hcv rna Search Results


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  • 91
    Thermo Fisher hcv rna
    Predicted values and experimental validation of the first step of the ratiometric approach. (a) Measured spectral transmittance (%) in the range of visible light (400–700 nm) for positive (solid blue line) and negative (solid purple line) RT-LAMP reaction solutions, each containing 0.7 mM of eriochrome black T (EBT) as the amplification indicator dye. Dashed lines correspond to normalized spectral responses for red (R), green (G), and blue (B) channels of an Exmor R CMOS sensor, a common sensor in cell phone cameras. (b–e) Analysis of the three possible RGB ratiometric combinations for positive and negative RT-LAMP reaction solutions. (b) The predicted RGB values and corresponding colors for positive and negative LAMP amplification reactions obtained by convoluting the transmittance spectrum and Exmor R spectral responses described in panel a. (c) The cropped and enlarged color images collected with an Apple iPhone 4S for positive and negative RT-LAMP reaction solutions containing 90 μM of EBT dye. (d) Predicted images and ratiometric values for positive and negative amplification reactions processed for each ratiometric combination, G/R, B/R, and G/B. (e) Experimental images and ratiometric values for positive and negative amplification reactions for each combination: G/R, B/R, and G/B. All experiments were performed with <t>HCV</t> <t>RNA</t> as template.
    Hcv Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 1441 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore hcv rna
    Analysis of intracellular and supernatant <t>HCV</t> <t>RNA</t> levels in core 70/91 mutants. In vitro -transcribed mutant and wild-type RNAs were transfected into Huh7 cells. Three days after transfection, RNA was extracted from cells (A) or culture supernatant (B)
    Hcv Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche hcv ribonucleic acid rna cobas taqman hcv test
    Analysis of intracellular and supernatant <t>HCV</t> <t>RNA</t> levels in core 70/91 mutants. In vitro -transcribed mutant and wild-type RNAs were transfected into Huh7 cells. Three days after transfection, RNA was extracted from cells (A) or culture supernatant (B)
    Hcv Ribonucleic Acid Rna Cobas Taqman Hcv Test, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche hcv rna hcv rna
    Serum <t>HCV</t> <t>RNA</t> levels (LIU/mL) during and after interferon-free treatment in the present study EOT, end of the treatment response.
    Hcv Rna Hcv Rna, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Roche qualitative hcv rna
    Preferences for <t>HCV</t> testing strategy. Half of respondents consider two-step testing strategy (see Figure 1 ) to be an optimal future testing approach in LMIC, while the other half prefer currently used two-step approach a . If one-step testing strategy is implemented, more than a half of respondents prefer to use HCV <t>RNA</t> test b
    Qualitative Hcv Rna, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 106 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche positive hcv ribonucleic acid rna polymerase chain reaction
    Preferences for <t>HCV</t> testing strategy. Half of respondents consider two-step testing strategy (see Figure 1 ) to be an optimal future testing approach in LMIC, while the other half prefer currently used two-step approach a . If one-step testing strategy is implemented, more than a half of respondents prefer to use HCV <t>RNA</t> test b
    Positive Hcv Ribonucleic Acid Rna Polymerase Chain Reaction, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore hcv ires rna
    Effect of NS5A on PKR activation by <t>HCV</t> <t>IRES</t> domains
    Hcv Ires Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    PrimerDesign Inc hcv rna
    <t>HCV</t> <t>RNA</t> Load in Brain and Liver Tissue
    Hcv Rna, supplied by PrimerDesign Inc, used in various techniques. Bioz Stars score: 92/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Abbott Laboratories hcv rna
    Distribution of <t>HCV-RNA</t> (A) and HCVAg (B) by HCV genotype. Significant differences between median values were observed only between genotypes 1 and 3 for both HCV-RNA (p = 0.028) and HCVAg (p = 0.0098).
    Hcv Rna, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 92/100, based on 592 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher optiquant hcv rna
    qRT-PCR of IFN-γ in chimpanzees infected with HEV or <t>HCV.</t> IFN-γ was tested by primer- and probe-specific TaqMan qPCR (see Table S1 in the supplemental material). Total <t>RNA</t> from liver biopsies was converted to cDNA, amplified, and tested
    Optiquant Hcv Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche amplicor hcv rna
    Mean values of results (expressed as log 10 <t>HCV</t> <t>RNA</t> copies per milliliter of serum) determined by our RT-PCR protocol (ABI Prism 7700 assay), the bDNA assay and the NGI method are comparable. (A) Comparison of totals; differences in mean values are not significant (ns). The percentages of samples positive by each method are given in the box. (B) Comparison of mean values for groups of different genotypes; differences are not significant.
    Amplicor Hcv Rna, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abbott Laboratories hcv rna asr
    Mean values of results (expressed as log 10 <t>HCV</t> <t>RNA</t> copies per milliliter of serum) determined by our RT-PCR protocol (ABI Prism 7700 assay), the bDNA assay and the NGI method are comparable. (A) Comparison of totals; differences in mean values are not significant (ns). The percentages of samples positive by each method are given in the box. (B) Comparison of mean values for groups of different genotypes; differences are not significant.
    Hcv Rna Asr, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher armored hcv rna
    Age related decline in prevalence of hepatitis C antibody in infants who had <t>anti-HCV</t> detected in their initial blood sample according to whether their mothers were positive for both <t>HCV-RNA</t> and anti-HCV or only had anti-HCV.
    Armored Hcv Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bayer AG versant hcv rna assay
    Age related decline in prevalence of hepatitis C antibody in infants who had <t>anti-HCV</t> detected in their initial blood sample according to whether their mothers were positive for both <t>HCV-RNA</t> and anti-HCV or only had anti-HCV.
    Versant Hcv Rna Assay, supplied by Bayer AG, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher hcv 1a armored rna
    Association between IFN Response, <t>HCV</t> <t>RNA</t> Levels, and Effect on Host Gene Expression in HCV-Infected Mice Intrahepatic HCV RNA levels were determined by quantitative RT-PCR as described in Materials and Methods. Total number of genes showing increased expression in HCV-infected mice relative to donor-matched uninfected mice is shown in gray bars, while the percent of induced genes that are IFN regulated is shown using black triangles.
    Hcv 1a Armored Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Predicted values and experimental validation of the first step of the ratiometric approach. (a) Measured spectral transmittance (%) in the range of visible light (400–700 nm) for positive (solid blue line) and negative (solid purple line) RT-LAMP reaction solutions, each containing 0.7 mM of eriochrome black T (EBT) as the amplification indicator dye. Dashed lines correspond to normalized spectral responses for red (R), green (G), and blue (B) channels of an Exmor R CMOS sensor, a common sensor in cell phone cameras. (b–e) Analysis of the three possible RGB ratiometric combinations for positive and negative RT-LAMP reaction solutions. (b) The predicted RGB values and corresponding colors for positive and negative LAMP amplification reactions obtained by convoluting the transmittance spectrum and Exmor R spectral responses described in panel a. (c) The cropped and enlarged color images collected with an Apple iPhone 4S for positive and negative RT-LAMP reaction solutions containing 90 μM of EBT dye. (d) Predicted images and ratiometric values for positive and negative amplification reactions processed for each ratiometric combination, G/R, B/R, and G/B. (e) Experimental images and ratiometric values for positive and negative amplification reactions for each combination: G/R, B/R, and G/B. All experiments were performed with HCV RNA as template.

