Hernandez Matthew M, Banu Radhika, Shrestha Paras, Gonzalez-Reiche Ana S, van de Guchte Adriana, Farrugia Keith, Sebra Robert, Gitman Melissa R, Nowak Michael D, Cordon-Cardo Carlos, Simon Viviana, van Bakel Harm, Sordillo Emilia Mia, Luna Nicolas, Ramirez Angie, Castañeda Sergio Andres, Patiño Luz Helena, Ballesteros Nathalia, Muñoz Marina, Ramírez Juan David, Paniz-Mondolfi Alberto E
Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
medRxiv. 2022 May 29:2022.05.28.22275691. doi: 10.1101/2022.05.28.22275691.
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 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 Bogotá, 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 (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, 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.
The 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.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体的特点是传播性和对治疗的反应存在差异。因此，区分它们对于监测、感染预防和患者护理至关重要。虽然全病毒基因组测序（WGS）是变体鉴定的“金标准”，但分子变体检测板越来越容易获得。然而，大多数检测板基于有限的靶点，且未经过全面评估。我们评估了高度多重的Agena MassARRAY SARS-CoV-2变体检测板v3在鉴定一组多样的391份SARS-CoV-2临床RNA标本中的变体时的诊断性能，这些标本是在美国纽约市以及哥伦比亚波哥大的我们的卫生系统中收集的（2020年9月2日至2022年3月2日）。我们证明，对于检测板上测试的11个变体呼叫中的9个（κ≥0.856）和30个靶点中的25个（κ≥0.820），该检测方法与WGS之间的评分者间一致性几乎达到完美水平。该检测方法对当代变体（如Iota、Alpha、Delta、奥密克戎[BA.1亚系]）具有高诊断敏感性（≥93.67%），对所有测试的11个变体（≥96.15%）和所有30个靶点（≥94.34%）具有高诊断特异性。此外，我们突出了不同的靶点模式，可用于识别检测板上尚未定义的变体，包括奥密克戎BA.2和其他亚系。这些发现例证了高度多重诊断检测板准确呼叫变体的能力以及靶点结果特征阐明新变体的潜力。
在监测工作有限且人群疫苗接种不一致的情况下，SARS-CoV-2持续传播导致出现了对公共卫生系统有独特影响的变体。因此，结合功能和临床研究，持续检测和鉴定对于为诊断和公共卫生措施提供信息至关重要。此外，在临床微生物实验室中WGS变得更易获得之前，用于识别变体的理想检测方法必须强大、提供高分辨率且能适应像SARS-CoV-2这样不断演变的病毒的特性。在此，我们突出了一种高度多重的商业检测方法在识别2020年9月2日至2022年3月2日期间在我们的卫生系统中寻求治疗的患者中传播的多种SARS-CoV-2谱系方面的诊断能力。该检测方法展示了核苷酸/氨基酸多态性的变体特异性特征，并强调了其在检测当代和新出现的SARS-CoV-2关注变体方面的实用性。
