A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants

Marisa C. Nielsen, Rafael R.G. Machado, Brooke M. Mitchell, Allan J. McConnell, Nehad I. Saada, Scott C. Weaver, Ping Ren

Research output: Contribution to journalArticlepeer-review

Abstract

Tracking new and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become increasingly important for public health responses, primarily because of variant-dependent transmission, disease severity, and treatment decisions. This evaluation compared Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV (I,II&IV) assays to detect known SARS-CoV-2 variants using traditional spike gene Sanger sequencing results as the gold standard reference. Both RNA extraction and extraction-free protocols were assessed. A total of 156 samples were included in this study. There was 100% (109/109) overall agreement (95% CI, 96.7%–100%) between the spike gene sequencing and the I,II&IV results using extracted RNA for the variants included in the Novaplex assay menus. The RNA extraction-free method was 91.7% (143/156) as sensitive (95% CI, 86.2%–95.5%) as the traditional RNA extraction method. Using the extraction-free method on samples with higher cycle threshold values (>30) resulted in some mutations not being detected, presumably due to lower nucleic acid concentrations in the original samples. In conclusion, the I,II&IV assays provide an accurate, rapid, and less labor-intensive method for detecting SARS-CoV-2 and identifying known variants of interest and concern. The RNA extraction-free method for samples with cycle threshold of <30 could be cost-effective for surveillance purposes. However, spike gene sequencing retains the advantage of detecting more and new variants.

Original languageEnglish (US)
Pages (from-to)455-461
Number of pages7
JournalJournal of Molecular Diagnostics
Volume24
Issue number5
DOIs
StatePublished - May 2022

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

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