Journal: Viruses

Article Title: Evaluation of a Lyophilized CRISPR-Cas12 Assay for a Sensitive, Specific, and Rapid Detection of SARS-CoV-2

doi: 10.3390/v13030420

Figure Lengend Snippet: Cross-reaction evaluation of Lyo-CRISPR SARS-CoV-2 kit with other respiratory pathogens.

Article Snippet: Respiratory syncytial virus , ATCC ® VR-1580DQ , 10 5 copies/mL , 0/3 , Negative , 3/3 , Valid.

Techniques: Concentration Assay

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Article Title: Neuraminidase delivered as an APC-targeted DNA vaccine induces protective antibodies against influenza.

doi: 10.1016/j.ymthe.2023.03.012

Figure Lengend Snippet: Figure 1. In vitro characterization of MHC class II-targeted heterodimeric DNA vaccines containing NA and/or HA (A) MHC class II-targeted heterodimeric acid/base (A/B) vaccine proteins consist of A and B chains, each having a targeting, dimerization, and antigenic unit. The targeting unit is either an scFv that binds MHC class II on APCs (scFvaMHCII, green) or a non-targeted control that binds the hapten NIP (scFvaNIP, white). The targeting units are genetically linked to a shortened hinge from human IgG3 (exon h1), allowing covalent disulfide bond formation between the A and B chains (black lines). The hinge is followed by a duplicated A (red) or B (blue) heterodimerization unit based on a modified Jun/Fos leucine zipper motif enriched for acidic or basic amino acids, respectively. The A and B chains are linked to antigenic units composed of NA (dark blue) or HA (orange) derived from influenza H1N1 PR8 virus. The heterodimeric vaccine proteins are named as

Article Snippet: The copy number of viral RNA was determined with quantitative genomic RNA from H1N1 PR8 (VR-95DQ, ATCC) and shown per microgram total tissue RNA.

Techniques: In Vitro, Vaccines, Control, Derivative Assay, Virus

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Article Title: Neuraminidase delivered as an APC-targeted DNA vaccine induces protective antibodies against influenza.

doi: 10.1016/j.ymthe.2023.03.012

Figure Lengend Snippet: Figure 2. MHC class II-targeted NA-bivalent heterodimers efficiently induce antibody responses after a single DNA vaccination (A) BALB/c mice were vaccinated once i.m. with 5 mg of each A and B plasmids (10 mg DNA in total) encoding the indicated heterodimeric vaccine proteins (box), followed immediately by EP. Blood was sampled at the indicated time points. (B) NA-specific (top) and HA-specific (bottom) IgG (left), IgG1 (center), and IgG2a (right) titers were measured by ELISA at the indicated time points after immunization. Statistical analysis compared targeted vs. non-targeted and antigen-bivalent vs. monovalent groups. (C) BALB/c mice were immunized once i.m./EP with different amounts of the indicated DNA vaccines. Serum was analyzed for NA-specific IgG responses 4 weeks post vaccination. (D) IgG responses specific for inactivated H1N1 PR8 virus (left), rec. NA protein (center), or rec. HA protein (right) in sera harvested 6 weeks post vaccination from

Article Snippet: The copy number of viral RNA was determined with quantitative genomic RNA from H1N1 PR8 (VR-95DQ, ATCC) and shown per microgram total tissue RNA.

Techniques: Enzyme-linked Immunosorbent Assay, Vaccines, Virus

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Article Title: Neuraminidase delivered as an APC-targeted DNA vaccine induces protective antibodies against influenza.

doi: 10.1016/j.ymthe.2023.03.012

Figure Lengend Snippet: Figure 4. A single DNA immunization with MHC class II-targeted NA/NA vaccines protects against homologous influenza virus challenge (A) BALB/c mice were immunized once i.m./EP and challenged with homologous influenza A H1N1 PR8 virus at week 2 (short term) or between weeks 6 and 10 (long term) after vaccination. (B–F) 50 mg of each A and B plasmids (total 100 mg, B), 5 mg/ plasmid (10 mg total, C–E), or 1 mg/plasmid (2 mg total, F) of the indicated DNA vaccines (box) were used. Mice were challenged with a lethal dose of 5 LD50 (B–D and F) or 100 LD50 (E) at week 9 (B), week 10 (C), week 2 (D and E), or week 6 (F). Weight (left, mean ± SEM) and survival (right) were monitored up to 12 days post challenge. n = 8 mice/group (B, C, E, and F) or n = 6 mice/group (D). Dead mice were assigned a weight of 75%. *p % 0.05, ***p % 0.001; two-way ANOVA (weight curve) or Mantel-Cox test (survival). Statistical analysis compared MHC class II- targeted NA/NA versus HA/HA as well as targeted versus non-targeted and anti- gen-bivalent versus -monovalent NA.

