Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory.
Andreas Lind, Regine Barlinn, Elisabeth Toverud Landaas, Lise Lima Andresen, Kirsti Jakobsen, Cathrine Fladeby, Mariann Nilsen, P��l Marius Bj��rnstad, Arvind Y M Sundaram, Teodora Ribarska, Fredrik M��ller, Gregor D Gilfillan, Mona Holberg-Petersen
Author Information
Andreas Lind: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
Regine Barlinn: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
Elisabeth Toverud Landaas: Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
Lise Lima Andresen: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
Kirsti Jakobsen: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
Cathrine Fladeby: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
Mariann Nilsen: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
P��l Marius Bj��rnstad: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
Arvind Y M Sundaram: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
Teodora Ribarska: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
Fredrik M��ller: Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
Gregor D Gilfillan: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
Mona Holberg-Petersen: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
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.