    Journal: ACS Nano

    Article Title: Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones

    doi: 10.1021/acsnano.5b07338

    Figure Lengend Snippet: Predicted values and experimental validation of the first step of the ratiometric approach. (a) Measured spectral transmittance (%) in the range of visible light (400–700 nm) for positive (solid blue line) and negative (solid purple line) RT-LAMP reaction solutions, each containing 0.7 mM of eriochrome black T (EBT) as the amplification indicator dye. Dashed lines correspond to normalized spectral responses for red (R), green (G), and blue (B) channels of an Exmor R CMOS sensor, a common sensor in cell phone cameras. (b–e) Analysis of the three possible RGB ratiometric combinations for positive and negative RT-LAMP reaction solutions. (b) The predicted RGB values and corresponding colors for positive and negative LAMP amplification reactions obtained by convoluting the transmittance spectrum and Exmor R spectral responses described in panel a. (c) The cropped and enlarged color images collected with an Apple iPhone 4S for positive and negative RT-LAMP reaction solutions containing 90 μM of EBT dye. (d) Predicted images and ratiometric values for positive and negative amplification reactions processed for each ratiometric combination, G/R, B/R, and G/B. (e) Experimental images and ratiometric values for positive and negative amplification reactions for each combination: G/R, B/R, and G/B. All experiments were performed with HCV RNA as template.

    Article Snippet: HCV Viral RNA Purification from AcroMetrix HCV High Control A total of 200 μL of plasma containing HCV RNA (viral load estimate provided by AcroMetrix: 1.1–3.5 IU/mL) was extracted using the QIAamp Viral RNA Mini Kit (QIAGEN, Inc., Valencia, CA, USA) according to the manufacturer’s instructions.

    Techniques: Amplification

    Validation of the robustness of the G/R ratiometric approach to different hardware (cell phone cameras) and lighting conditions. (a–g) Enlarged and cropped color images (top two rows of each individual panel) captured by an unmodified cell phone camera from positive (+) and negative (−) RT-LAMP reactions at 2-fold increases in EBT concentration from 10.9 μM to 1.4 mM (1 = 0.011 mM; 2 = 0.022 mM; 3 = 0.044 mM, 4 = 0.088 mM, 5 = 0.175 mM; 6 = 0.35 mM; 7 = 0.7 mM; 8 = 1.4 mM). Positive wells are blue and negative wells are purple. After G/R ratiometric processing (bottom two rows of each individual panel), negative wells are black. Regions I, II, III in each panel indicate the effect of dye concentration: (II) acceptable concentration range for visualization (green regions); (I) concentrations too low for visualization (white regions); and (III) concentrations too high for visualization (red regions). (a–d) Images captured by four common cell phones under fluorescent light: (a) Apple iPhone 4S, (b) HTC inspire 4G, (c) Motorola Moto G, and (d) Nokia 808 PureView. (e–g) Images captured by an Apple iPhone 4S under three additional light conditions: (e) incandescent light, (f) direct sunlight, and (g) indirect sunlight. All experiments were performed with HCV RNA as a clinically relevant target. All images were acquired with unmodified cell phone cameras. Detailed information for the G/R ratiometric process (Figure S2) and additional cell phone camera images (Figure S3) are provided in the Supporting Information .

    Journal: ACS Nano

    Article Title: Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones

    doi: 10.1021/acsnano.5b07338

    Figure Lengend Snippet: Validation of the robustness of the G/R ratiometric approach to different hardware (cell phone cameras) and lighting conditions. (a–g) Enlarged and cropped color images (top two rows of each individual panel) captured by an unmodified cell phone camera from positive (+) and negative (−) RT-LAMP reactions at 2-fold increases in EBT concentration from 10.9 μM to 1.4 mM (1 = 0.011 mM; 2 = 0.022 mM; 3 = 0.044 mM, 4 = 0.088 mM, 5 = 0.175 mM; 6 = 0.35 mM; 7 = 0.7 mM; 8 = 1.4 mM). Positive wells are blue and negative wells are purple. After G/R ratiometric processing (bottom two rows of each individual panel), negative wells are black. Regions I, II, III in each panel indicate the effect of dye concentration: (II) acceptable concentration range for visualization (green regions); (I) concentrations too low for visualization (white regions); and (III) concentrations too high for visualization (red regions). (a–d) Images captured by four common cell phones under fluorescent light: (a) Apple iPhone 4S, (b) HTC inspire 4G, (c) Motorola Moto G, and (d) Nokia 808 PureView. (e–g) Images captured by an Apple iPhone 4S under three additional light conditions: (e) incandescent light, (f) direct sunlight, and (g) indirect sunlight. All experiments were performed with HCV RNA as a clinically relevant target. All images were acquired with unmodified cell phone cameras. Detailed information for the G/R ratiometric process (Figure S2) and additional cell phone camera images (Figure S3) are provided in the Supporting Information .

    Article Snippet: HCV Viral RNA Purification from AcroMetrix HCV High Control A total of 200 μL of plasma containing HCV RNA (viral load estimate provided by AcroMetrix: 1.1–3.5 IU/mL) was extracted using the QIAamp Viral RNA Mini Kit (QIAGEN, Inc., Valencia, CA, USA) according to the manufacturer’s instructions.

    Techniques: Concentration Assay

    Experimental validation of two-step SlipChip devices for single molecule counting with an unmodified cell phone camera. (a) A flow-chart of detection of single molecules in two-step SlipChip: (i) 5 nL amplification wells are loaded with amplification reaction solution (RXN) and 9.5 nL detection wells are loaded with indicator dye (DYE). (ii) After amplification, a slip is performed and the RXN and DYE wells are combined. (iii) Immediately after mixing, positive reaction solutions become blue, while negative reactions remain purple. The readout is imaged by an unmodified cell phone camera. (iv) Ratiometric image processing (G/R process) provides a single binary result (positive or negative). (b) Stereoscope image of the device before the amplification and readout wells are merged (arrow designates direction of slip). (c) Stereoscope, (d) cell phone camera and (e) fluorescent images after the device is slipped and the wells are merged. (f) Stereoscope and (g) cell phone camera images after G/R image processing. (h) Correlation between fluorescence counts and cell phone (G/R processed) counts. Colors were enhanced in figure panels b–d, and f for clarity of publication; raw images were used in all ratiometric analyses. In these experiments, HCV RNA was amplified by dRT-LAMP.

    Journal: ACS Nano

    Article Title: Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones

    doi: 10.1021/acsnano.5b07338

    Figure Lengend Snippet: Experimental validation of two-step SlipChip devices for single molecule counting with an unmodified cell phone camera. (a) A flow-chart of detection of single molecules in two-step SlipChip: (i) 5 nL amplification wells are loaded with amplification reaction solution (RXN) and 9.5 nL detection wells are loaded with indicator dye (DYE). (ii) After amplification, a slip is performed and the RXN and DYE wells are combined. (iii) Immediately after mixing, positive reaction solutions become blue, while negative reactions remain purple. The readout is imaged by an unmodified cell phone camera. (iv) Ratiometric image processing (G/R process) provides a single binary result (positive or negative). (b) Stereoscope image of the device before the amplification and readout wells are merged (arrow designates direction of slip). (c) Stereoscope, (d) cell phone camera and (e) fluorescent images after the device is slipped and the wells are merged. (f) Stereoscope and (g) cell phone camera images after G/R image processing. (h) Correlation between fluorescence counts and cell phone (G/R processed) counts. Colors were enhanced in figure panels b–d, and f for clarity of publication; raw images were used in all ratiometric analyses. In these experiments, HCV RNA was amplified by dRT-LAMP.

    Article Snippet: HCV Viral RNA Purification from AcroMetrix HCV High Control A total of 200 μL of plasma containing HCV RNA (viral load estimate provided by AcroMetrix: 1.1–3.5 IU/mL) was extracted using the QIAamp Viral RNA Mini Kit (QIAGEN, Inc., Valencia, CA, USA) according to the manufacturer’s instructions.

    Techniques: Single Molecule Counting, Flow Cytometry, Amplification, Fluorescence

    Analysis of intracellular and supernatant HCV RNA levels in core 70/91 mutants. In vitro -transcribed mutant and wild-type RNAs were transfected into Huh7 cells. Three days after transfection, RNA was extracted from cells (A) or culture supernatant (B)

    Journal: Journal of Virology

    Article Title: Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91 ▿Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91 ▿ §

    doi: 10.1128/JVI.02583-10

    Figure Lengend Snippet: Analysis of intracellular and supernatant HCV RNA levels in core 70/91 mutants. In vitro -transcribed mutant and wild-type RNAs were transfected into Huh7 cells. Three days after transfection, RNA was extracted from cells (A) or culture supernatant (B)

    Article Snippet: For the detection of HCV RNA in culture supernatant, the supernatant was passed through a 0.45-μm filter (Millex-HA, Millipore, Bedford, MA) and stored at −80°C until use.

