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

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 transmissible 2 and 35% more lethal 3 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.A rapid increase in the proportion of SARS-CoV-2 samples with SGTF was identified in regions of England affected by B.1.1.7,and, after validation with whole genome sequencing, SGTF was determined to be a reliable marker of B.1.1.7 across the country. 2 To quantify the spread of B.1.1.7 in the Greater Toronto Area, we tracked SGTF prevalence between December 2020 and March 2021.