Alliance for Pandemic Preparedness

May 10, 2021

Precision Health Diagnostic and Surveillance Network Uses S Gene Target Failure (SGTF) Combined with Sequencing Technologies to Identify Emerging SARS-CoV-2 Variants

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  • [Pre-print, not peer-reviewed] A genomic surveillance algorithm developed to combine RT-PCR and sequencing technologies to identify SARS-CoV-2 variants of concern found the frequency of S Gene Target Failure (SGTF) exponentially to 47% and 48% by the last week of March 2021, in both Puerto Rico and US laboratories, respectively. SGTF is used as a proxy for the SARS-CoV-2 B.1.1.7 variant. This increase in SGTF prevalence was concurrent with an increase in variants of concern among all SARS-CoV-2 sequences from Puerto Rico uploaded to GISAID (n = 461). The frequency of the B.1.1.7 variant increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021. 

Guerrero-Preston et al. (May 7, 2021). Precision Health Diagnostic and Surveillance Network Uses S Gene Target Failure (SGTF) Combined with Sequencing Technologies to Identify Emerging SARS-CoV-2 Variants. Pre-print downloaded May 10 from https://doi.org/10.1101/2021.05.04.21256012