    Techniques: In Vitro, Mutagenesis, Transfection

    Effects of core mutant HCV on SOCS1 and SOCS3 expression in Huh7 cells. Expression levels of SOCS1 (A) or SOCS3 (B) in Huh7 cells transfected with the wild type or the core mutant JFH1. Three days posttransfection, total cellular RNA was isolated and

    Journal: Journal of Virology

    Article Title: Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91 ▿Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91 ▿ §

    doi: 10.1128/JVI.02583-10

    Figure Lengend Snippet: Effects of core mutant HCV on SOCS1 and SOCS3 expression in Huh7 cells. Expression levels of SOCS1 (A) or SOCS3 (B) in Huh7 cells transfected with the wild type or the core mutant JFH1. Three days posttransfection, total cellular RNA was isolated and

    Article Snippet: For the detection of HCV RNA in culture supernatant, the supernatant was passed through a 0.45-μm filter (Millex-HA, Millipore, Bedford, MA) and stored at −80°C until use.

    Techniques: Mutagenesis, Expressing, Transfection, Isolation

    Endocytosis pathway for purified LVP. (A) A total of 200,000 copies of HCV RNA from purified LVP were incubated for 3 h with 50,000 HepG2 cells grown for 24 h in LPDS or FCS. Internalized HCV RNA was calculated after suramin treatment. (B) A total of 500,000 copies of HCV RNA from purified LVP were incubated with 20,000 N1 or FH fibroblasts for 3 h before suramin treatment and quantitation of internalized HCV RNA. Error bars indicated standard deviations.

    Journal: Journal of Virology

    Article Title: Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles

    doi: 10.1128/JVI.76.14.6919-6928.2002

    Figure Lengend Snippet: Endocytosis pathway for purified LVP. (A) A total of 200,000 copies of HCV RNA from purified LVP were incubated for 3 h with 50,000 HepG2 cells grown for 24 h in LPDS or FCS. Internalized HCV RNA was calculated after suramin treatment. (B) A total of 500,000 copies of HCV RNA from purified LVP were incubated with 20,000 N1 or FH fibroblasts for 3 h before suramin treatment and quantitation of internalized HCV RNA. Error bars indicated standard deviations.

    Article Snippet: For kinetic and uptake experiments, HCV RNA-containing particles bound to cell surface receptors after the incubation period and three washings with PBS-0.2% BSA were removed by incubation with 10 mM suramin (Sigma) in PBS at 4°C for 1 h. Cells were washed three times in PBS and harvested in 350 μl of RNeasy kit lysis buffer.

    Techniques: Purification, Incubation, Quantitation Assay

    Kinetics of internalization of immunoglobulin-positive purified LPV. (A) After 3 h of incubation at 37°C with purified LVP and extensive washing, PLC cells were subjected to suramin treatment at 4°C. The number of HCV RNA copies after suramin treatment is representative of internalized purified LVP. As uptake does not occur at 4°C, the HCV RNA copy number remaining associated with cells following incubation at 4°C and subsequent suramin treatment is indicative of the efficiency of suramin. The efficiency of suramin treatment was greater than 95% (data not shown). Data are expressed as HCV RNA copy number per microgram of protein. (B and C) Purified LVP were incubated with PLC cells for various periods of time before suramin treatment and quantitation of internalized HCV RNA. (B) Incubation with 50,000 copies of HCV RNA from purified LVP. (C) Incubation with 200,000 copies of HCV RNA from purified LVP. Data are representative of three independent experiments. Error bars indicated standard deviations.

    Journal: Journal of Virology

    Article Title: Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles

    doi: 10.1128/JVI.76.14.6919-6928.2002

    Figure Lengend Snippet: Kinetics of internalization of immunoglobulin-positive purified LPV. (A) After 3 h of incubation at 37°C with purified LVP and extensive washing, PLC cells were subjected to suramin treatment at 4°C. The number of HCV RNA copies after suramin treatment is representative of internalized purified LVP. As uptake does not occur at 4°C, the HCV RNA copy number remaining associated with cells following incubation at 4°C and subsequent suramin treatment is indicative of the efficiency of suramin. The efficiency of suramin treatment was greater than 95% (data not shown). Data are expressed as HCV RNA copy number per microgram of protein. (B and C) Purified LVP were incubated with PLC cells for various periods of time before suramin treatment and quantitation of internalized HCV RNA. (B) Incubation with 50,000 copies of HCV RNA from purified LVP. (C) Incubation with 200,000 copies of HCV RNA from purified LVP. Data are representative of three independent experiments. Error bars indicated standard deviations.

    Article Snippet: For kinetic and uptake experiments, HCV RNA-containing particles bound to cell surface receptors after the incubation period and three washings with PBS-0.2% BSA were removed by incubation with 10 mM suramin (Sigma) in PBS at 4°C for 1 h. Cells were washed three times in PBS and harvested in 350 μl of RNeasy kit lysis buffer.

    Techniques: Purification, Incubation, Planar Chromatography, Quantitation Assay

    Immunodetection of HCV core protein in purified and delipidated LVP. (A) Control immunoelectron microscopy with an irrelevant primary monoclonal antibody and a gold-labeled secondary antibody. No significant labeled antibody binding occurred. (B) Immunoelectron microscopy of Tween 80-treated LVP with anti-HCV core protein monoclonal antibody 19D9D6 and a 10-nm-gold-labeled secondary antibody. The binding of core protein-specific antibody on the particles can be seen. (C) Western blot of purified and delipidated LVP. Ether-butanol-treated LVP corresponding to 3 × 10 6 HCV RNA copies (lane a), HepG2 cells (negative control) (lane b), and HepG2 cells stably transfected with HCV core cDNA (positive control) (lane c) are shown. Detection of HCV core protein was performed with monoclonal antibody 19D9D6.

    Journal: Journal of Virology

    Article Title: Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles

    doi: 10.1128/JVI.76.14.6919-6928.2002

    Figure Lengend Snippet: Immunodetection of HCV core protein in purified and delipidated LVP. (A) Control immunoelectron microscopy with an irrelevant primary monoclonal antibody and a gold-labeled secondary antibody. No significant labeled antibody binding occurred. (B) Immunoelectron microscopy of Tween 80-treated LVP with anti-HCV core protein monoclonal antibody 19D9D6 and a 10-nm-gold-labeled secondary antibody. The binding of core protein-specific antibody on the particles can be seen. (C) Western blot of purified and delipidated LVP. Ether-butanol-treated LVP corresponding to 3 × 10 6 HCV RNA copies (lane a), HepG2 cells (negative control) (lane b), and HepG2 cells stably transfected with HCV core cDNA (positive control) (lane c) are shown. Detection of HCV core protein was performed with monoclonal antibody 19D9D6.

    Article Snippet: For kinetic and uptake experiments, HCV RNA-containing particles bound to cell surface receptors after the incubation period and three washings with PBS-0.2% BSA were removed by incubation with 10 mM suramin (Sigma) in PBS at 4°C for 1 h. Cells were washed three times in PBS and harvested in 350 μl of RNeasy kit lysis buffer.

    Techniques: Immunodetection, Purification, Immuno-Electron Microscopy, Labeling, Binding Assay, Western Blot, Negative Control, Stable Transfection, Transfection, Positive Control

    Cell association and uptake of purified LVP. (A) A total of 50,000 copies of HCV RNA from serum, fraction (fract.) 1 (whole fraction containing lipoproteins and LVP), fraction 2 (whole fraction depleted of immunoglobulin-positive LVP but containing lipoproteins and remaining immunoglobulin-negative LVP), and purified (pur.) LVP were incubated with PLC cells (50,000 cells/well). Cell association was quantified after 3 h of incubation and extensive washing and expressed as HCV RNA copy number per well. Data are representative of three independent experiments. (B and C) Purified LVP (50,000 HCV RNA copies) were coincubated with increasing amount of VLDL from a noninfected donor (B) or with increasing ratios of protein A-coated magnetic beads saturated with purified human IgG to purified LVP (C). Quantitation of cell-associated HCV RNA was performed after 3 h of incubation. ip, immunopurified LVP. Error bars indicated standard deviations.

