Rapid screening for SARS-CoV-2 VOC Alpha (202012/01, B.1.1.7) using the Allplex SARS-CoV-2 / FluA / FluB / RSV test

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Int J Infect Dis. October 7, 2021: S1201-9712 ​​(21) 00792-X. doi: 10.1016 / j.ijid.2021.10.005. Online ahead of print.

ABSTRACT

BACKGROUND: The emergence of variants of SARS-CoV-2 (VOC) of concern for increased transmissibility and potentially capable of evading the immune system, warrants for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR tests for routine diagnostic purposes, leading to particular profiles that can be used for rapid variant screening. In this work, we report a particular profile observed with the Allplex ™ SARS-CoV-2 / FluA / FluB / RSV and VOC Alpha assay (202012/01, line B.1.1.7, also named VOC-UK), which was the first SARS-CoV-2 VOC identified.

METHODS: Samples were analyzed by two RT-qPCR assays: the Allplex ™ SARS-CoV-2 / FluA / FluB / RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT- PCR (Thermo Fisher Scientifics, USA). Definition of the SARS-CoV-2 variant was achieved by Sanger sequencing of relevant regions of the S gene and, in some cases, whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION ( Oxford Nanopore Technologies, Oxford, United Kingdom) or a MiSeq ILLUMINA platform (San Diego, California, United States).

RESULTS: Of 173 SARS-CoV-2 positive samples, all of the B.1.1.7 line (N = 71) showed a mean difference in Cq between the N and S gene of + 11 ± 2 (range, +8 / + 15). None of the other specimens, including several different lineages (wild type for the regions analyzed, N = 22; Gamma, N = 63; Delta, N = 9; B.1.258, N = 3; B.1.160, N = 3; B.1.177.7, N = 1; B.1.1.420, N = 1), showed a similar difference in the values ​​of Cq.

CONCLUSIONS: The particular pattern of delayed N gene positivity could provide a practical method for screening for Alpha VOCs, concurrent with viral detection, when using the Allplex ™ SARS-CoV-2 / FluA / FluB / RSV assay.

IDPM: 34628023 | DOI: 10.1016 / j.ijid.2021.10.005


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