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 - The Danish COVID-19 Genome Consortium (DCGC)
A2 - Andersen, Kasper S.
A2 - Andersen, Martin H.
A2 - Berg, Amalie
A2 - Bielidt, Susanne R.
A2 - Dall, Sebastian M.
A2 - Dvarionaite, Erika
A2 - Hansen, Susan H.
A2 - Jørgensen, Vibeke R.
A2 - Kirkegaard, Rasmus H.
A2 - Saei, Wagma
A2 - Nicolajsen, Trine B.
A2 - Østergaard, Stine K.
A2 - Brøndum, Rasmus F.
A2 - Bøgsted, Martin
A2 - Hose, Katja
A2 - Sagi, Tomer
A2 - Pakanec, Miroslaw
A2 - Fuglsang-Damgaard, David
A2 - Mølvadgaard, Mette
A2 - Krarup, Henrik
A2 - Nielsen, Marc T.K.
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 - 2022/10
Y1 - 2022/10
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.
UR - http://www.scopus.com/inward/record.url?scp=85139364519&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0274889
DO - 10.1371/journal.pone.0274889
M3 - Journal article
C2 - 36197885
AN - SCOPUS:85139364519
SN - 1932-6203
VL - 17
JO - PLOS ONE
JF - PLOS ONE
IS - 10
M1 - e0274889
ER -