    Journal: Journal of Virology

    Article Title: Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles

    doi: 10.1128/JVI.76.14.6919-6928.2002

    Figure Lengend Snippet: Cell association and uptake of purified LVP. (A) A total of 50,000 copies of HCV RNA from serum, fraction (fract.) 1 (whole fraction containing lipoproteins and LVP), fraction 2 (whole fraction depleted of immunoglobulin-positive LVP but containing lipoproteins and remaining immunoglobulin-negative LVP), and purified (pur.) LVP were incubated with PLC cells (50,000 cells/well). Cell association was quantified after 3 h of incubation and extensive washing and expressed as HCV RNA copy number per well. Data are representative of three independent experiments. (B and C) Purified LVP (50,000 HCV RNA copies) were coincubated with increasing amount of VLDL from a noninfected donor (B) or with increasing ratios of protein A-coated magnetic beads saturated with purified human IgG to purified LVP (C). Quantitation of cell-associated HCV RNA was performed after 3 h of incubation. ip, immunopurified LVP. Error bars indicated standard deviations.

    Article Snippet: For kinetic and uptake experiments, HCV RNA-containing particles bound to cell surface receptors after the incubation period and three washings with PBS-0.2% BSA were removed by incubation with 10 mM suramin (Sigma) in PBS at 4°C for 1 h. Cells were washed three times in PBS and harvested in 350 μl of RNeasy kit lysis buffer.

    Techniques: Purification, Incubation, Planar Chromatography, Magnetic Beads, Quantitation Assay

    Characterization of LVP binding to the LDL receptor. Purified LVP (6.6 × 10 6 HCV RNA copies) were incubated for 1 h with 200 μg of purified human IgG/ml. A total of 300,000 HCV RNA copies were diluted in FCS-free medium supplemented with 0.2% BSA and 50 μg of each anti-ApoB or anti-ApoE monoclonal antibody/ml alone or together. The samples were allowed to stand at room temperature for 1 h with rocking. The samples were then incubated for 45 min on 40,000 HepG2 cells that had been grown for 24 h in medium supplemented with LPDS. Quantitation of cell-associated HCV RNA was then performed. Monoclonal antibodies were 4G3 (anti-ApoB), 5E11 (anti-ApoB), and 1D7 (anti-ApoE). The P value for a comparison of results obtained with the control and the pool of antibodies was

    Journal: Journal of Virology

    Article Title: Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles

    doi: 10.1128/JVI.76.14.6919-6928.2002

    Figure Lengend Snippet: Characterization of LVP binding to the LDL receptor. Purified LVP (6.6 × 10 6 HCV RNA copies) were incubated for 1 h with 200 μg of purified human IgG/ml. A total of 300,000 HCV RNA copies were diluted in FCS-free medium supplemented with 0.2% BSA and 50 μg of each anti-ApoB or anti-ApoE monoclonal antibody/ml alone or together. The samples were allowed to stand at room temperature for 1 h with rocking. The samples were then incubated for 45 min on 40,000 HepG2 cells that had been grown for 24 h in medium supplemented with LPDS. Quantitation of cell-associated HCV RNA was then performed. Monoclonal antibodies were 4G3 (anti-ApoB), 5E11 (anti-ApoB), and 1D7 (anti-ApoE). The P value for a comparison of results obtained with the control and the pool of antibodies was

    Article Snippet: For kinetic and uptake experiments, HCV RNA-containing particles bound to cell surface receptors after the incubation period and three washings with PBS-0.2% BSA were removed by incubation with 10 mM suramin (Sigma) in PBS at 4°C for 1 h. Cells were washed three times in PBS and harvested in 350 μl of RNeasy kit lysis buffer.

    Techniques: Binding Assay, Purification, Incubation, Quantitation Assay

    Serum HCV RNA levels (LIU/mL) during and after interferon-free treatment in the present study EOT, end of the treatment response.

    Journal: Oncotarget

    Article Title: Interferon-free treatment for patients with chronic hepatitis C and autoimmune liver disease: higher SVR rates with special precautions for deterioration of autoimmune hepatitis

    doi: 10.18632/oncotarget.24391

    Figure Lengend Snippet: Serum HCV RNA levels (LIU/mL) during and after interferon-free treatment in the present study EOT, end of the treatment response.

    Article Snippet: Measurement of HCV RNA HCV RNA was measured by COBAS TaqMan HCV assay version 2.0 (Roche Diagnostics, Tokyo, Japan), with a lower limit of quantification of 15 IU/mL.

    Techniques:

    The laboratory testing algorithm used for identifying hepatitis C virus and hepatitis B virus infection. HBV = hepatitis B virus, HBc = hepatitis B core; HBs = hepatitis B surface; HCV = hepatitis C virus; RNA = ribonucleic acid.

    Journal: Annals of Family Medicine

    Article Title: Detecting Hepatitis B and C by Combined Public Health and Primary Care Birth Cohort Testing

    doi: 10.1370/afm.2166

    Figure Lengend Snippet: The laboratory testing algorithm used for identifying hepatitis C virus and hepatitis B virus infection. HBV = hepatitis B virus, HBc = hepatitis B core; HBs = hepatitis B surface; HCV = hepatitis C virus; RNA = ribonucleic acid.

    Article Snippet: When a screening test was positive, subsequent tests included the following: HCV ribonucleic acid (RNA) (COBAS, Ampliprep/COBAS, Taqman HCV Quantitative Test, version 2.0, Roche Diagnostics) and/or immunoblot (Mikrogen), a hepatitis B surface antigen (HBsAg) test, and an antihepatitis B surface (anti-HBs) test (HBsAg II and Anti-HBs, Roche Diagnostics) (see ).

    Techniques: Infection

    Longitudinal virological results following discordant or inconsistent TMA results at week 12 or week 20 of treatment Patients included in this analysis were those who: (left panel) had HCV RNA-positive results at baseline, had TMA-discordant (+/-) results at week 12, and subsequent virological results available at weeks 20 OR, (right panel) had HCV RNA-positive results at week 12, had TMA-discordant (+/-) results at week 20, and subsequent virological results available at week 24. Positive samples (+) were defined as those that were PCR-positive or TMA-positive (singly or in duplicate). Negative samples (-) were defined as those that were TMA-negative (singly or in duplicate). TMA-discordant or inconsistent results at both weeks 12 and 20 were more likely to be followed by TMA-negative than positive results (19 negative vs 2 positive, p

    Journal: Hepatology (Baltimore, Md.)

    Article Title: Interpretation of Positive TMA Test Results from PCR-Negative Samples Obtained after Treatment of Chronic Hepatitis C

    doi: 10.1002/hep.22487

    Figure Lengend Snippet: Longitudinal virological results following discordant or inconsistent TMA results at week 12 or week 20 of treatment Patients included in this analysis were those who: (left panel) had HCV RNA-positive results at baseline, had TMA-discordant (+/-) results at week 12, and subsequent virological results available at weeks 20 OR, (right panel) had HCV RNA-positive results at week 12, had TMA-discordant (+/-) results at week 20, and subsequent virological results available at week 24. Positive samples (+) were defined as those that were PCR-positive or TMA-positive (singly or in duplicate). Negative samples (-) were defined as those that were TMA-negative (singly or in duplicate). TMA-discordant or inconsistent results at both weeks 12 and 20 were more likely to be followed by TMA-negative than positive results (19 negative vs 2 positive, p

    Article Snippet: Subjects with detectable HCV RNA at week 20 by PCR were deemed to be nonresponders to peginterferon/ribavirin and treatment was discontinued at week 24.

