S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021

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A novel variant of SARS-CoV-2, B.1.1.7, originally discovered in the UK, is rapidly overtaking wild-type SARS-CoV-2 globally,1 due to a substantial transmission advantage. This variant is estimated to be 40% to 80% more transmissible2 and 35% more lethal3 than the wild-type virus.

Deletion of amino acids 69 and 70 within the spike (S) gene of SARS-CoV-2 B.1.1.7, sometimes attributable to the N501Y mutation, can result in an undetectable S-gene target (S-gene target failure, SGTF) for some real-time reverse transcriptase-polymerase chain reaction (RT-PCR) testing methods.

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