Journal: PeerJ

Article Title: Nationwide wastewater sequencing surveillance of SARS-CoV-2 lineages: validation against clinical data across 28 U.S. states

doi: 10.7717/peerj.20941

Figure Lengend Snippet: Spearman rank correlation coefficient between wastewater abundances and clinical abundances of SARS-CoV-2 lineages. All correlations were positive and significant after a Bonferroni correction, indicating clear agreement. Lower correlation coefficients are thought to be a result of either limited data points (BA) or ongoing epidemiological dynamics (LF, KP) for more recent lineages.

Article Snippet: For all sequencing runs, SARS-CoV-2 gRNA (ATCC VR-1986D), an early isolate of the original SARS-CoV-2 virus from March of 2020 in Washington, is used as a positive control (GenBank: MT246667.1 ).

Techniques:

Journal: PeerJ

Article Title: Nationwide wastewater sequencing surveillance of SARS-CoV-2 lineages: validation against clinical data across 28 U.S. states

doi: 10.7717/peerj.20941

Figure Lengend Snippet: Box and whisker plot of days from average emergence (defined as the date in which a lineage represented over 10% of the total abundance of lineages in at least 5 of our sites) for each SARS-CoV-2 lineage lineage. Each dot represents an individual WWTP. A larger spread indicates a slower spread across the country. Negative values represent an earlier emergence. Each of these dates is calculated with respect to each lineage’s average emergence across all sites.

Article Snippet: For all sequencing runs, SARS-CoV-2 gRNA (ATCC VR-1986D), an early isolate of the original SARS-CoV-2 virus from March of 2020 in Washington, is used as a positive control (GenBank: MT246667.1 ).

Techniques: Whisker Assay

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: Lyo-CRISPR SARS-CoV-2 assay. ( A ) Processing scheme, including the reagents and equipment required for performing the following three steps: RNA extraction using spin columns or by treating the samples with lysis buffer and heat, to be used as input in the reverse transcription (RT) and isothermal amplification reactions and CRISPR-Cas12 detection for N gene by fluorescence. Resuspension with nuclease-free water is required to hydrate the lyophilized beads containing all components for isothermal amplification and CRISPR detection. ( B ) Workflow scheme showing the entire process at molecular level. PBS: Phosphate Buffered Saline buffer; min: minutes; Lyo: lyophilized; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; CRISPR: clustered regularly interspaced short palindromic repeats; sgRNA: single guide RNA; F-Q reporter: fluorophore-quencher reporter.

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

Techniques: CRISPR, RNA Extraction, Lysis, Reverse Transcription, Amplification, Fluorescence, Saline

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: Agreement between GeneFinder RT-qPCR and Lyo-CRISPR SARS-CoV-2 kit results for testing samples extracted with spin column ( n = 210) and samples in lysis buffer ( n = 30) from hospitalized patients.

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

Techniques: Lysis

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, Virus

Journal: Scientific Reports

Article Title: Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation

doi: 10.1038/s41598-023-34220-w

Figure Lengend Snippet: List of commercially available molecular standards (nucleic acid solutions) used in analysis of the specificity of the three studied RT-qPCR assays.

Article Snippet: Quantitative Genomic RNA from Human parainfluenza virus 2 strain Greer , ATCC-VR-92DQ.

Techniques: Virus

Journal: Scientific Reports

Article Title: Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation

doi: 10.1038/s41598-023-34220-w

Figure Lengend Snippet: List of commercially available molecular standards (nucleic acid solutions) used in analysis of the specificity of the three studied RT-qPCR assays.

Article Snippet: Quantitative Genomic RNA from Human coronavirus 229E , ATCC-VR-740DQ.

Techniques: Virus

Journal: Scientific Reports

Article Title: Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation

doi: 10.1038/s41598-023-34220-w

Figure Lengend Snippet: RT-qPCR amplification parameters for Novel Coronavirus (2019-nCoV) Real Time Multiplex RT-PCR Kit (Liferiver), Vitassay qPCR SARS-CoV-2 (Vitassay) and TaqPath COVID‑19 CE-IVD RT-PCR Kit (Thermo Fisher Scientific).

Article Snippet: Quantitative Genomic RNA from Human coronavirus 229E , ATCC-VR-740DQ.