    Techniques: Polymerase Chain Reaction

    Frequency of Phenotypic Resistance Profiles in Patients who Relapse by Prior Response and Subtype in Phase 3 Studies (includes the T12/PR arm of ADVANCE and pooled TVR arms of REALIZE). Relapse was defined as HCV RNA > 25 IU/mL during follow-up after

    Journal: PLoS ONE

    Article Title: Hepatitis C Viral Evolution in Genotype 1 Treatment-Na?ve and Treatment-Experienced Patients Receiving Telaprevir-Based Therapy in Clinical Trials

    doi: 10.1371/journal.pone.0034372

    Figure Lengend Snippet: Frequency of Phenotypic Resistance Profiles in Patients who Relapse by Prior Response and Subtype in Phase 3 Studies (includes the T12/PR arm of ADVANCE and pooled TVR arms of REALIZE). Relapse was defined as HCV RNA > 25 IU/mL during follow-up after

    Article Snippet: HCV RNA Quantitation and Subtyping Plasma HCV RNA levels were determined using the Roche COBAS TaqMan® HCV/HPS assay (Version 2.0) for Phase 3 trials.

    Techniques:

    Phenotypic Resistance Profiles in Patients Who Did Not Achieve SVR with a TVR-based Regimen. Data from ADVANCE include only the T12PR arm and data from REALIZE include pooled TVR arms. Higher-level resistance (red) is defined as > 25-fold increase in IC 50 and lower-level resistance (yellow) is defined as 3- to 25-fold increase in IC 50 from wild-type. Grey (n/a) indicates patients with no sequence data available due to HCV RNA levels below the LOD of the sequencing assay or lost-to-follow-up.

    Journal: PLoS ONE

    Article Title: Hepatitis C Viral Evolution in Genotype 1 Treatment-Na?ve and Treatment-Experienced Patients Receiving Telaprevir-Based Therapy in Clinical Trials

    doi: 10.1371/journal.pone.0034372

    Figure Lengend Snippet: Phenotypic Resistance Profiles in Patients Who Did Not Achieve SVR with a TVR-based Regimen. Data from ADVANCE include only the T12PR arm and data from REALIZE include pooled TVR arms. Higher-level resistance (red) is defined as > 25-fold increase in IC 50 and lower-level resistance (yellow) is defined as 3- to 25-fold increase in IC 50 from wild-type. Grey (n/a) indicates patients with no sequence data available due to HCV RNA levels below the LOD of the sequencing assay or lost-to-follow-up.

    Article Snippet: HCV RNA Quantitation and Subtyping Plasma HCV RNA levels were determined using the Roche COBAS TaqMan® HCV/HPS assay (Version 2.0) for Phase 3 trials.

    Techniques: Sequencing

    Treatment Outcome in Patients from Phase 3 Telaprevir Studies. Data from ADVANCE includes only the T12PR arm and data from REALIZE includes pooled TVR arms. ‘Other’ includes patients with missing SVR assessment and patients with HCV RNA > 25 IU/mL at last study dose but who did not have viral breakthrough. ‘Relapse’ here is calculated using a denominator of total number of patients, and so differs from a relapse rate calculated in Figure 8 which uses patients with undetectable HCV RNA at the end of treatment. ‘SVR’ rates here are calculated as in the INCIVEK USPI, which utilized the last recorded HCV RNA assessment; in case of missing data, the last HCV RNA assessment from week 12 of follow-up onward was used. For the determination of SVR and relapse rates, the lower limit of quantification (

    Journal: PLoS ONE

    Article Title: Hepatitis C Viral Evolution in Genotype 1 Treatment-Na?ve and Treatment-Experienced Patients Receiving Telaprevir-Based Therapy in Clinical Trials

    doi: 10.1371/journal.pone.0034372

    Figure Lengend Snippet: Treatment Outcome in Patients from Phase 3 Telaprevir Studies. Data from ADVANCE includes only the T12PR arm and data from REALIZE includes pooled TVR arms. ‘Other’ includes patients with missing SVR assessment and patients with HCV RNA > 25 IU/mL at last study dose but who did not have viral breakthrough. ‘Relapse’ here is calculated using a denominator of total number of patients, and so differs from a relapse rate calculated in Figure 8 which uses patients with undetectable HCV RNA at the end of treatment. ‘SVR’ rates here are calculated as in the INCIVEK USPI, which utilized the last recorded HCV RNA assessment; in case of missing data, the last HCV RNA assessment from week 12 of follow-up onward was used. For the determination of SVR and relapse rates, the lower limit of quantification (

    Article Snippet: HCV RNA Quantitation and Subtyping Plasma HCV RNA levels were determined using the Roche COBAS TaqMan® HCV/HPS assay (Version 2.0) for Phase 3 trials.

    Techniques:

    The distribution of timing of HCV RNA undetectable after the initiation of treatment at weeks 2, 4, 8, and 12 in comparison with TaqMan and qualitative Amplicor assays . SVR, sustained virological response.

    Journal: BMC Gastroenterology

    Article Title: Excellent superiority and specificity of COBAS TaqMan HCV assay in an early viral kinetic change during pegylated interferon alpha-2b plus ribavirin treatment

    doi: 10.1186/1471-230X-10-38

    Figure Lengend Snippet: The distribution of timing of HCV RNA undetectable after the initiation of treatment at weeks 2, 4, 8, and 12 in comparison with TaqMan and qualitative Amplicor assays . SVR, sustained virological response.

    Article Snippet: Determination of HCV RNA level During the treatment period (the initial 12 weeks: at week 2, week 4, week 8, and week 12), we retrospectively determined serum HCV RNA level by both COBAS TaqMan HCV assay (TaqMan) (Roche Diagnostics) and COBAS Amplicor HCV Monitor Test v2.0 using the 10-fold dilution method (Amplicor 10-fold method) (Roche Diagnostics) in each patient.

    Techniques:

    Long-term FU with liver elasticity measurement using Fibroscan and testings of HCV-RNA with a highly sensitive method in patients with a sustained virological response. The values of two patients with positive HCV-RNA at FU, indicative of occult infection, are shown with filled circles. EOT, end of treatment; FU, follow-up; HCV, hepatitis C virus.

    Journal: European Journal of Gastroenterology & Hepatology

    Article Title: Long-term follow-up after cure from chronic hepatitis C virus infection shows occult hepatitis and a risk of hepatocellular carcinoma in noncirrhotic patients

    doi: 10.1097/MEG.0000000000001316

    Figure Lengend Snippet: Long-term FU with liver elasticity measurement using Fibroscan and testings of HCV-RNA with a highly sensitive method in patients with a sustained virological response. The values of two patients with positive HCV-RNA at FU, indicative of occult infection, are shown with filled circles. EOT, end of treatment; FU, follow-up; HCV, hepatitis C virus.

    Article Snippet: HCV-RNA detection At FU, all patients were screened for HCV-RNA by PCR using the routine method of the MagNA Pure LC system/COBAS TaqMan HCV test (Roche Diagnostics, Mannheim, Germany), with a sensitivity of 15 IU/ml for the HCV WHO Standard.

    Techniques: Infection

    Mean Log 10 HCV RNA levels during the first 24 weeks of treatment by time on study (weeks) and treatment group

    Journal: Gastroenterology

    Article Title: The Combination of Ribavirin and Peginterferon Is Superior to Peginterferon and Placebo for Children and Adolescents Chronic Hepatitis C

    doi: 10.1053/j.gastro.2010.10.047

    Figure Lengend Snippet: Mean Log 10 HCV RNA levels during the first 24 weeks of treatment by time on study (weeks) and treatment group

    Article Snippet: HCV RNA levels were measured at entry and weeks 1, 3, 5, 12, 24, 48, and 72 using a high-throughput quantitative assay (Cobas® TaqMan® HCV Test, v2.0.with High Pure System (Research Use Only) for Viral Nucleic Acid extraction, (Roche Molecular Systems, Pleasanton, CA) which has a lower limit of quantification of 25 IU/mL and a lower limit of detection of 10 IU/mL in EDTA plasma.

