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

The Danish COVID-19 Genome Consortium (DCGC)

doi:10.1371/journal.pone.0274889

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

The Danish COVID-19 Genome Consortium (DCGC)

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5 Citations (Scopus)

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Abstract

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.

Original language	English
Article number	e0274889
Journal	PLoS ONE
Volume	17
Issue number	10
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0274889
Publication status	Published - 2022

Bibliographical note

Publisher Copyright:
© 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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Cite this

@article{314912c00dc14718ad655afe08511712,

title = "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",

abstract = "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.",

author = "Randi Jessen and Line Nielsen and Larsen, {Nicolai Balle} and Cohen, {Arieh Sierra} and Vithiagaran Gunalan and Ellinor Marving and Alonzo Alfaro-N{\'u}{\~n}ez and Charlotta Polacek and Anders Fomsgaard and Katja Spiess and Ari, {Halenur Bayhan} and Kristina Finneisen and Benfeldt, {Caroline M{\o}lsted} and Andersen, {Kasper S.} and Andersen, {Martin H.} and Amalie Berg and Bielidt, {Susanne R.} and Dall, {Sebastian M.} and Erika Dvarionaite and Hansen, {Susan H.} and J{\o}rgensen, {Vibeke R.} and Kirkegaard, {Rasmus H.} and Wagma Saei and Nicolajsen, {Trine B.} and {\O}stergaard, {Stine K.} and Br{\o}ndum, {Rasmus F.} and Martin B{\o}gsted and Katja Hose and Tomer Sagi and Miroslaw Pakanec and David Fuglsang-Damgaard and Mette M{\o}lvadgaard and Henrik Krarup and Svarrer, {Christina W.} and Christiansen, {Mette T.} and Berit Lilje and Tang, {Man Hung E.} and Ng, {Kim L.} and Edslev, {Sofie M.} and Schneider, {Uffe V.} and Pedersen, {Martin S.} and Kristian Sch{\o}nning and Lene Nielsen and Nilsson, {Line L.} and Friis, {Martin B.} and Thomas Sundelin and Hansen, {Thomas A.} and Skov, {Marianne N.} and Anders Jensen and Andersen, {Dorte T.} and {The Danish COVID-19 Genome Consortium (DCGC)}",

note = "Publisher Copyright: {\textcopyright} 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.",

year = "2022",

doi = "10.1371/journal.pone.0274889",

language = "English",

volume = "17",

journal = "PLoS ONE",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "10 ",

}

TY - JOUR

T1 - 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

AU - Jessen, Randi

AU - Nielsen, Line

AU - Larsen, Nicolai Balle

AU - Cohen, Arieh Sierra

AU - Gunalan, Vithiagaran

AU - Marving, Ellinor

AU - Alfaro-Núñez, Alonzo

AU - Polacek, Charlotta

AU - Fomsgaard, Anders

AU - Spiess, Katja

AU - Ari, Halenur Bayhan

AU - Finneisen, Kristina

AU - Benfeldt, Caroline Mølsted

AU - Andersen, Kasper S.

AU - Andersen, Martin H.

AU - Berg, Amalie

AU - Bielidt, Susanne R.

AU - Dall, Sebastian M.

AU - Dvarionaite, Erika

AU - Hansen, Susan H.

AU - Jørgensen, Vibeke R.

AU - Kirkegaard, Rasmus H.

AU - Saei, Wagma

AU - Nicolajsen, Trine B.

AU - Østergaard, Stine K.

AU - Brøndum, Rasmus F.

AU - Bøgsted, Martin

AU - Hose, Katja

AU - Sagi, Tomer

AU - Pakanec, Miroslaw

AU - Fuglsang-Damgaard, David

AU - Mølvadgaard, Mette

AU - Krarup, Henrik

AU - Svarrer, Christina W.

AU - Christiansen, Mette T.

AU - Lilje, Berit

AU - Tang, Man Hung E.

AU - Ng, Kim L.

AU - Edslev, Sofie M.

AU - Schneider, Uffe V.

AU - Pedersen, Martin S.

AU - Schønning, Kristian

AU - Nielsen, Lene

AU - Nilsson, Line L.

AU - Friis, Martin B.

AU - Sundelin, Thomas

AU - Hansen, Thomas A.

AU - Skov, Marianne N.

AU - Jensen, Anders

AU - Andersen, Dorte T.

AU - The Danish COVID-19 Genome Consortium (DCGC)

N1 - Publisher Copyright: © 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.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

U2 - 10.1371/journal.pone.0274889

DO - 10.1371/journal.pone.0274889

M3 - Journal article

C2 - 36197885

AN - SCOPUS:85139364519

VL - 17

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 10

M1 - e0274889

ER -