Immunofluorescence staining of infected Calu-3 cells with an antibody against SARS-COV-2 nucleocapsid and spike proteins. Scale bars: 40 µm. D) Immunofluorescence staining for nucleocapsid protein combined with viral RNA FISH in pre-VOC, Omicron BA.1 and additional Omicron isolates corresponding to BA.1, BA.5 and JN.1 subvariants. E) Representative bioanalyzer traces showing similar levels of 18S and 28S rRNA between infected and mock samples.

Article Snippet: Samples were immunolabeled with an anti-nucleocapsid primary antibody (Sinobiological, 40143-MM05-100) and an Alexa Fluor 647-conjugated secondary antibody as previously described After.

Techniques: Sequencing, Flow Cytometry, Immunofluorescence, Staining, Infection

Journal: bioRxiv

Article Title: Comparative profiling of SARS-CoV-2 variant infections reveals diverse impacts on host cell RNA and RNA binding protein distribution and regulation

doi: 10.64898/2026.01.22.701202

Figure Lengend Snippet: A) Schematic of the experimental workflow used in this study. B) Architecture of the SARS-CoV-2 genome, with binding sites of FISH probe sets indicated by color triangles. C) Immunofluorescence staining of infected Calu-3 cells with an antibody against SARS-CoV-2 nucleocapsid protein (N-protein) combined with viral RNA smiFISH. Scale bar: 40 µm. D) Mean of total viral RNA FISH and nucleocapsid IF intensities per infected cell, as shown performed in ( C ), with standard deviation across n=3 replicates . E) Viral RNA smiFISH conducted on control or infected Calu-3 cells using the indicated probes specific targeting the ORF1ab (green) or ORF-N (magenta) sub-genomic regions. Scale bar: 20 µm. F) Location of RT-qPCR primers used to assess ORF1ab and ORF N sub-genomic RNA expressions and corresponding RT-qPCR 2 -ΔΔCt results using pre-VOC as the reference. Data represents n=3 replicates. Statistical significance is denoted as follow: * p<0.05, ** p<0.005, *** p<0.0005. G) Viral RNA smiFISH targeting positive-sense (+) and negative-sense (-) viral RNA, combined with immunofluorescence co-labeling with the 9D5 antibody detecting dsRNA structures. Scale bar: 10 µm.

Article Snippet: Samples were immunolabeled with an anti-nucleocapsid primary antibody (Sinobiological, 40143-MM05-100) and an Alexa Fluor 647-conjugated secondary antibody as previously described After.

Techniques: Binding Assay, Immunofluorescence, Staining, Infection, Standard Deviation, Control, Quantitative RT-PCR, Labeling

Journal: bioRxiv

Article Title: Comparative profiling of SARS-CoV-2 variant infections reveals diverse impacts on host cell RNA and RNA binding protein distribution and regulation

doi: 10.64898/2026.01.22.701202

Figure Lengend Snippet: A) Number of total proteins (A) or ISG (B) detected across Mock and infected conditions. Proteins significantly up- and downregulated following infection (padj < 0.05, log2-fold change > 1 or < −1) are highlighted in red and blue, respectively. B) Two-dimensional kernel density estimates of RNA log2 fold changes versus protein log2 fold changes for each condition (solid contours; p < 0.05). The density maximum for each condition is indicated by a cross. Dashed lines represent linear regressions, and the corresponding Pearson correlation coefficients (R) are annotated. C) Number of genes binned by their RNA and protein relative expression for each variant. ‘up’ and ‘down’: log2 fold-change > 1 and < −1, respectively, and adjusted p-value < 0.05. nc: not significantly changed. Numbers indicate the gene count per bin. Bubble sizes represent the percentage of differentially expressed genes, either at the RNA of protein level. Colors encode the combined direction of RNA and protein expression change (concordant up, concordant down or discordant changes). D) Heatmap showing the standardized degradation rate of proteins upregulated (up, padj<0.05 and fold-change>1.2), not changed (nc) or downregulated (down, padj<0.05 and fold-change<0.8) across infections, and the corresponding number of proteins. E) Clustermap of standardized, batch-corrected protein intensities across individual replicates (N=4) and conditions for each SRP component. F) Immunofluorescence staining of IRF2 and N-protein in uninfected Calu-3 cells (mock) or in cells infected with pre-VOC or Omicron viruses. G) Fluorescent OPP staining of infected cells combined with nucleocapsid immunofluorescence. OPP(-): negative control without OPP. OPP(+): mock cells with OPP. Scale bar represents 20 µm.

