Journal: Chemical Science

Article Title: Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

doi: 10.1039/d2sc06665c

Figure Lengend Snippet: Examples of commercial molecular diagnostic assays for the detection of SARS-CoV-2 a

Article Snippet: Agena Bioscience, Inc. , MassARRAY SARS-CoV-2 Panel , rRT-PCR, MALDI-TOF , N gene (N1, N2, and N3 regions), ORF1, and ORF1ab , Nasopharyngeal swabs, oropharyngeal swabs, nasal and mid-turbinate swabs , 310–2500 copies per mL , 98.9% , 100% , H , .

Techniques: Diagnostic Assay, Amplification, Reverse Transcription, Reverse Transcription Polymerase Chain Reaction, Microarray, Hybridization, Kinetic Assay, Helicase-dependent Amplification

Journal: Chemical Science

Article Title: Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

doi: 10.1039/d2sc06665c

Figure Lengend Snippet: Comparison of the three types of SARS-CoV-2 antibody assay diagnostic kits

Article Snippet: Agena Bioscience, Inc. , MassARRAY SARS-CoV-2 Panel , rRT-PCR, MALDI-TOF , N gene (N1, N2, and N3 regions), ORF1, and ORF1ab , Nasopharyngeal swabs, oropharyngeal swabs, nasal and mid-turbinate swabs , 310–2500 copies per mL , 98.9% , 100% , H , .

Techniques: Comparison, Diagnostic Assay, Clinical Proteomics, Enzyme-linked Immunosorbent Assay, High Throughput Screening Assay

Journal: Chemical Science

Article Title: Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

doi: 10.1039/d2sc06665c

Figure Lengend Snippet: Types of SARS-CoV-2 pseudovirus neutralizing tests

Article Snippet: Agena Bioscience, Inc. , MassARRAY SARS-CoV-2 Panel , rRT-PCR, MALDI-TOF , N gene (N1, N2, and N3 regions), ORF1, and ORF1ab , Nasopharyngeal swabs, oropharyngeal swabs, nasal and mid-turbinate swabs , 310–2500 copies per mL , 98.9% , 100% , H , .

Techniques: Plasmid Preparation, Expressing, Virus, Luciferase, Mutagenesis, Clinical Proteomics, Bioprocessing

Journal: medRxiv

Article Title: Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward

doi: 10.1101/2021.08.05.21261562

Figure Lengend Snippet: Evolution of SARS-CoV-2 infections distributed across time for persons with exposures in a single inpatient unit. A. Number scale at the bottom of the figure indicates sequential days with indicated breaks in the scale. Blue bars represent days spent in the indicated rooms on a single medical-surgical unit. Circles represent patients; square, a family member; hexagon, a healthcare worker. Numbers within shapes indicate PCR Ct. Red fill indicates positive PCR test; green fill, negative PCR; * within green circle indicates a negative antigen test. Negative numbers in circles represent days prior to the beginning of the timeline. V, vaccinated; UV, unvaccinated; Nd appearing after V- or UV- represents number of days on the outbreak unit. A, asymptomatic at time of diagnosis; S, symptomatic at time of diagnosis. Open circles indicate the onset of symptoms prior to diagnosis. The first diagnosed patient is designated as Index. B. Location of rooms. Letters correspond to rooms identified in . Grey rectangles represent beds and together depict 1-bed, 2-bed, and 3-bed rooms.

Article Snippet: Variants were identified by MassARRAY SARS-CoV-2 Variant Panel (36-plex PCR, Agena BioScience) for most breakthrough cases after June 2021 Viral genomic sequencing was performed by the Jackson Laboratory.

Techniques: Biomarker Discovery

Journal: medRxiv

Article Title: Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward

doi: 10.1101/2021.08.05.21261562

Figure Lengend Snippet: PCR cycle threshold (Ct) in breakthrough infections with the Delta variant vs earlier variants of SARS-CoV-2. Shown are the mean ± standard deviation for the two groups. * p = .003.

Article Snippet: Variants were identified by MassARRAY SARS-CoV-2 Variant Panel (36-plex PCR, Agena BioScience) for most breakthrough cases after June 2021 Viral genomic sequencing was performed by the Jackson Laboratory.

