A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants
ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS...
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-10-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01736-22 |
| _version_ | 1797990000603693056 |
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| author | Matthew M. Hernandez Radhika Banu Paras Shrestha Ana S. Gonzalez-Reiche Adriana van de Guchte Keith Farrugia Robert Sebra Melissa R. Gitman Michael D. Nowak Carlos Cordon-Cardo Viviana Simon Harm van Bakel Emilia Mia Sordillo Nicolas Luna Angie Ramirez Sergio Andres Castañeda Luz Helena Patiño Nathalia Ballesteros Marina Muñoz Juan David Ramírez Alberto E. Paniz-Mondolfi |
| author_facet | Matthew M. Hernandez Radhika Banu Paras Shrestha Ana S. Gonzalez-Reiche Adriana van de Guchte Keith Farrugia Robert Sebra Melissa R. Gitman Michael D. Nowak Carlos Cordon-Cardo Viviana Simon Harm van Bakel Emilia Mia Sordillo Nicolas Luna Angie Ramirez Sergio Andres Castañeda Luz Helena Patiño Nathalia Ballesteros Marina Muñoz Juan David Ramírez Alberto E. Paniz-Mondolfi |
| author_sort | Matthew M. Hernandez |
| collection | DOAJ |
| description | ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the “gold standard” for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern. |
| first_indexed | 2024-04-11T08:28:26Z |
| format | Article |
| id | doaj.art-ed4bb5d41c7b4562ad9a1264c662cd64 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-11T08:28:26Z |
| publishDate | 2022-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-ed4bb5d41c7b4562ad9a1264c662cd642022-12-22T04:34:37ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-10-0110510.1128/spectrum.01736-22A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 VariantsMatthew M. Hernandez0Radhika Banu1Paras Shrestha2Ana S. Gonzalez-Reiche3Adriana van de Guchte4Keith Farrugia5Robert Sebra6Melissa R. Gitman7Michael D. Nowak8Carlos Cordon-Cardo9Viviana Simon10Harm van Bakel11Emilia Mia Sordillo12Nicolas Luna13Angie Ramirez14Sergio Andres Castañeda15Luz Helena Patiño16Nathalia Ballesteros17Marina Muñoz18Juan David Ramírez19Alberto E. Paniz-Mondolfi20Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USACentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaDepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USADepartment of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USAABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the “gold standard” for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.https://journals.asm.org/doi/10.1128/spectrum.01736-22RT-PCRMALDI-TOFSARS-CoV-2variant panelmultiplexOmicron |
| spellingShingle | Matthew M. Hernandez Radhika Banu Paras Shrestha Ana S. Gonzalez-Reiche Adriana van de Guchte Keith Farrugia Robert Sebra Melissa R. Gitman Michael D. Nowak Carlos Cordon-Cardo Viviana Simon Harm van Bakel Emilia Mia Sordillo Nicolas Luna Angie Ramirez Sergio Andres Castañeda Luz Helena Patiño Nathalia Ballesteros Marina Muñoz Juan David Ramírez Alberto E. Paniz-Mondolfi A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants Microbiology Spectrum RT-PCR MALDI-TOF SARS-CoV-2 variant panel multiplex Omicron |
| title | A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants |
| title_full | A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants |
| title_fullStr | A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants |
| title_full_unstemmed | A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants |
| title_short | A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants |
| title_sort | robust highly multiplexed mass spectrometry assay to identify sars cov 2 variants |
| topic | RT-PCR MALDI-TOF SARS-CoV-2 variant panel multiplex Omicron |
| url | https://journals.asm.org/doi/10.1128/spectrum.01736-22 |
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