A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern

Randi Jessen, Line Nielsen, Nicolai Balle Larsen, Arieh Sierra Cohen, Vithiagaran Gunalan, Ellinor Marving, Alonzo Alfaro-Núñez, Charlotta Polacek, Anders Fomsgaard, Katja Spiess*, The Danish COVID-19 Genome Consortium (DCGC), Kasper S. Andersen (Medlem af forfattergruppering), Martin H. Andersen (Medlem af forfattergruppering), Amalie Berg (Medlem af forfattergruppering), Susanne R. Bielidt (Medlem af forfattergruppering), Sebastian M. Dall (Medlem af forfattergruppering), Erika Dvarionaite (Medlem af forfattergruppering), Susan H. Hansen (Medlem af forfattergruppering), Vibeke R. Jørgensen (Medlem af forfattergruppering), Rasmus H. Kirkegaard (Medlem af forfattergruppering)Wagma Saei (Medlem af forfattergruppering), Trine B. Nicolajsen (Medlem af forfattergruppering), Stine K. Østergaard (Medlem af forfattergruppering), Rasmus F. Brøndum (Medlem af forfattergruppering), Martin Bøgsted (Medlem af forfattergruppering), Katja Hose (Medlem af forfattergruppering), Tomer Sagi (Medlem af forfattergruppering), Miroslaw Pakanec (Medlem af forfattergruppering), David Fuglsang-Damgaard (Medlem af forfattergruppering), Mette Mølvadgaard (Medlem af forfattergruppering), Henrik Krarup (Medlem af forfattergruppering), Marc T.K. Nielsen (Medlem af forfattergruppering)


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Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.

TidsskriftPLOS ONE
Udgave nummer10
Antal sider12
StatusUdgivet - okt. 2022

Bibliografisk note

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© 2022 Jessen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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