Techniques: Amplification, Multiplex Assay

Journal: Cell Discovery

Article Title: Zika virus propagation and release in human fetal astrocytes can be suppressed by neutral sphingomyelinase-2 inhibitor GW4869

doi: 10.1038/s41421-018-0017-2

Figure Lengend Snippet: Human fetal astrocytes were infected with ZIKV strains MR766 or PRVABC59 at the indicated MOI for 24 h, washed, then cultured for another 24 h. Supernatant from uninfected Vero cells was used for mock-infected control. a – h At the experimental endpoint, ICC of flavivirus antigen (green color) was performed. DAPI (blue color) was used as a nuclear counterstain. Panels are representative of three separate donors. Scale bar: 100 µm. Images were acquired through a Zeiss LSM 710 confocal microscope. i ZIKV-positive cells in a – h were quantified and shown as percentage of total cells in the culture. j RNA was isolated and expression ZIKV RNA was determined through real-time RT-PCR. Data were normalized to GAPDH and presented as fold change compared to mock-infected control. ** p < 0.001; *** p < 0.0001 as compared to mock-infected control

Article Snippet: Quantitative Genomic RNA from ZIKV (ATCC) was used as standard for viral copy determination. f After GW4869 treatment, cell-free culture supernatants were added to Vero cells and overlaid with Agar gel.

Techniques: Infection, Cell Culture, Control, Microscopy, Isolation, Expressing, Quantitative RT-PCR

Journal: Cell Discovery

Article Title: Zika virus propagation and release in human fetal astrocytes can be suppressed by neutral sphingomyelinase-2 inhibitor GW4869

doi: 10.1038/s41421-018-0017-2

Figure Lengend Snippet: Astrocytes were infected with ZIKV stains PRVABC59 and treated with doses of GW4869 ranging from 2 μM to 10 μM. After 24 h, the cultures were washed and treated with same doses of GW4869 in fresh medium for another 24 h. a Experimental scheme. b – d EVs were isolated from culture supernatants and visualized through NanoSight ( b ). Quantifications of NanoSight data. *** p < 0.0001 in comparison to ZIKV group (ANOVA, n = 5) ( c ). The levels of flotillin-2 and Alix in EVs, as well as the levels of GFAP and β-actin in WCL were determined by Western blot ( d ). e ZIKA RNA was detected in total cellular RNA through real-time RT-PCR. Data were normalized to GAPDH and presented as fold change compared to ZIKV group. f – i Immunocytochemistry of flavivirus antigen was performed on the ZIKV-infected astrocytes. DAPI was used as a nuclear counterstain. Results are representative of three independent experiments. Scale bar: 50 μm. j Quantification of immunofluorescence data was performed with counting flavivirus antigen in infected cells. k ZIKA RNA was detected in total RNA isolated from cell-free supernatants through real-time RT-PCR. l , m After GW4869 treatment, cell-free culture supernatants were added to Vero cells and overlaid with Agar gel. Viral PFU was determined at 4-day post inoculation through crystal violet staining ( l ). Viral plaques were manually counted and calculated as PFU/ml ( m ). * p < 0.05; *** p < 0. 001, as compared to the ZIKV group

Article Snippet: Quantitative Genomic RNA from ZIKV (ATCC) was used as standard for viral copy determination. f After GW4869 treatment, cell-free culture supernatants were added to Vero cells and overlaid with Agar gel.

Techniques: Infection, Isolation, Comparison, Western Blot, Quantitative RT-PCR, Immunocytochemistry, Immunofluorescence, Staining

Journal: Cell Discovery

Article Title: Zika virus propagation and release in human fetal astrocytes can be suppressed by neutral sphingomyelinase-2 inhibitor GW4869

doi: 10.1038/s41421-018-0017-2

Figure Lengend Snippet: Astrocytes were infected with ZIKV stains MR766 and treated with doses of GW4869 ranging from 2 μM to 10 μM. After 24 h, the cultures were washed and treated with same doses of GW4869 in fresh medium for another 24 h. a – c EVs were isolated from culture supernatants and visualized through NanoSight ( a ). Quantifications of NanoSight data. *** p < 0.0001 in comparison to ZIKV group (ANOVA, n = 5) ( b ). The levels of flotillin-2 and tTG in EVs, as well as the levels of β-actin in WCL were determined by Western blot ( c ). d ZIKA RNA was detected in total cellular RNA through real-time RT-PCR. Data were normalized to GAPDH and presented as fold change compared to ZIKV group. e ZIKA RNA was detected in total RNA isolated from cell-free supernatants through real-time RT-PCR. Quantitative Genomic RNA from ZIKV (ATCC) was used as standard for viral copy determination. f After GW4869 treatment, cell-free culture supernatants were added to Vero cells and overlaid with Agar gel. Viral PFU were determined at 4-day post inoculation through crystal violet staining

Article Snippet: Quantitative Genomic RNA from ZIKV (ATCC) was used as standard for viral copy determination. f After GW4869 treatment, cell-free culture supernatants were added to Vero cells and overlaid with Agar gel.

Techniques: Infection, Isolation, Comparison, Western Blot, Quantitative RT-PCR, Staining