First FDA-Authorized COVID-19 Test Identifies Specific SARS-CoV-2 Lineages

Growing concern over fast spreading, novel variants of the SARS-CoV-2 coronavirus, such as the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1, Brazil), Delta (B.1.617.2) and Omicron (B.1.1.529) strains, highlights the need for more sequencing to detect mutations quickly and prevent the spread of new strains. Now, the U.S. Food and Drug Administration (FDA) has authorized the first test for the identification and differentiation of SARS-CoV-2 Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages, which are genetic variations in circulating virus strains.

LabCorp Diagnostics (Burlington, NC, USA) has received an emergency use authorization (EUA) from the FDA for its VirSeq SARS-CoV-2 NGS Test on the PacBio Sequel II sequencing system. The system provides access to high throughput, cost effective, highly accurate long-read sequencing. VirSeq SARS-CoV-2 NGS Test can identify specific SARS-CoV-2 strains in patient samples.

The VirSeq SARS-CoV-2 NGS Test is a PacBio Sequel II-based whole genome sequencing assay used for the determination of PANGO lineage from extracted RNA of SARS-CoV-2 positive samples identified using Labcorp’s COVID-19 RT-PCR Test or Labcorp SARS-CoV-2 & Influenza A/B Assay. The SARS-CoV-2 probe set used in the assay contains ~1000 tiled Molecular Loop Inversion Probes (MIPS) designed to amplify RNA that has been reverse transcribed to cDNA from 99.6% of the SARS-CoV-2 genome with most bases covered by 22 MIPs. The product synthesized in-between the MIPS is enriched and has sample specific molecular barcodes added via amplification followed by sequencing.

The test could be used by health care providers if they believe, based on a patient medical history and other diagnostic information, that strain-specific information could help determine appropriate patient treatment. The test is not intended to be used in a primary diagnosis of SARS-CoV-2 infection, to confirm the presence of infection, or for identification of specific SARS-CoV-2 genomic mutations.

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