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. 2021 Aug:141:104906.
doi: 10.1016/j.jcv.2021.104906. Epub 2021 Jul 7.

Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory

Andreas Lind  1 , Regine Barlinn  1 , Elisabeth Toverud Landaas  2 , Lise Lima Andresen  1 , Kirsti Jakobsen  1 , Cathrine Fladeby  1 , Mariann Nilsen  1 , Pål Marius Bjørnstad  3 , Arvind Y M Sundaram  3 , Teodora Ribarska  3 , Fredrik Müller  2 , Gregor D Gilfillan  3 , Mona Holberg-Petersen  1
Affiliations

Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory

Andreas Lind et al. J Clin Virol. 2021 Aug.

Abstract

Objectives: The emerging SARS-CoV-2 variants of concern (VoC), B.1.1.7, B.1.351 and P.1, with increased transmission and/or immune evasion, emphasise the need for broad and rapid variant monitoring. Our high-volume laboratory introduced a PCR variant assay (Variant PCR) in January 2021 based on the protocol by Vogels et al. STUDY DESIGN: To assess whether Variant PCR could be used for rapid B.1.1.7, B.1.351 and P.1 screening, all positive SARS-CoV-2 airway samples were prospectively tested in parallel using both the Variant PCR and whole genome sequencing (WGS).

Results: In total 1,642 SARS-CoV-2 positive samples from individual patients were tested within a time span of 4 weeks. For all samples with valid results from both Variant PCR and WGS, no VoC was missed by Variant PCR (totalling 399 VoC detected). Conversely, all of the samples identified as "other lineages" (i.e., "non-VoC lineages") by the Variant PCR, were confirmed by WGS.

Conclusions: The Variant PCR based on the protocol by Vogels et al., is an effective method for rapid screening for VoC, applicable for most diagnostic laboratories within a pandemic setting. WGS is still required to confirm the identity of certain variants and for continuous surveillance of emerging VoC.

Keywords: B.1.1.7; B.1.351; P.1; SARS-CoV-2; Variants screening; Whole Genome Sequencing (WGS).

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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.

Figures

Fig 1
Fig. 1
Total number of SARS-CoV-2 positive samples (red bars), number of samples with the B.1.1.7 variant (blue bars) and % of the B.1.1.7 lineage of all positive samples (green line) on a daily basis from 25 January to 19 February (Observation period) and from 20 February to 7 March 2021 (Follow-up period) using Variant PCR.
See this image and copyright information in PMC

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