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