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A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants
Matthew M. Hernandez; Radhika Banu; Paras Shrestha; Ana S. Gonzalez-Reiche; Adriana van de Guchte; Keith Farrugia; Robert Sebra; Mount Sinai PSP Study Group; Melissa R Gitman; Michael D Nowak; Carlos Cordon-Cardo; Viviana Simon; Harm van Bakel; Emilia M Sordillo; Nicolás Luna; Angie Ramírez; Sergio Castañeda; Luz H Patiño; Nathalia Ballesteros; Marina Muñoz; Juan David Ramírez; Alberto E Paniz Mondolfi.
Afiliación
  • Matthew M. Hernandez; Icahn School of Medicine at Mount Sinai
  • Radhika Banu; Icahn School of Medicine at Mount Sinai
  • Paras Shrestha; Icahn School of Medicine at Mount Sinai
  • Ana S. Gonzalez-Reiche; Icahn School of Medicine at Mount Sinai
  • Adriana van de Guchte; Icahn School of Medicine at Mount Sinai
  • Keith Farrugia; Icahn School of Medicine at Mount Sinai
  • Robert Sebra; Icahn School of Medicine at Mount Sinai
  • Mount Sinai PSP Study Group; Icahn School of Medicine at Mount Sinai
  • Melissa R Gitman; Icahn School of Medicine at Mount Sinai
  • Michael D Nowak; Icahn School of Medicine at Mount Sinai
  • Carlos Cordon-Cardo; Icahn School of Medicine at Mount Sinai
  • Viviana Simon; Icahn School of Medicine
  • Harm van Bakel; Icahn School of Medicine at Mount Sinai
  • Emilia M Sordillo; Icahn School of Medicine at Mount Sinai
  • Nicolás Luna; Universidad del Rosario
  • Angie Ramírez; Universidad del Rosario
  • Sergio Castañeda; Universidad del Rosario
  • Luz H Patiño; Universidad del Rosario
  • Nathalia Ballesteros; Universidad del Rosario
  • Marina Muñoz; Universidad del Rosario
  • Juan David Ramírez; Icahn School of Medicine at Mount Sinai
  • Alberto E Paniz Mondolfi; Icahn School of Medicine
Preprint en En | PREPRINT-MEDRXIV | ID: ppmedrxiv-22275691
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 viral 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(R) 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 as well as in Bogota, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls ({kappa} [≥] 0.856) and 25 of 30 targets ({kappa} [≥] 0.820) tested on the panel. The assay had a high diagnostic sensitivity ([≥]93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants ([≥]96.15%) and all 30 targets ([≥]94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. ImportanceThe continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform 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 highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.
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Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-MEDRXIV Tipo de estudio: Diagnostic_studies / Experimental_studies / Prognostic_studies Idioma: En Año: 2022 Tipo del documento: Preprint
Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-MEDRXIV Tipo de estudio: Diagnostic_studies / Experimental_studies / Prognostic_studies Idioma: En Año: 2022 Tipo del documento: Preprint