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Here, we report the combination of PCRs specific for heavily mutated sites in the<jats:italic>spike<\/jats:italic>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<jats:italic>spike<\/jats:italic>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 \u03b2-coronavirus in years to come.<\/jats:p>","DOI":"10.1007\/s00430-022-00728-7","type":"journal-article","created":{"date-parts":[[2022,1,21]],"date-time":"2022-01-21T15:02:34Z","timestamp":1642777354000},"page":"71-77","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Rapid and sensitive identification of omicron by variant-specific PCR and nanopore sequencing: paradigm for diagnostics of emerging SARS-CoV-2 variants"],"prefix":"10.1007","volume":"211","author":[{"given":"Christopher","family":"D\u00e4chert","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7016-0470","authenticated-orcid":false,"given":"Maximilian","family":"Muenchhoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4435-6861","authenticated-orcid":false,"given":"Alexander","family":"Graf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna","family":"Autenrieth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabine","family":"Bender","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helga","family":"Mairhofer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0942-0637","authenticated-orcid":false,"given":"Paul R.","family":"Wratil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Thieme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5112-9507","authenticated-orcid":false,"given":"Stefan","family":"Krebs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natascha","family":"Grzimek-Koschewa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3994-2332","authenticated-orcid":false,"given":"Helmut","family":"Blum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1384-8946","authenticated-orcid":false,"given":"Oliver T.","family":"Keppler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,21]]},"reference":[{"key":"728_CR1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.27561","author":"RK Mohapatra","year":"2021","unstructured":"Mohapatra RK, Sarangi AK, Kandi V et al (2021) Omicron (B.1.1.529 variant of SARS-CoV-2); an emerging threat: current global scenario. 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