On November 26, 2021, the World Health Organization classified B.1.1.529 as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC), named omicron. Spike-gene dropouts in conventional SARS-CoV-2 PCR systems have been reported over the last weeks as indirect diagnostic evidence for the identification of omicron. Here, we report the combination of PCRs specific for heavily mutated sites in the spike gene and nanopore-based full-length genome sequencing for the rapid and sensitive identification of the first four COVID-19 patients diagnosed in Germany to be infected with omicron on November 28, 2021. This study will assist the unambiguous laboratory-based diagnosis and global surveillance for this highly contagious VoC with an unprecedented degree of humoral immune escape. Moreover, we propose that specialized diagnostic laboratories should continuously update their assays for variant-specific PCRs in the spike gene of SARS-CoV-2 to readily detect and diagnose emerging variants of interest and VoCs. The combination with established nanopore sequencing procedures allows both the rapid confirmation by whole genome sequencing as well as the sensitive identification of newly emerging variants of this pandemic β-coronavirus in years to come.

2021 年 11 月 26 日，世界卫生组织将 B.1.1.529 归类为严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 关注变种 (VoC)，命名为 omicron。过去几周有报道称，传统 SARS-CoV-2 PCR 系统中的Spike基因丢失，作为识别 omicron 的间接诊断证据。在此，我们报告了针对刺突基因中严重突变位点的特异性 PCR 与基于纳米孔的全长基因组测序的组合，用于快速、灵敏地识别 11 月在德国诊断出的首批 4 名感染 omicron 的 COVID-19患者2021 年 2 月 28 日。这项研究将有助于对这种具有前所未有的体液免疫逃逸程度的高度传染性 VoC 进行明确的实验室诊断和全球监测。此外，我们建议专业诊断实验室应不断更新 SARS-CoV-2刺突基因中变异特异性 PCR 的检测方法，以便轻松检测和诊断感兴趣的新出现变异和 VoC。与已建立的纳米孔测序程序相结合，既可以通过全基因组测序进行快速确认，也可以在未来几年内灵敏地识别这种大流行性β冠状病毒的新出现的变种。