Article Snippet: The copy number of viral RNA was determined with quantitative genomic RNA from H1N1 PR8 (VR-95DQ, ATCC) and shown per microgram total tissue RNA.

Techniques: Vaccines, Virus, Plasmid Preparation

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Article Title: Neuraminidase delivered as an APC-targeted DNA vaccine induces protective antibodies against influenza.

doi: 10.1016/j.ymthe.2023.03.012

Figure Lengend Snippet: Figure 5. MHC class II-targeted NA DNA vaccine induces superior NA-specific antibody responses compared with conventional inactivated virus after one vaccination (A, B) BALB/c mice were immunized once i.m. with 0.2, 1, or 5 mg of formalin-inactivated H1N1 PR8 virus or with 5 mg/ plasmid (10 mg total) of the indicated DNA vaccines, fol- lowed by EP (box). (A) NA-specific (left) and HA-specific (right) titers were measured by ELISA at the indicated time points after immunization. Mean ± SEM is shown. (B) Mice were challenged with 5 LD50 H1N1 PR8 virus 11 week post vaccination. Weight (left, mean ± SEM) and survival (right) were monitored up to 12 days post challenge. Dead mice were assigned a weight of 75%; n = 8 mice/group. Statistical analysis compared the different doses of inactivated virus with DNA vaccination with MHC class II-targeted NA and/or HA. **p % 0.01, ***p % 0.001; two-way ANOVA (IgG titers, weight curve) or Mantel-Cox test (survival).

Article Snippet: The copy number of viral RNA was determined with quantitative genomic RNA from H1N1 PR8 (VR-95DQ, ATCC) and shown per microgram total tissue RNA.

Techniques: Virus, Plasmid Preparation, Vaccines, Enzyme-linked Immunosorbent Assay

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Article Title: Neuraminidase delivered as an APC-targeted DNA vaccine induces protective antibodies against influenza.

doi: 10.1016/j.ymthe.2023.03.012

Figure Lengend Snippet: Figure 6. Vaccine-induced NA-specific antibodies mediate protection against homologous influenza infection, inhibit NA enzymatic activity, and block viral replication (A–D) BALB/c mice were immunized once i.m./EP with 50 mg each of A and B plasmids (100 mg total) as indicated. (A) Pooled sera (350 mL) from mice 5 weeks after vaccination were transferred i.p. to naive BALB/c mice. One day after transfer, mice were challenged with 2.5 LD50 H1N1 PR8 virus. (B) 2 weeks after vaccination with the indicated DNA vaccines, mice were challenged with 5 LD50 H1N1 PR8 virus. Starting on day 12 after vaccination, mice were treated with anti-CD4 and anti- CD8 mAbs or isotype-matched control mAbs every second day. n = 8 mice/group; weight (left, mean ± SEM) and survival (right) were monitored up to 12 days post challenge, and dead mice were assigned a weight of 75% (A and B). (C) Neutrali- zation of influenza A H1N1 PR8 virus by serum from vaccinated mice (box) obtained 4 weeks after immunization was measured by microneutralization assay and is shown as IC50. (D) The same sera were tested for ability to inhibit NA enzyme activity by ELLA, using a reassorted influenza A H6N1 virus containing NA from H1N1 PR8. IC50 is indicated. (E and F) BALB/c mice were immunized once i.m./EP with 50 mg of each A and B plasmids (100 mg total, E) or 5 mg of each A and B plasmids (10 mg total, F) as indicated. Mice were challenged with homologous H1N1 PR8 virus 6 weeks after vaccination, and lungs were harvested on day 5 post challenge. Viral loads were determined by qRT-PCR (left), showing gene copy number per micro- gram total tissue RNA, and by measuring in vitro cell culture infectivity (right), pre- sented as 50% tissue culture infectious dose (TCID50) per milliliter of lung homog- enates. Individual mice and mean ± SEM are shown; n = 4–6 mice/group (C–F). *p % 0.05, **p % 0.01, ***p % 0.001; two-way ANOVA (weight curve), Mantel-Cox test (survival), Kruskal-Wallis multiple-comparisons test with Dunn’s correction (C and D, TCID50), or multiple-comparisons one-way ANOVA with Tukey’s correction (copy number).

Article Snippet: The copy number of viral RNA was determined with quantitative genomic RNA from H1N1 PR8 (VR-95DQ, ATCC) and shown per microgram total tissue RNA.

