Rapid and sensitive identification of omicron by variant-specific PCR and nanopore sequencing: paradigm for diagnostics of emerging SARS-CoV-2 variants

• DOI: 10.1007/s00430-022-00728-7
• Publication Date: 2022-01-21T15:02:34Z
• Authors: Christopher Dächert; Maximilian Muench...; Alexander Graf; Hanna Autenrieth; Sabine Bender; Helga Mairhofer; Paul R. Wratil; Susanne Thieme; Stefan Krebs; Natascha Grzimek-...; Helmut Blum; Oliver T. Keppler
• Keywords: Molecular diagnostics; Identification; 2019-20 coronavirus outbreak

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 last weeks indirect diagnostic evidence for identification Here, we report combination PCRs specific heavily mutated sites spike gene and nanopore-based full-length genome sequencing rapid sensitive first four COVID-19 patients diagnosed Germany to be infected with omicron on 28, 2021. This study will assist unambiguous laboratory-based diagnosis global surveillance this highly contagious VoC an unprecedented degree humoral immune escape. Moreover, propose that specialized laboratories should continuously update their assays variant-specific readily detect diagnose emerging variants interest VoCs. The established nanopore procedures allows both confirmation by whole well newly pandemic β-coronavirus years come.