Techniques: Variant Assay, Standard Deviation

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Workflow and molecular principle of SARS-CoV-2 RNA detection in FFPE tissue by MALDI-TOF mass spectrometry. RNA extraction from FFPE placental and amniotic tissue was performed using the Maxwell RSC RNA FFPE Kit (Promega) according to manufacturer’s instructions. Extracted viral RNA is then reverse transcribed into cDNA and amplified by a one-step RT-PCR reaction. The figure schematically depicts specific amplification of the SARS-CoV-2 targets N1 and N2. The forward primers are indicated in green, the reverse primers in blue. Thereafter, PCR products are treated with the shrimp alkaline phosphatase (SAP) enzyme to remove unincorporated nucleotides (dNTPs). Next, a single nucleotide extension reaction is performed, in which target-specific extension primers are elongated by a single mass-modified terminator nucleotide (A, T, C or G) complementary to the cDNA template sequence. The extension products (EP) are then analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) using the MassARRAY system (Agena Bioscience) and mass spectra of the SARS-CoV-2-specific detected cDNA fragments are generated. In the absence of viral RNA, RT-PCR as well as single nucleotide extension reactions cannot be performed and consequently, no cDNA fragments are detected by MALDI-TOF analysis. EP: extension product; UEP: unextended extension primer.

Article Snippet: For detection of the SARS-CoV-2 variants the Research Use Only (RUO) MassARRAY ® SARS-CoV-2 Variant Panel v1 (Agena Bioscience) was used.

Techniques: RNA Detection, Mass Spectrometry, RNA Extraction, Reverse Transcription, Amplification, One Step RT-PCR, Modification, Sequencing, Generated, Reverse Transcription Polymerase Chain Reaction

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Genomic targets of the MassARRAY SARS-CoV-2 Panels . ( A ): The CE-IVD-certified MassARRAY SARS-CoV-2 Panel targets 5 genomic regions within the SARS-CoV-2 genome: ORF1, ORF1ab, N1, N2 and N3 (indicated by red arrows). The detection of at least 2 targets is required for the result “SARS-CoV-2 positive”. ORF, open reading frame; S, spike; E, envelope; M, membrane; N, nucleocapsid. ( B ): The MassARRAY SARS-CoV-2 Variant Panel v1 targets 20 specific mutations (indicated by red arrows) within the spike gene allowing the identification of 5 different SARS-CoV-2 variants. For detection of the British (B.1.1.7) variant at least 6 out of the 8 mutations H69_70 del, Y144del, N501Y, A570D, P681H, T716I, S982A, D1118H are required while for detection of the South African (B.1.351) variant at least 6 out of the 8 mutations L18F, D80A, D215G, L242_L244del, K417N, E484K, N501Y and A701V are required. The 4 mutations L18F, K417T, E484K and N501Y identify the Brazilian (P.1) variant and the 4 mutations H69_70del, Y453F, N501T and I692V allow the identification of the Danish (Mink) variant (3 out of 4 mutations required). The mutation D614G evolved very early during the pandemic spread in 2020 and is present in all variants.

Article Snippet: For detection of the SARS-CoV-2 variants the Research Use Only (RUO) MassARRAY ® SARS-CoV-2 Variant Panel v1 (Agena Bioscience) was used.

Techniques: Membrane, Variant Assay, Mutagenesis

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Representative mass spectra of a positive sample analyzed by the CE-IVD-certified MassARRAY SARS-CoV-2 Panel. The different mass spectra display intensity and mass (in daltons) of the SARS-CoV-2 -specific cDNA fragments ORF1, ORF1ab, N1, N2 and N3. Additionally, the mass spectrum of the MS2 phage control is depicted. The red box highlights the unextended extension primer peak, whereas the blue box highlights the peak corresponding to the extension product. UEP: unextended extension primer; EP: extension product.

Article Snippet: For detection of the SARS-CoV-2 variants the Research Use Only (RUO) MassARRAY ® SARS-CoV-2 Variant Panel v1 (Agena Bioscience) was used.

