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

Author(s)

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

• Document type: Journal article
• Source: JOURNAL OF MOLECULAR DIAGNOSTICS; v. 24, n. 5, p. 7-pg., 2022-05-12.

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. (J Mol Diagn 2022, 24: 455-461; https://doi.org/10.1016/ j.jmoldx.2022.02.001) (AU)

• FAPESP's process: 19/27803-2 - Immune-mediated mayaro virus protection from wild-type chikungunya virus infection
• Grantee: Rafael Rahal Guaragna Machado
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)