    Techniques:

    Preferences for HCV testing strategy. Half of respondents consider two-step testing strategy (see Figure 1 ) to be an optimal future testing approach in LMIC, while the other half prefer currently used two-step approach a . If one-step testing strategy is implemented, more than a half of respondents prefer to use HCV RNA test b

    Journal: BMC Infectious Diseases

    Article Title: Optimising diagnosis of viraemic hepatitis C infection: the development of a target product profile

    doi: 10.1186/s12879-017-2770-5

    Figure Lengend Snippet: Preferences for HCV testing strategy. Half of respondents consider two-step testing strategy (see Figure 1 ) to be an optimal future testing approach in LMIC, while the other half prefer currently used two-step approach a . If one-step testing strategy is implemented, more than a half of respondents prefer to use HCV RNA test b

    Article Snippet: Currently available commercial quantitative and qualitative HCV RNA or HCV cAg assays are focused on centralized laboratory infrastructure (e.g. Roche COBAS Taqman HCV assay, Abbott RealTime HCV assay, Hologic Aptima® HCV Quant Dx Assay) [ ].

    Techniques:

    Information about respondents. Professional profiles of 36 respondents to the HCV RNA and cAg TPPs

    Journal: BMC Infectious Diseases

    Article Title: Optimising diagnosis of viraemic hepatitis C infection: the development of a target product profile

    doi: 10.1186/s12879-017-2770-5

    Figure Lengend Snippet: Information about respondents. Professional profiles of 36 respondents to the HCV RNA and cAg TPPs

    Article Snippet: Currently available commercial quantitative and qualitative HCV RNA or HCV cAg assays are focused on centralized laboratory infrastructure (e.g. Roche COBAS Taqman HCV assay, Abbott RealTime HCV assay, Hologic Aptima® HCV Quant Dx Assay) [ ].

    Techniques:

    Preferred sensitivity and acceptable trade-offs between sensitivity and price. Over 50% of respondents see current price of HBV DNA, HCV RNA, and to a lesser extent HCV cAg, is seen as a major barrier to scale up the testing a . Half of respondents consider that 95% as an acceptable diagnostic sensitivity for a one-step diagnostic test whereas 43% prefer 98% b . Respondents were willing to pay more for a higher sensitivity and were willing to compromise on sensitivity for a cheap test c and d

    Journal: BMC Infectious Diseases

    Article Title: Optimising diagnosis of viraemic hepatitis C infection: the development of a target product profile

    doi: 10.1186/s12879-017-2770-5

    Figure Lengend Snippet: Preferred sensitivity and acceptable trade-offs between sensitivity and price. Over 50% of respondents see current price of HBV DNA, HCV RNA, and to a lesser extent HCV cAg, is seen as a major barrier to scale up the testing a . Half of respondents consider that 95% as an acceptable diagnostic sensitivity for a one-step diagnostic test whereas 43% prefer 98% b . Respondents were willing to pay more for a higher sensitivity and were willing to compromise on sensitivity for a cheap test c and d

    Article Snippet: Currently available commercial quantitative and qualitative HCV RNA or HCV cAg assays are focused on centralized laboratory infrastructure (e.g. Roche COBAS Taqman HCV assay, Abbott RealTime HCV assay, Hologic Aptima® HCV Quant Dx Assay) [ ].

    Techniques: Diagnostic Assay

    Preference for the HCV diagnostic test and the test of cure to be the same or different. Almost half of respondents preferred that the diagnostic test and test of cure be the same and about two thirds of these preferred that it be a decentralized (i.e. near-patient) HCV RNA test

    Journal: BMC Infectious Diseases

    Article Title: Optimising diagnosis of viraemic hepatitis C infection: the development of a target product profile

    doi: 10.1186/s12879-017-2770-5

    Figure Lengend Snippet: Preference for the HCV diagnostic test and the test of cure to be the same or different. Almost half of respondents preferred that the diagnostic test and test of cure be the same and about two thirds of these preferred that it be a decentralized (i.e. near-patient) HCV RNA test

    Article Snippet: Currently available commercial quantitative and qualitative HCV RNA or HCV cAg assays are focused on centralized laboratory infrastructure (e.g. Roche COBAS Taqman HCV assay, Abbott RealTime HCV assay, Hologic Aptima® HCV Quant Dx Assay) [ ].

    Techniques: Diagnostic Assay

    Effect of NS5A on PKR activation by HCV IRES domains

    Journal: Journal of molecular biology

    Article Title: Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

    doi: 10.1016/j.jmb.2010.04.059

    Figure Lengend Snippet: Effect of NS5A on PKR activation by HCV IRES domains

    Article Snippet: In PKR inhibition studies by HCV IRES RNA, poly I:C (Sigma) of approximate size 30-200 bp was used as an activator of PKR.

    Techniques: Activation Assay

    Inhibition and activation of PKR by full-length HCV IRES RNA (1-388). (a) Inhibition of poly I:C-mediated activation of PKR by HCV IRES. The amount of poly I:C in all lanes was 1 μg/mL, and concentrations of HCV IRES were 0.08, 0.16, 0.32, 0.64, 1.25, 2.5, 5 and 10 μM. No-RNA/no-poly I:C and no-HCV IRES lanes are included. Phosphorylation activities are provided under the gel and were normalized relative to the lane in which only poly I:C was present. (b) Activation of PKR by HCV IRES. RNA concentrations were 0.02, 0.04, 0.08, 0.16, 0.32, 0.64, 1.25, 2.5, and 5 μM. A no RNA lane is included. Phosphorylation activities were normalized to the most reactive lane, 0.64 μM IRES. For both (a) and (b), 10% SDS-PAGE gels are shown, with position of phosphorylated PKR (p-PKR) indicated, and graphical representations of phosphorylation activities as a function of full-length IRES concentration are provided.

    Journal: Journal of molecular biology

    Article Title: Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

    doi: 10.1016/j.jmb.2010.04.059

    Figure Lengend Snippet: Inhibition and activation of PKR by full-length HCV IRES RNA (1-388). (a) Inhibition of poly I:C-mediated activation of PKR by HCV IRES. The amount of poly I:C in all lanes was 1 μg/mL, and concentrations of HCV IRES were 0.08, 0.16, 0.32, 0.64, 1.25, 2.5, 5 and 10 μM. No-RNA/no-poly I:C and no-HCV IRES lanes are included. Phosphorylation activities are provided under the gel and were normalized relative to the lane in which only poly I:C was present. (b) Activation of PKR by HCV IRES. RNA concentrations were 0.02, 0.04, 0.08, 0.16, 0.32, 0.64, 1.25, 2.5, and 5 μM. A no RNA lane is included. Phosphorylation activities were normalized to the most reactive lane, 0.64 μM IRES. For both (a) and (b), 10% SDS-PAGE gels are shown, with position of phosphorylated PKR (p-PKR) indicated, and graphical representations of phosphorylation activities as a function of full-length IRES concentration are provided.

    Article Snippet: In PKR inhibition studies by HCV IRES RNA, poly I:C (Sigma) of approximate size 30-200 bp was used as an activator of PKR.

    Techniques: Inhibition, Activation Assay, SDS Page, Concentration Assay

    Activation of PKR by multiple domains of HCV IRES. (a) PKR activation assays of domains I-II (1-130) (left panel) and III-IV (131-388) (right panel). RNA concentrations for both panels were 0.3, 0.6, 1.3, 2.5, and 5.0 μM. (b) PKR activation assay of domain II (39-119) alone. RNA concentrations were 0.15, 0.3, 0.6, 1.3, 2.5, 5 and 10 μM. For both (a) and (b), 10% SDS-PAGE gels are shown, with position of phosphorylated PKR (p-PKR) indicated. A no-RNA lane and 79 bp dsRNA lane are included. Phosphorylation activities are normalized to the 79 bp lane and are noted under the gel. (c) Graphical representation of phosphorylation activities from panels (a) and (b) as a function of RNA concentration.