Techniques: Control

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Detection of SARS-CoV-2 RNA in placental and amniotic tissue. Placental and amniotic tissue were analyzed by MALDI-TOF MS using the CE-IVD-certified MassARRAY SARS-CoV-2 Panel ( A ) and by RT-PCR using the EURORealTime SARS-CoV-2 Kit ( B ). ( A ): The plots display the intensity of the peaks corresponding to the 5 targets ORF1, ORF1ab, N1, N2 and N3 included in the CE-IVD-certified MassARRAY SARS-CoV-2 Panel. The intensity threshold considering a peak as detected is 5. All 5 SARS-CoV-2 targets were detected in both placental and amniotic tissue. ( B ). The graphs show the fluorescence intensity ( y -axis) for each cycle ( x -axis) of the real-time amplification of the SARS-CoV-2 -specific target regions (amplification curve). The amplification curve of the positive control (PC) is highlighted in green, the one of the negative control (NC) in red. The crossing point (Cp) value is indicated for both placental tissue (p.tissue) and amniotic tissue (a.tissue).

Article Snippet: For detection of the SARS-CoV-2 variants the Research Use Only (RUO) MassARRAY ® SARS-CoV-2 Variant Panel v1 (Agena Bioscience) was used.

Techniques: Reverse Transcription Polymerase Chain Reaction, Fluorescence, Amplification, Positive Control, Negative Control

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: SARS-CoV-2 variant analysis of amniotic and placental tissue by MALDI-TOF MS. Placental and amniotic tissue were analyzed by MALDI-TOF MS using the MassARRAY SARS-CoV-2 Variant Panel v1. The figure shows the specific mutations within the SARS-CoV-2 spike gene that are assigned to the different variants B 1.1.7 ( A ), B 1.351 ( B ), P.1 ( C ) and Cluster 5/Mink ( D ). Detected mutations in placental tissue (p.tissue), amniotic tissue (a.tissue), positive controls (PC) B 1.1.7 and B 1.351 and negative control (NC) are illustrated by green-colored squares.

Article Snippet: For detection of the SARS-CoV-2 variants the Research Use Only (RUO) MassARRAY ® SARS-CoV-2 Variant Panel v1 (Agena Bioscience) was used.

Techniques: Variant Assay, Negative Control

Journal: Diagnostics

Article Title: Rapid Evaluation of the Xpert ® Xpress CoV-2 plus and Xpert ® Xpress CoV-2/Flu/RSV plus Tests

doi: 10.3390/diagnostics13010034

Figure Lengend Snippet: ( a ) Xpert ® Xpress CoV-2 plus workflow and ( b ) Xpert ® Xpress CoV-2/Flu/RSV plus workflow. 2 o : secondary; LOD: limit of detection; n: number; SOC: standard of care; VOC: SARS-CoV-2 variants of concern.

Article Snippet: These specimens were selected by COVID-19 wave and were previously genotyped by the AllPlex SARS-CoV-2 Variants I and II and NovaPlex SARS-CoV-2 Variants V tests (all Seegene, Seoul, Republic of Korea) and/or TaqMan SARS-CoV-2 Mutation Panels (Thermo Fisher Scientific, Waltham, MA, USA) and/or MassARRAY SARS-CoV-2 Variant Panel v3 (RUO) (MassARRAY; Agena Biosciences, San Diego, CA, USA), or by next generation sequencing performed at the NICD.

Techniques:

Journal: Diagnostics

Article Title: Rapid Evaluation of the Xpert ® Xpress CoV-2 plus and Xpert ® Xpress CoV-2/Flu/RSV plus Tests

doi: 10.3390/diagnostics13010034

Figure Lengend Snippet: Regression analysis of the Xpert ® Xpress SARS-CoV-2, Xpert ® Xpress CoV-2 plus and Xpert ® Xpress CoV-2/Flu/RSV tests, including the equation of the line and R 2 values. ( a ) Xpert ® Xpress SARS-CoV-2 and Xpert ® Xpress CoV-2 plus ; ( b ) Xpert ® Xpress CoV-2/Flu/RSV plus .

Article Snippet: These specimens were selected by COVID-19 wave and were previously genotyped by the AllPlex SARS-CoV-2 Variants I and II and NovaPlex SARS-CoV-2 Variants V tests (all Seegene, Seoul, Republic of Korea) and/or TaqMan SARS-CoV-2 Mutation Panels (Thermo Fisher Scientific, Waltham, MA, USA) and/or MassARRAY SARS-CoV-2 Variant Panel v3 (RUO) (MassARRAY; Agena Biosciences, San Diego, CA, USA), or by next generation sequencing performed at the NICD.

Techniques: