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

Autor: Dächert C; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany., Muenchhoff M; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany., Graf A; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.; Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany., Autenrieth H; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany., Bender S; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany., Mairhofer H; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany., Wratil PR; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany., Thieme S; Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany., Krebs S; Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany., Grzimek-Koschewa N; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany., Blum H; Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany., Keppler OT; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany. keppler@mvp.lmu.de.
Jazyk: angličtina
Zdroj: Medical microbiology and immunology [Med Microbiol Immunol] 2022 Feb; Vol. 211 (1), pp. 71-77. Date of Electronic Publication: 2022 Jan 21.
DOI: 10.1007/s00430-022-00728-7
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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