    Journal: Journal of molecular biology

    Article Title: Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

    doi: 10.1016/j.jmb.2010.04.059

    Figure Lengend Snippet: Activation of PKR by multiple domains of HCV IRES. (a) PKR activation assays of domains I-II (1-130) (left panel) and III-IV (131-388) (right panel). RNA concentrations for both panels were 0.3, 0.6, 1.3, 2.5, and 5.0 μM. (b) PKR activation assay of domain II (39-119) alone. RNA concentrations were 0.15, 0.3, 0.6, 1.3, 2.5, 5 and 10 μM. For both (a) and (b), 10% SDS-PAGE gels are shown, with position of phosphorylated PKR (p-PKR) indicated. A no-RNA lane and 79 bp dsRNA lane are included. Phosphorylation activities are normalized to the 79 bp lane and are noted under the gel. (c) Graphical representation of phosphorylation activities from panels (a) and (b) as a function of RNA concentration.

    Article Snippet: In PKR inhibition studies by HCV IRES RNA, poly I:C (Sigma) of approximate size 30-200 bp was used as an activator of PKR.

    Techniques: Activation Assay, SDS Page, Concentration Assay

    Activation of PKR and phosphorylation of eIF2α by multiple domains of HCV IRES. (a) PKR/eIF2α phosphorylation by full-length (1-388) HCV IRES. For both − and + eIF2α lanes, IRES concentrations were 0.625, 1.25, and 2.5 μM. (b) PKR/eIF2α phosphorylation by domains III-IV (131-388). For both − and + eIF2α lanes, domains III-IV concentrations were 0.625, 1.25, 2.5, 5, and 10 μM. (c) PKR/eIF2α phosphorylation by domain II (39-119). For both − and + eIF2α lanes, domain II concentrations were 0.625, 1.25, 2.5, 5, and 10 μM. For all panels, 10% SDS-PAGE gels are presented, and positions of phosphorylated PKR (p-PKR) and phosphorylated eIF2α (p-eIF2α) are indicated. When present, eIF2α was in 10-fold excess over PKR. PKR activation for all gels was normalized to the 79 bp (-eIF2α) PKR band in panel (c), and eIF2α phosphorylation for all gels was normalized to the 79 bp (+eIF2α) eIF2α band in panel (c). These values are provided under the gel.

    Journal: Journal of molecular biology

    Article Title: Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

    doi: 10.1016/j.jmb.2010.04.059

    Figure Lengend Snippet: Activation of PKR and phosphorylation of eIF2α by multiple domains of HCV IRES. (a) PKR/eIF2α phosphorylation by full-length (1-388) HCV IRES. For both − and + eIF2α lanes, IRES concentrations were 0.625, 1.25, and 2.5 μM. (b) PKR/eIF2α phosphorylation by domains III-IV (131-388). For both − and + eIF2α lanes, domains III-IV concentrations were 0.625, 1.25, 2.5, 5, and 10 μM. (c) PKR/eIF2α phosphorylation by domain II (39-119). For both − and + eIF2α lanes, domain II concentrations were 0.625, 1.25, 2.5, 5, and 10 μM. For all panels, 10% SDS-PAGE gels are presented, and positions of phosphorylated PKR (p-PKR) and phosphorylated eIF2α (p-eIF2α) are indicated. When present, eIF2α was in 10-fold excess over PKR. PKR activation for all gels was normalized to the 79 bp (-eIF2α) PKR band in panel (c), and eIF2α phosphorylation for all gels was normalized to the 79 bp (+eIF2α) eIF2α band in panel (c). These values are provided under the gel.

    Article Snippet: In PKR inhibition studies by HCV IRES RNA, poly I:C (Sigma) of approximate size 30-200 bp was used as an activator of PKR.

    Techniques: Activation Assay, SDS Page

    HCV RNA Load in Brain and Liver Tissue

    Journal: Gastroenterology

    Article Title: Hepatitis C Virus Infects the Endothelial Cells of the Blood-Brain Barrier

    doi: 10.1053/j.gastro.2011.11.028

    Figure Lengend Snippet: HCV RNA Load in Brain and Liver Tissue

    Article Snippet: Quantification of HCV RNA from matched samples of white and grey matter, cerebellum, medulla, liver, and plasma revealed that, in clinical samples with detectable brain HCV, the viral load was 1000- to 10,000-fold lower in brain compared with liver from the same subject.

    Techniques:

    HCV RNA and antigen expression in brain endothelial and hepatoma cells. hCMEC/D3 and Huh-7 cells were infected with HCVcc SA13/JFH for12hours, and unbound virus was removed by washing. ( A ) HCV RNA copies and ( B ) the frequency of NS5A-positive cells were

    Journal: Gastroenterology

    Article Title: Hepatitis C Virus Infects the Endothelial Cells of the Blood-Brain Barrier

    doi: 10.1053/j.gastro.2011.11.028

    Figure Lengend Snippet: HCV RNA and antigen expression in brain endothelial and hepatoma cells. hCMEC/D3 and Huh-7 cells were infected with HCVcc SA13/JFH for12hours, and unbound virus was removed by washing. ( A ) HCV RNA copies and ( B ) the frequency of NS5A-positive cells were

    Article Snippet: Quantification of HCV RNA from matched samples of white and grey matter, cerebellum, medulla, liver, and plasma revealed that, in clinical samples with detectable brain HCV, the viral load was 1000- to 10,000-fold lower in brain compared with liver from the same subject.

    Techniques: Expressing, Infection

    Distribution of HCV-RNA (A) and HCVAg (B) by HCV genotype. Significant differences between median values were observed only between genotypes 1 and 3 for both HCV-RNA (p = 0.028) and HCVAg (p = 0.0098).

    Journal: BMC Infectious Diseases

    Article Title: HCV core antigen and HCV-RNA in HIV/HCV co-infected patients with different HCV genotypes

    doi: 10.1186/1471-2334-14-222

    Figure Lengend Snippet: Distribution of HCV-RNA (A) and HCVAg (B) by HCV genotype. Significant differences between median values were observed only between genotypes 1 and 3 for both HCV-RNA (p = 0.028) and HCVAg (p = 0.0098).

    Article Snippet: The current standard for diagnosing an active HCV infection is the detection and quantification of HCV-RNA, also recommended to monitor the antiviral treatment.

    Techniques:

    Correlation between HCVAg and HCV-RNA on 315 samples from patients with HCV RNA > 12 IU/ml. Values are reported on a logarithmic scale and with different symbols according to genotype. The correlation coefficient (Spearman) was 0.869.

    Journal: BMC Infectious Diseases

    Article Title: HCV core antigen and HCV-RNA in HIV/HCV co-infected patients with different HCV genotypes

    doi: 10.1186/1471-2334-14-222

    Figure Lengend Snippet: Correlation between HCVAg and HCV-RNA on 315 samples from patients with HCV RNA > 12 IU/ml. Values are reported on a logarithmic scale and with different symbols according to genotype. The correlation coefficient (Spearman) was 0.869.

    Article Snippet: The current standard for diagnosing an active HCV infection is the detection and quantification of HCV-RNA, also recommended to monitor the antiviral treatment.

    Techniques:

    Monitoring profiles from three patients co-infected by HCV and HIV. The values of HCV-RNA and HCVAg are expressed on a logarithmic scale as IU/mL and fmol/L. respectively. The trends of the two parameters in the two patients described in Figure 3 A and B were almost identical whereas the patient in Figure 3 C showed a persistence of HCVAg positivity and a virological relapse on the following draw. Dotted line: HCVAg; solid line: HCV-RNA.

    Journal: BMC Infectious Diseases

    Article Title: HCV core antigen and HCV-RNA in HIV/HCV co-infected patients with different HCV genotypes

    doi: 10.1186/1471-2334-14-222

    Figure Lengend Snippet: Monitoring profiles from three patients co-infected by HCV and HIV. The values of HCV-RNA and HCVAg are expressed on a logarithmic scale as IU/mL and fmol/L. respectively. The trends of the two parameters in the two patients described in Figure 3 A and B were almost identical whereas the patient in Figure 3 C showed a persistence of HCVAg positivity and a virological relapse on the following draw. Dotted line: HCVAg; solid line: HCV-RNA.