Techniques: Infection, Activity Assay, Blocking Assay, Virus, Vaccines, Control, Microneutralization Assay, Quantitative RT-PCR, In Vitro, Cell Culture

Journal: STAR Protocols

Article Title: qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples

doi: 10.1016/j.xpro.2020.100102

Figure Lengend Snippet: Appropriate and Inappropriate qRT-PCR Curves for Samples (A) Representation of curves for N1 gene in one patient sample. Each curve represents one technical replicate (i.e., one well) of the qRT-PCR run. The curve labeled with an asterisk (∗) denotes what one would expect if N1 transcript is not present in the sample. The curve labeled with yellow arrow head represents a spurious curve with a C T value of 5.594 likely due to technical artifact. (B) Technical duplicate curves generated for N1 gene in one positive patient sample. These curves, with C T value of 31.131, are what one would expect if the qRT-PCR run identified SARS-CoV-2 viral genomic RNA present in patient samples.

Article Snippet: Please note however, that it is possible to obtain full-length SARS-CoV-2 genomic RNA from ATCC (Cat. No. VR-1986D) to use in lieu of or addition to the TaqPath COVID-19 Combo Kit positive control.

Techniques: Quantitative RT-PCR, Labeling, Generated

Journal: STAR Protocols

Article Title: qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples

doi: 10.1016/j.xpro.2020.100102

Figure Lengend Snippet:

Article Snippet: Please note however, that it is possible to obtain full-length SARS-CoV-2 genomic RNA from ATCC (Cat. No. VR-1986D) to use in lieu of or addition to the TaqPath COVID-19 Combo Kit positive control.

Techniques: Reverse Transcription, Adhesive, Multiplex Assay, Software, Real-time Polymerase Chain Reaction

Journal: Scientific Data

Article Title: Human pathogen nucleic acids in wastewater solids from 191 wastewater treatment plants in the United States

doi: 10.1038/s41597-024-03969-8

Figure Lengend Snippet: Positive controls used in the study for non-SARS-CoV-2 targets, Gene blocks are dsDNA molecules with the target sequence purchased from Integrated DNA Technologies (IDT, Coralville, Iowa).

Article Snippet: Enterovirus D68 (EVD68) , Genome Polyprotein (VP1) , ATCC VR-1826DQ and ATCC VR-1823D Gene Blocks.

Techniques: Sequencing, Positive Control, Virus, Membrane, Control, Blocking Assay

Journal: Scientific Reports

Article Title: Rapid and accurate detection of SARS-CoV-2 using the RHAM technology

doi: 10.1038/s41598-023-49733-7

Figure Lengend Snippet: Evaluation of RHAM specificity. ( A ) The specificity of RHAM targeting Orf1ab was evaluated by testing the nucleic acids of other respiratory pathogens, ( B ) The specificity of RHAM targeting N gene was evaluated by testing the nucleic acids of other respiratory pathogens. All pathogens including coronavirus (HKU1, OC43, NL63, 229E), SARS coronavirus, MERS coronavirus, influenza A H1N1, H5N1, H7N9, and H9N2, influenza B virus, respiratory syncytial virus types A and B, human parainfluenza virus type II, adenovirus types 3 and 7, enterovirus EV71, Mycoplasma pneumoniae , Epstein-Barr virus, human cytomegalovirus, and Mycobacterium tuberculosis . 10 μL of nucleic acid was added to the RHAM reaction mixture (25 μL reaction volume).

Article Snippet: MERS coronavirus (ATCC, VR-3248SD), coronavirus OC43 (ATCC, VR-1558D), HKU1 (ATCC, VR-3262SD), 229E (ATCC, VR-740DQ), NL63 (ATCC, VR-3263SD), SARS coronavirus (ATCC, VR-3280SD), influenza A H1N1 (ATCC, VR-1469), H5N1 (ATCC, VR-1647), influenza B Virus (ATCC, VR-1735D), respiratory syncytial virus type A (ATCC, VR-1804DQ) and B (ATCC, 1850DQ), human parainfluenza virus type II (ATCC, VR-92DQ), adenovirus type 3 (ATCC, VR-3DQ) and 7 (ATCC, VR-7DQ), enterovirus EV71 (ATCC, VR-1775DQ), Mycoplasma pneumoniae (ATCC, 29342), human cytomegalovirus (ATCC, VR-1590), and Mycobacterium tuberculosis (ATCC 25177) were purchased from the ATCC SARS-CoV-2 RNA (GBW(E)091098) was purchased from the National Institute of Metrology (China, CNRN).

Techniques: Virus