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.
Publisher
Public Library of Science (PLoS)
Reference21 articles.
1. WHO.int [Internet]. Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern [cited 2021 November 26]. Available from: https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
2. outbreak.info [Internet]. A standardized, open-source database of COVID-19 resources and epidemiology data [cited 2022 July 12]. Available from: https://outbreak.info/
3. WHO.int [Internet]. World Health Organisation [cited 2022 April 21]. Available from: https://www.who.int/
4. Mutational and phylogenetic analyses of the two lineages of the Omicron variant;S Majumdar;J Med Virol,2022
5. Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022.;J Fonager;Eurosurveillance.,2022
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