massarray sars cov 2 variant panel v3 ruo  (agena bioscience)

Journal: Diagnostics (Basel, Switzerland)

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: Figure 2. 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 R2 values. (a) Xpert®

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: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Detection of viral variants by the Agena MassARRAY SARS-CoV-2 Variant Panel. (A) SARS-CoV-2 genome with nucleotide positions from 5′-to-3′ direction depicted above. S gene polymorphisms targeted by the variant panel (lollipops) and corresponding amino acids are depicted below. (B) A color map depicts algorithms of target combinations that defined 16 distinct SARS-CoV-2 variants on the panel. Variant results are depicted (left) and included the WHO designation (e.g., Omicron, Delta, etc.) and corresponding PANGO lineage assignments. Note that the B.1.526.1 variant was redesignated B.1.637 to distinguish it from the Iota variant lineage ( https://cov-lineages.org/lineage_list.html , accessed April 26, 2022). The minimum number of targets required to support the corresponding variant result is indicated (right). Target results are depicted as colored cells indicating amino acid positions that did not contribute to the defined variant identity algorithm (gray). The remaining three colors reflect native amino acids (e.g., unchanged from Wuhan-Hu-1 reference) (yellow), detectable amino acid polymorphisms (red), and drop out of the given target (green), all of which contributed to the variant identity algorithm. (C) Phylogenetic composition of 391 clinical specimen viral RNA recovered for diagnostic evaluation of the variant panel. The numbers of each lineage tested are depicted in brackets.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Variant Assay, Diagnostic Assay

Journal: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Diagnostic sensitivity and specificity of the Agena MassARRAY SARS-CoV-2 Variant panel. (A) Diagnostic sensitivity and (B) diagnostic specificity of 11 variant calls on the panel are depicted. The number of specimens that correspond with each variant according to WGS is annotated in brackets. Depiction of (C) diagnostic sensitivity and (D) diagnostic specificity of each of 30 distinct panel targets. The number of specimens that correspond with each amino acid polymorphism according to WGS is annotated in brackets for each target. Asterisks (*) indicate targets for which dropout results were excluded from analyses (see Materials and Methods). For target N501Y, a separate diagnostic analysis was conducted excluding BA.1 specimens (“N501Y_Excl-BA.1”). Error bars reflect 95% CI in all four panels. ND, not determined.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Diagnostic Assay, Variant Assay

Journal: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Target result patterns of undefined variants on the Agena MassARRAY SARS-CoV-2 Variant Panel. (A) A color map depicts the observed target results for three undefined SARS-CoV-2 variants tested on the panel: Lambda (C.37), Mu (B.1.621), and Omicron (BA.2). Distinct target patterns were observed among each of the variant types are depicted. Cells indicate the distinct target results, including detectable native amino acid (gray), detection of target polymorphism (red), and target dropout (green). The number of specimens that yielded each of the distinct target result patterns is indicated on the right as well as the output variant ID result generated by the variant panel software. (B) A heatmap depicts the measured prevalence of each variant panel target substitution among publicly available Omicron sublineage genomes as of May 6, 2022.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Variant Assay, Generated, Software

Journal: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Detection of viral variants by the Agena MassARRAY SARS-CoV-2 Variant Panel. (A) SARS-CoV-2 genome with nucleotide positions from 5′-to-3′ direction depicted above. S gene polymorphisms targeted by the variant panel (lollipops) and corresponding amino acids are depicted below. (B) A color map depicts algorithms of target combinations that defined 16 distinct SARS-CoV-2 variants on the panel. Variant results are depicted (left) and included the WHO designation (e.g., Omicron, Delta, etc.) and corresponding PANGO lineage assignments. Note that the B.1.526.1 variant was redesignated B.1.637 to distinguish it from the Iota variant lineage ( https://cov-lineages.org/lineage_list.html , accessed April 26, 2022). The minimum number of targets required to support the corresponding variant result is indicated (right). Target results are depicted as colored cells indicating amino acid positions that did not contribute to the defined variant identity algorithm (gray). The remaining three colors reflect native amino acids (e.g., unchanged from Wuhan-Hu-1 reference) (yellow), detectable amino acid polymorphisms (red), and drop out of the given target (green), all of which contributed to the variant identity algorithm. (C) Phylogenetic composition of 391 clinical specimen viral RNA recovered for diagnostic evaluation of the variant panel. The numbers of each lineage tested are depicted in brackets.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Variant Assay, Diagnostic Assay

Journal: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Diagnostic sensitivity and specificity of the Agena MassARRAY SARS-CoV-2 Variant panel. (A) Diagnostic sensitivity and (B) diagnostic specificity of 11 variant calls on the panel are depicted. The number of specimens that correspond with each variant according to WGS is annotated in brackets. Depiction of (C) diagnostic sensitivity and (D) diagnostic specificity of each of 30 distinct panel targets. The number of specimens that correspond with each amino acid polymorphism according to WGS is annotated in brackets for each target. Asterisks (*) indicate targets for which dropout results were excluded from analyses (see Materials and Methods). For target N501Y, a separate diagnostic analysis was conducted excluding BA.1 specimens (“N501Y_Excl-BA.1”). Error bars reflect 95% CI in all four panels. ND, not determined.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Diagnostic Assay, Variant Assay

Journal: Microbiology Spectrum

Article Title: A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

doi: 10.1128/spectrum.01736-22

Figure Lengend Snippet: Target result patterns of undefined variants on the Agena MassARRAY SARS-CoV-2 Variant Panel. (A) A color map depicts the observed target results for three undefined SARS-CoV-2 variants tested on the panel: Lambda (C.37), Mu (B.1.621), and Omicron (BA.2). Distinct target patterns were observed among each of the variant types are depicted. Cells indicate the distinct target results, including detectable native amino acid (gray), detection of target polymorphism (red), and target dropout (green). The number of specimens that yielded each of the distinct target result patterns is indicated on the right as well as the output variant ID result generated by the variant panel software. (B) A heatmap depicts the measured prevalence of each variant panel target substitution among publicly available Omicron sublineage genomes as of May 6, 2022.

Article Snippet: We recovered residual viral RNA from all 391 specimens from −80°C storage to undergo testing on the Agena MassARRAY SARS-CoV-2 Variant Panel v3 ( https://www.agenabio.com/products/panel/coronavirus-sars-cov-2-variant-detection-research-panel , accessed April 5, 2022).

Techniques: Variant Assay, Generated, Software

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