Article Snippet: Samples were immunolabeled with an anti-nucleocapsid primary antibody (Sinobiological, 40143-MM05-100) and an Alexa Fluor 647-conjugated secondary antibody as previously described After.

Techniques: Infection, Expressing, Variant Assay, Immunofluorescence, Staining, Negative Control

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: PABPC1 is identified as a RNA-binding protein of positive-sense RNA (+ssRNA) viruses through multi-omics analysis and high-throughput screening (A) Schematic overview of the multi-omics and high-throughput screening strategy used to identify SARS-CoV-2 RNA-binding proteins (RBPs). (B) Heatmap of SARS-CoV-2 RNA-binding proteins across nine independent datasets, proteins detected in four or more datasets are highlighted in red. (C) Bar plot of 94 high-confidence RBPs. (D) Venn diagram showing shared and virus-specific RNA-binding proteins among SARS-CoV-2, HCoV-OC43, DENV, and RV. (E) Heatmap of integration of five genome-wide screens and literature curation identifies 49 RBPs that significantly affect SARS-CoV-2 replication. (F) Schematic of RBPs knockdown and SARS-CoV-2 ΔN-GFP-HiBiT replicon delivery particles (RDPs) infection workflow. (G-H) Knockdown of selected RBPs in Caco-2-N cells followed by qPCR measurement of SARS-CoV-2 E and ORF1ab expression.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: RNA Binding Assay, Biomarker Discovery, High Throughput Screening Assay, Virus, Genome Wide, Knockdown, Infection, Expressing

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: PABPC1 restricts the replication of SARS-CoV-2, HCoV-OC43 and MHV, but not ZIKV. (A) qPCR analysis of SARS-CoV-2 E and ORF1ab RNA level at 12, 24, 36, and 48 h post-infection in Caco-2-N cells with PABPC1 knockdown. (B) qPCR analysis of HCoV-OC43 M and N RNA level at 12, 24, 36, and 48 h post-infection in RD cells with PABPC1 knockdown. (C) qPCR analysis of MHV E and N RNA level at 12, 24, 36, and 48 h post-infection in Neuro2a cells with PABPC1 knockdown. (D) qPCR analysis of ZIKV M and E RNA level at 12, 24, 36, and 48 h post-infection in A549 cells with PABPC1 knockdown. (E) RIP-qPCR analysis of SARS-CoV-2 gene enrichment in IgG and PABPC1 immunoprecipitated samples following SARS-CoV-2 RDPs infection. (F) RIP-qPCR analysis of HCoV-OC43 gene enrichment in IgG and PABPC1 immunoprecipitated samples following HCoV-OC43 infection. (G) RIP-qPCR analysis of MHV gene enrichment in IgG and PABPC1 immunoprecipitated samples following MHV infection. (H) RIP-qPCR analysis of ZIKV gene enrichment in IgG and PABPC1 immunoprecipitated samples following ZIKV infection. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Infection, Knockdown, Immunoprecipitation, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: PABPC1 depletion enhances coronavirus replication in vitro. (A) Western blot analysis confirming PABPC1 knockdown in Caco-2 cells. Cells were subsequently infected with SARS-CoV-2 at an MOI = 0.02, and viral RNA levels of the N and E genes were quantified by qPCR at 24 h (B) and 48 h (C) post-infection. Western blot analysis confirming PABPC1 knockout in Caco-2 cells (D) and Huh7 cells (E). (F-I) qPCR analysis of RNA levels of N or E in cell or supernatant from wild-type Caco-2 or PABPC1 knockout cells and wild-type Huh7 or PABPC1 knockout cells, with infection by SARS-CoV-2 at an MOI = 0.02 for 24 h. (J-K) Immunofluorescence analysis of N protein (red) in wild-type Caco-2 or PABPC1 knockout cells and wild-type Huh7 or PABPC1 knockout cells, with infection by SARS-CoV-2. Scale bar, 100 μm. (L) RNA-seq analysis of SARS-CoV-2 and human genome mapping rates in wild-type and PABPC1 knockout Caco-2 cells, with infection by SARS-CoV-2. (M) Bar plot showing counts per million (CPM) of individual SARS-CoV-2 genes in wild-type and PABPC1 knockout Caco-2 cells. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3) derived from three independent experiments. NS, not significant for P > 0.05, * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: In Vitro, Western Blot, Knockdown, Infection, Knock-Out, Immunofluorescence, RNA Sequencing, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: Pharmacological inhibition of PABPC1–poly(A) interaction enhances coronavirus replication in vitro and in vivo. (A) Schematic representation of small-molecule inhibitors 1,10-Phen and ML324 competitively binding to PABPC1. (B-C) qPCR analysis of SARS-CoV-2 E and N RNA levels in Caco-2-N cells pretreated with 1,10-Phen or ML324 for 24 h, followed by infection with SARS-CoV-2 ΔN-GFP-HiBiT RDPs at an MOI of 0.001. (D) Schematic representation of Sftpc-N-hACE2 mice pretreated with 1,10-Phen or ML324, followed by intranasal infection with SARS-CoV-2 RDPs. Black arrows indicate intraperitoneal injection of 1,10-Phen or ML324, and blue arrows indicate intranasal administration of SARS-CoV-2 RDPs. (E) Line graph showing body weight changes in Sftpc-N-hACE2 mice. Mice were treated with saline (control) or the small-molecule inhibitors 1,10-Phen or ML324 prior to SARS-CoV-2 RDPs infection, n=5. (F) qPCR analysis of SARS-CoV-2 E RNA levels in the lung of Sftpc-N-hACE2 mice, n=5. (G) Pathology scores of lungs from saline-treated, 1,10-Phen-treated, and ML324-treated mice, n=5. (H) Representative H&E-stained lung sections from uninfected, saline-treated, 1,10-Phen-treated, and ML324-treated mice, n=5. Scale bar, 2000 and 200 µm. Scale bar, 2000 and 200 µm. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3 in B-C, n = 5 in E-G) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Inhibition, In Vitro, In Vivo, Binding Assay, Infection, Injection, Saline, Control, Staining, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: PABPC1 directly binds coronavirus RNA and selectively accelerates the decay of short poly(A)-tailed viral transcripts. (A) RIP-seq analysis of SARS-CoV-2 and human genome mapping rates in input and PABPC1 immunoprecipitated (IP) samples from Caco-2-N cells, with or without SARS-CoV-2 RDPs infection. (B) Integrative Genomics Viewer (IGV) tracks showing read distributions from RIP-seq and input samples along the SARS-CoV-2 positive-sense RNA genome. (C) EMSA analysis of SARS-CoV-2 M RNA binding to purified GST–PABPC1 protein. (D) Stability analysis of RNA of SARS-CoV-2 M gene in Caco-2 WT or PABPC1 -/- cells with treatment of actinomycin D (ActD) for another 0, 2, 4, and 6 h. (E) Tail-length distribution of viral mRNAs in Caco-2 WT or PABPC1 -/- cells with infection of SARS-CoV-2. (F) Violin plots showing the poly(A) tail length distributions of human and SARS-CoV-2 mRNAs. (G) Line graph showing RNA retention measured by qPCR in cells with or without PABPC1 knockdown after transfection of luciferase gene containing different poly(A) tail lengths. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Immunoprecipitation, Infection, RNA Binding Assay, Purification, Knockdown, Transfection, Luciferase, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: PABPC1-EXD2 interaction drives the degradation of viral RNA. (A) Scatter plot showing identification of PABPC1-interacting proteins by IP-MS, with six RNA metabolism factors highlighted. (B) qPCR analysis of SARS-CoV-2 E gene RNA levels following knockdown of PABPC1-interacting proteins and infection with SARS-CoV-2 RDPs. (C) Co-immunoprecipitation analysis of PABPC1-HA and EXD2-Flag co-expressed in HEK293T cells. (D) GST pulldown analysis of bacterially expressed and purified PABPC1-GST and EXD2-His proteins. (E) Fluorescence images showing co-localization of PABPC1-GFP and EXD2-mCherry. Scale bar, 100 µm. Schematic representation of PABPC1 (F) and EXD2 (G) truncation constructs. Co-immunoprecipitation analysis of PABPC1 truncation fragments co-expressed with full-length EXD2 in HEK293T cells (H), and of EXD2 truncation fragments co-expressed with full-length PABPC1 (I). Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Protein-Protein interactions, Knockdown, Infection, Immunoprecipitation, Purification, Fluorescence, Construct, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: EXD2 mediates antiviral activity through 3’-5’ exonuclease activity. (A-C) Kinetics of HiBiT luminescence, GFP fluorescence, and qPCR analysis of SARS-CoV-2 E and ORF1ab RNA levels in Caco-2-N cells following EXD2 knockdown and infection with SARS-CoV-2 RDPs. (D) Relative luciferase activity of the SARS-CoV-2-Luc reporter in cells transfected with 100 ng, 200 ng, or 500 ng of EXD2-Flag. (E) Relative luciferase activity of the SARS-CoV-2-Luc reporter in cells transfected with 500 ng of EXD2 truncation fragments. (F) Schematic representation of EXD2 and ΔEXD2. (G) Agarose gel electrophoresis analysis of SARS-CoV-2 M RNA following incubation with full-length EXD2 or the exonuclease-deficient ΔEXD2 protein. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Activity Assay, Fluorescence, Knockdown, Infection, Luciferase, Transfection, Agarose Gel Electrophoresis, Incubation, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: The fusion protein of the key functional domains of PABPC1 and EXD2 inhibits SARS-CoV-2 and MHV replication as a novel nucleic acid therapeutic. (A) Schematic representation illustrating that co-expression of PABPC1 and EXD2 suppresses SARS-CoV-2 RDPs replication. (B) Schematic representation and Western blot analysis of the PABPC1–EXD2 fusion protein. (C) AlphaFold3-predicted structure of the PABPC1–EXD2 fusion protein. (D) Relative luciferase activity of the SARS-CoV-2-Luc reporter in cells transfected with 100 ng, 200 ng, or 500 ng of RRM1-4-EXD2-Flag. (E-G) GFP fluorescence, qPCR analysis of SARS-CoV-2 E and ORF1ab RNA levels, and kinetics of HiBiT luminescence in Caco-2-N cells transfected with RRM1-4–EXD2-Flag and infected with SARS-CoV-2 RDPs. (H) Characterization of lipid nanoparticle (LNP)-encapsulated fusion mRNA. (I) qPCR analysis of SARS-CoV-2 E RNA levels in Caco-2-N cells following LNP treatment and infection with SARS-CoV-2 RDPs. (J) qPCR analysis of MHV N RNA levels in Neruo2a cells following LNP treatment and infection with MHV. Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3 in D, F-G, I-J) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Functional Assay, Expressing, Western Blot, Luciferase, Activity Assay, Transfection, Fluorescence, Infection, Two Tailed Test, Derivative Assay

