New SARS-CoV-2 variants have recently emerged in the UK, South Africa, and Brazil containing multiple mutations in the segment of the virus genome that encodes the spike protein.
AusDiagnostics’ two independent SARS-CoV-2 assays in respiratory MT-PCR panels were evaluated for mutations in priming sites with reference to the sequences of the UK, South Africa and Brazil SARS-CoV-2 variants.
Two out of 109 sequences in the UK variant clade B.1.1.7 (201.501Y.V1) had independent mutations in the AusDiagnostics priming sites. One out of 20 sequences in the South Africa variant clade B.1.351 (20H.501y.V2) had a mutation in one of the AusDiagnostics priming sites. Due to the position of these mutations, the two current SARS-CoV-2 assays will perform normally against the UK and South African variants.
AusDiagnostics SARS-CoV-2 assays should perform normally against the Brazilian variant as there are no nucleotide changes in the priming sites or in the amplicon compared to the reference strain.
AusDiagnostics continues to monitor the effects of emerging variants on its assays. A number of alternative assays for SARS-CoV-2 have already been validated which would enable a rapid response to future significant changes in the SARS-CoV-2 genome.
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