Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA.
Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
Sci Rep. 2023 May 10;13(1):7612. doi: 10.1038/s41598-023-34188-7.
Epidemiologic surveillance of circulating SARS-CoV-2 variants is essential to assess impact on clinical outcomes and vaccine efficacy. Whole genome sequencing (WGS), the gold-standard to identify variants, requires significant infrastructure and expertise. We developed a digital droplet polymerase chain reaction (ddPCR) assay that can rapidly identify circulating variants of concern/interest (VOC/VOI) using variant-specific mutation combinations in the Spike gene. To validate the assay, 800 saliva samples known to be SARS-CoV-2 positive by RT-PCR were used. During the study (July 2020-March 2022) the assay was easily adaptable to identify not only existing circulating VAC/VOI, but all new variants as they evolved. The assay can discriminate nine variants (Alpha, Beta, Gamma, Delta, Eta, Epsilon, Lambda, Mu, and Omicron) and sub-lineages (Delta 417N, Omicron BA.1, BA.2). Sequence analyses confirmed variant type for 124/124 samples tested. This ddPCR assay is an inexpensive, sensitive, high-throughput assay that can easily be adapted as new variants are identified.
对循环 SARS-CoV-2 变体进行流行病学监测对于评估其对临床结果和疫苗效果的影响至关重要。全基因组测序（WGS）是识别变体的金标准，但需要大量的基础设施和专业知识。我们开发了一种数字液滴聚合酶链反应（ddPCR）检测方法，该方法可以使用 Spike 基因中的变体特异性突变组合，快速识别关注/感兴趣的变体（VOC/VOI）。为了验证该检测方法，我们使用了 800 份经 RT-PCR 确认为 SARS-CoV-2 阳性的唾液样本。在研究期间（2020 年 7 月至 2022 年 3 月），该检测方法可以轻松适应识别不仅现有的循环 VOC/VOI，还可以识别随着变异而进化的所有新变体。该检测方法可以区分 9 种变体（Alpha、Beta、Gamma、Delta、Eta、Epsilon、Lambda、Mu 和 Omicron）和亚系（Delta 417N、Omicron BA.1、BA.2）。序列分析证实了 124/124 个测试样本的变体类型。这种 ddPCR 检测方法是一种廉价、敏感、高通量的检测方法，可以轻松适应新变体的识别。
