A Qualitative RT-PCR Assay for the Specific Identification of the SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern

Abstract

Objectives: The aim of this study was to develop a RT-PCR assay for the specific detection of the SARS-CoV-2 Omicron variant as a rapid alternative to sequencing.

Methods: A RT-PCR was designed in silico and validated using characterised clinical samples containing Omicron (both BA.1 and BA.2 sub-lineages) and the Omicron synthetic RNA genome. As negative controls, SARS-CoV-2 positive clinical samples collected in May 2020, and synthetic RNA genomes of the isolate Wuhan Hu-1 and of the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Iota (B.1.526), Epsilon (B.1.429) and Delta (B.1.617.2) SARS-CoV-2 variants were used.

Results: Experiments performed using as templates the synthetic RNA genomes demonstrate the high specificity of the PCR-method for the SARS-CoV-2 Omicron variant. Despite the synthetic RNAs were used at high copy numbers, specific signal was mainly detected with the Omicron synthetic genome. Only a non-specific late signal was detected using the Alpha variant genome but these results were considered negligible as this variant has been replaced by the delta variant and it is not circulating anymore in the world. Using our method, we confirmed the presence of Omicron on clinical samples containing this variant but not other SARS-CoV-2 lineages. The method is highly sensitive and can detect up to 1 cp of the Omicron virus per µl.

Conclusions: The method presented here, in combination with other methods in use for detection of SARS-CoV-2, can be used for an early identification of Omicron variant.

Note:
Funding: This work was funded by the Joint Research Centre as part of its Work Programme that reflects the strategic objectives of the European Commission towards the fight against COVID-19.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: Exemption for review by the ethical committee system and informed consent was given by the Committee on Biomedical Research Ethics - Capital region in accordance with Danish law on assay development projects. The ethical approval was also under general informed consent of the university hospital of Geneva (HUG) for anonymized use of left over materials. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Keywords: RT-PCR, Coronavirus, SARS-CoV-2, Omicron, specific detection