Department of Pathology, University of Texas Medical Branch, Galveston, Texas.
World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
J Mol Diagn. 2022 May;24(5):455-461. doi: 10.1016/j.jmoldx.2022.02.001. Epub 2022 Feb 24.
Tracking new and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become increasingly important for public health responses, primarily because of variant-dependent transmission, disease severity, and treatment decisions. This evaluation compared Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV (I,II&IV) assays to detect known SARS-CoV-2 variants using traditional spike gene Sanger sequencing results as the gold standard reference. Both RNA extraction and extraction-free protocols were assessed. A total of 156 samples were included in this study. There was 100% (109/109) overall agreement (95% CI, 96.7%-100%) between the spike gene sequencing and the I,II&IV results using extracted RNA for the variants included in the Novaplex assay menus. The RNA extraction-free method was 91.7% (143/156) as sensitive (95% CI, 86.2%-95.5%) as the traditional RNA extraction method. Using the extraction-free method on samples with higher cycle threshold values (>30) resulted in some mutations not being detected, presumably due to lower nucleic acid concentrations in the original samples. In conclusion, the I,II&IV assays provide an accurate, rapid, and less labor-intensive method for detecting SARS-CoV-2 and identifying known variants of interest and concern. The RNA extraction-free method for samples with cycle threshold of <30 could be cost-effective for surveillance purposes. However, spike gene sequencing retains the advantage of detecting more and new variants.
跟踪新出现的严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）变体对于公共卫生应对措施变得越来越重要，主要是因为变体依赖性传播、疾病严重程度和治疗决策。本评估比较了 Seegene 技术公司的 Novaplex SARS-CoV-2 变体 I、II 和 IV（I、II&IV）检测试剂盒，使用传统的刺突基因 Sanger 测序结果作为金标准参考，来检测已知的 SARS-CoV-2 变体。评估了 RNA 提取和无提取两种方案。本研究共纳入了 156 个样本。对于 Novaplex 检测试剂盒中包含的变体，使用提取 RNA 时，刺突基因测序与 I、II&IV 结果之间的总符合率为 100%（109/109）（95%置信区间，96.7%-100%）。无 RNA 提取方法的灵敏度为 91.7%（143/156）（95%置信区间，86.2%-95.5%），与传统 RNA 提取方法相当。对于循环阈值（Ct 值）>30 的样本使用无提取方法，可能会导致一些突变无法被检测到，推测是由于原始样本中的核酸浓度较低。总之，I、II&IV 检测试剂盒为检测 SARS-CoV-2 并识别已知的重要和关注的变体提供了一种准确、快速且劳动强度较低的方法。对于 Ct 值<30 的样本，无 RNA 提取方法在监测方面可能具有成本效益。然而，刺突基因测序仍然具有检测更多和新变体的优势。
