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. 2022 Feb:300:114428.
doi: 10.1016/j.jviromet.2021.114428. Epub 2021 Dec 11.

Utility of a commercial RT-qPCR assay to detect SARS-CoV-2 gene variations as an indicator of lineages

Camino Trobajo-Sanmartín  1 , Ana Miqueleiz  2 , María Eugenia Portillo  2 , Miguel Fernández-Huerta  2 , Ana Navascués  2 , Jesús Castilla  3 , Carmen Ezpeleta  2
Affiliations

Utility of a commercial RT-qPCR assay to detect SARS-CoV-2 gene variations as an indicator of lineages

Camino Trobajo-Sanmartín et al. J Virol Methods. 2022 Feb.

Abstract

Background: The World Health Organization (WHO) recommended RT-qPCR tests as the reference technique for SARS-CoV-2 molecular detection, however with the rapid spread of the infection, mutations in specific RT-qPCR target regions have been widely described could allow the presumptive identification.

Objective: In this study, we evaluated the analytical performance of the Allplex™SARS-CoV-2/FluA/FluB/RSV assay for the additional presumptive identification of SARS-CoV-2 variants in a real-life setting.

Results: We observed gene-specific changes in the cycle threshold (Ct) of the N and RdRp genes compared with the Ct yielded for the S gene when the SARS-CoV-2 testing was performed Allplex™SARS-CoV-2/FluA/FluB/RSV assay. Seventeen samples showed Ct variations in the N and/or RdRp. In 10 cases, the N gene was affected, delayed or negative and in 14 cases, the RdRp gene showed a delay or negative concerning the S gene. A delay in the Ct of both genes (RdRp and N) was observed in six cases. Sequencing determined that all samples identified as B.1.1.7 showed changes in the PCR curves of the N and RdRp. However, samples identified as B.1.177 only showed variations for the RdRp gene.

Conclusions: Allplex™SARS-CoV-2/FluA/FluB/RSV assay, the diagnosis could presumably allow the rapid assignment of lineages B.1.1.7 and B.1.177, and emphasizes the importance of exhaustive surveillance for circulating variants of the SARS-CoV-2 virus to reduce community transmission.

Keywords: N gene; RdRp gene; SARS-CoV-2; Variants.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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