    Article Snippet: The current standard for diagnosing an active HCV infection is the detection and quantification of HCV-RNA, also recommended to monitor the antiviral treatment.

    Techniques: Infection

    Kinetics of HCV RNA in different group of patients at different time points (week 0, 1, 2, 4, 8). The median HCV RNA level and relative range are reported with black circle for responder and with white circle for treatment-failing patients. Statistic “p” values are reported at each time points.

    Journal: Scientific Reports

    Article Title: Baseline and Breakthrough Resistance Mutations in HCV Patients Failing DAAs

    doi: 10.1038/s41598-017-15987-1

    Figure Lengend Snippet: Kinetics of HCV RNA in different group of patients at different time points (week 0, 1, 2, 4, 8). The median HCV RNA level and relative range are reported with black circle for responder and with white circle for treatment-failing patients. Statistic “p” values are reported at each time points.

    Article Snippet: Viral load decrease in responder and treatment-failing patients was compared at the baseline, 1, 2, 4 and 8 weeks, and after stopping with the using Abbott HCV-RNA assay (Abbott Park, Illinois, U.S.A.).

    Techniques:

    qRT-PCR of IFN-γ in chimpanzees infected with HEV or HCV. IFN-γ was tested by primer- and probe-specific TaqMan qPCR (see Table S1 in the supplemental material). Total RNA from liver biopsies was converted to cDNA, amplified, and tested

    Journal: Journal of Virology

    Article Title: Pathogenesis of Hepatitis E Virus and Hepatitis C Virus in Chimpanzees: Similarities and Differences ▿Pathogenesis of Hepatitis E Virus and Hepatitis C Virus in Chimpanzees: Similarities and Differences ▿ †

    doi: 10.1128/JVI.01205-10

    Figure Lengend Snippet: qRT-PCR of IFN-γ in chimpanzees infected with HEV or HCV. IFN-γ was tested by primer- and probe-specific TaqMan qPCR (see Table S1 in the supplemental material). Total RNA from liver biopsies was converted to cDNA, amplified, and tested

    Article Snippet: A quantity standard line representing a 6-log range was constructed with the OptiQuant HCV RNA (Acrometrix, Benicia, CA) nucleic acid test reference panel.

    Techniques: Quantitative RT-PCR, Infection, Real-time Polymerase Chain Reaction, Amplification

    Mean values of results (expressed as log 10 HCV RNA copies per milliliter of serum) determined by our RT-PCR protocol (ABI Prism 7700 assay), the bDNA assay and the NGI method are comparable. (A) Comparison of totals; differences in mean values are not significant (ns). The percentages of samples positive by each method are given in the box. (B) Comparison of mean values for groups of different genotypes; differences are not significant.

    Journal: Journal of Clinical Microbiology

    Article Title: High-Throughput Real-Time Reverse Transcription-PCR Quantitation of Hepatitis C Virus RNA

    doi:

    Figure Lengend Snippet: Mean values of results (expressed as log 10 HCV RNA copies per milliliter of serum) determined by our RT-PCR protocol (ABI Prism 7700 assay), the bDNA assay and the NGI method are comparable. (A) Comparison of totals; differences in mean values are not significant (ns). The percentages of samples positive by each method are given in the box. (B) Comparison of mean values for groups of different genotypes; differences are not significant.

    Article Snippet: Seventy-four patients were HCV RNA positive by a commercial quantitative HCV RNA test with a detection limit of 102 copies/ml (Amplicor HCV-RNA; Roche Molecular Systems) and five were negative.

    Techniques: Reverse Transcription Polymerase Chain Reaction

    Schematic representation of the transcription fragment from the 5′ NCR of HCV. Oligonucleotide primers C149 and C342 were used for amplification by RT-PCR. Primers C24 and C339 were hybridized to the RNA transcript to assess its integrity. FT275 is the dual-labeled probe. R, reporter; Q, quencher; nt, nucleotides.

    Journal: Journal of Clinical Microbiology

    Article Title: High-Throughput Real-Time Reverse Transcription-PCR Quantitation of Hepatitis C Virus RNA

    doi:

    Figure Lengend Snippet: Schematic representation of the transcription fragment from the 5′ NCR of HCV. Oligonucleotide primers C149 and C342 were used for amplification by RT-PCR. Primers C24 and C339 were hybridized to the RNA transcript to assess its integrity. FT275 is the dual-labeled probe. R, reporter; Q, quencher; nt, nucleotides.

    Article Snippet: Seventy-four patients were HCV RNA positive by a commercial quantitative HCV RNA test with a detection limit of 102 copies/ml (Amplicor HCV-RNA; Roche Molecular Systems) and five were negative.

    Techniques: Amplification, Reverse Transcription Polymerase Chain Reaction, Labeling

    Standard curve of the input RNA concentration in serial dilutions of the first reference standard versus C T . Each dot represents the result of triplicate PCR amplifications for each dilution. The stars represent the results of PCR amplification of samples containing unknown quantities of HCV RNA tested by this method. R was equal to 0.999, and the slope was −3.429.

    Journal: Journal of Clinical Microbiology

    Article Title: High-Throughput Real-Time Reverse Transcription-PCR Quantitation of Hepatitis C Virus RNA

    doi:

    Figure Lengend Snippet: Standard curve of the input RNA concentration in serial dilutions of the first reference standard versus C T . Each dot represents the result of triplicate PCR amplifications for each dilution. The stars represent the results of PCR amplification of samples containing unknown quantities of HCV RNA tested by this method. R was equal to 0.999, and the slope was −3.429.

    Article Snippet: Seventy-four patients were HCV RNA positive by a commercial quantitative HCV RNA test with a detection limit of 102 copies/ml (Amplicor HCV-RNA; Roche Molecular Systems) and five were negative.

    Techniques: Concentration Assay, Polymerase Chain Reaction, Amplification

    Age related decline in prevalence of hepatitis C antibody in infants who had anti-HCV detected in their initial blood sample according to whether their mothers were positive for both HCV-RNA and anti-HCV or only had anti-HCV.

    Journal: Journal of medical virology

    Article Title: Prospective Cohort Study of Mother-to-Infant Infection and Clearance of Hepatitis C in Rural Egyptian Villages

    doi: 10.1002/jmv.21480

    Figure Lengend Snippet: Age related decline in prevalence of hepatitis C antibody in infants who had anti-HCV detected in their initial blood sample according to whether their mothers were positive for both HCV-RNA and anti-HCV or only had anti-HCV.

    Article Snippet: Quantitative controls consisting of known copy numbers generated from Armored HCV RNA (Ambion, Austin, TX) were run with each reaction.

    Techniques:

    Association between IFN Response, HCV RNA Levels, and Effect on Host Gene Expression in HCV-Infected Mice Intrahepatic HCV RNA levels were determined by quantitative RT-PCR as described in Materials and Methods. Total number of genes showing increased expression in HCV-infected mice relative to donor-matched uninfected mice is shown in gray bars, while the percent of induced genes that are IFN regulated is shown using black triangles.

    Journal: PLoS Pathogens

    Article Title: Host-Specific Response to HCV Infection in the Chimeric SCID-beige/Alb-uPA Mouse Model: Role of the Innate Antiviral Immune Response

    doi: 10.1371/journal.ppat.0020059

    Figure Lengend Snippet: Association between IFN Response, HCV RNA Levels, and Effect on Host Gene Expression in HCV-Infected Mice Intrahepatic HCV RNA levels were determined by quantitative RT-PCR as described in Materials and Methods. Total number of genes showing increased expression in HCV-infected mice relative to donor-matched uninfected mice is shown in gray bars, while the percent of induced genes that are IFN regulated is shown using black triangles.

    Article Snippet: Primer and probe sets for absolute quantification of intrahepatic viral load were designed based on sequences of HCV 1a armored RNA (Ambion Diagnostics, Austin, Texas, United States) using Primer Express (version 3).

    Techniques: Expressing, Infection, Mouse Assay, Quantitative RT-PCR