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Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023. | LitMetric

AI Article Synopsis

  • * The Alpha variant, which emerged in late 2020, featured a S-gene deletion leading to a testing anomaly called S-gene target failure (SGTF).
  • * Recently, the XBB.1.5 sublineage with S-gene target presence (SGTP) has emerged, showing rapid growth in the northeastern U.S. during the dominance of the Omicron BA.5 variants exhibiting SGTF.

Article Abstract

Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a spike gene (S-gene) deletion (Δ69-70) in the N-terminal region, which might compensate for immune escape mutations that impair infectivity (1), resulted in reduced or failed S-gene target amplification in certain multitarget reverse transcription-polymerase chain reaction (RT-PCR) assays, a pattern referred to as S-gene target failure (SGTF) (2). The predominant U.S. SARS-CoV-2 lineages have generally alternated between SGTF and S-gene target presence (SGTP), which alongside genomic sequencing, has facilitated early monitoring of emerging variants. During a period when Omicron BA.5-related sublineages (which exhibit SGTF) predominated, an XBB.1.5 sublineage with SGTP has rapidly expanded in the northeastern United States and other regions.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9927069PMC
http://dx.doi.org/10.15585/mmwr.mm7205e2DOI Listing

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