Journal: bioRxiv

Article Title: Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

doi: 10.64898/2026.01.12.699136

Figure Lengend Snippet: Inflammatory stimuli upregulate PABPC1 and EXD2 Expression (A) qPCR analysis of PABPC1 and EXD2 mRNA levels in Caco-2 cells following infection with SARS-CoV-2. (B) RNA-seq analysis of PABPC1 and EXD2 counts per million (CPM) in Caco-2 cells following SARS-CoV-2 infection. (C) RNA-seq analysis of fold changes in PABPC1 and EXD2 expression in Caco-2 cells at 0, 1, 4, 7, 12, 24, and 48 h post SARS-CoV-2 infection. (D) RNA-seq analysis of FPKM values for PABPC1 and EXD2 expression in SARS-CoV-2-infected patients and healthy controls. (E) Schematic representation of K18-hACE2 mice intranasally infected with SARS-CoV-2 BA.2 and lung collection at 3, 5, and 7 days post-infection. (F) Line graph showing body weight changes in K18-hACE2 mice, n=6. (G) qPCR analysis of SARS-CoV-2 E and N RNA levels in the lung of K18-hACE2 mice, n=6. (H) GSEA enrichment analysis of pathways in lungs of K18-hACE2 mice at 3, 5, and 7 days post SARS-CoV-2 BA.2 infection. (I) Representative H&E-stained lung sections from uninfected mice and mice at 3, 5, and 7 days post-infection, n=6. Scale bar, 200 µm. (J) qPCR analysis of IL-1 β, IL-6 and IL-8 mRNA levels in lungs of K18-hACE2 mice at 3, 5, and 7 days post SARS-CoV-2 BA.2 infection. (K) qPCR analysis of PABPC1 and EXD2 mRNA levels in lungs of K18-hACE2 mice at 3, 5, and 7 days post SARS-CoV-2 BA.2 infection. (L) Schematic representation of C57BL/6J mice sacrificed 1 day after intraperitoneal injection of LPS for lung collection. (M) GSEA enrichment analysis of signaling pathways in the lungs of C57BL/6J mice following intraperitoneal injection of LPS. (N) Volcano plot analysis of differential gene expression in the lungs of C57BL/6J mice before and after LPS treatment (fold change > 2, P < 0.05). Data are representative of three independent experiments and were analyzed by two-tailed unpaired t test. Graphs show the mean ± SD (n = 3 in A-C; n = 5 in F-G, J-K) derived from three independent experiments. NS, not significant for P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Cells were then incubated with mouse anti–SARS-CoV-2 Nucleocapsid antibody (Sino Biological, 40143-MM05) diluted in 1% BSA at 37 °C for 1 h, followed by three washes with PBS.

Techniques: Expressing, Infection, RNA Sequencing, Staining, Injection, Protein-Protein interactions, Gene Expression, Two Tailed Test, Derivative Assay