In Silico Design of Specific Primer Sets for the Detection of B.1.1.529 SARS-CoV-2 Variant of Concern (Omicron)

On 26 November 2021, the World Health Organization (WHO) classified variant B.1.1.529, reported earlier by the South African authorities as “Variant of Concern” with the name Omicron. The decision was taken because Omicron is bearing a number of mutations with a potential impact on its transmissibility, severity of disease following infection, as well as on the effectiveness of immune protection resulting from both vaccines and natural infection. In this paper, we present an in silico developed RT-PCR based detection method (named OmMet) that was designed to be highly specific for the detection of the Omicron variant. Bioinformatic prediction tests demonstrate that the sequences in the primer sets are highly accurate, and do not match with genetic sequences of other viruses, including other coronaviruses or SARS-CoV-2 variants. The methodology presented does not rely on S-gene target failure (SGTF) of existing RT-PCR assays, widely used currently, but allows the direct specific identification of the variant B.1.1.529 (Omicron).