Easier, faster assay enables many more laboratories to identify COVID-19 variants

Date:
March 31, 2022
Source:
Elsevier
Summary:
Using a commercially available test and simplified process, any
laboratory that can run a real-time PCR assay can detect known
SARS-CoV- 2 variants in patient samples, researchers report.



FULL STORY ==========================================================================
A new study has found that the Novaplex SARS-CoV-2 Variant I, II, and
IV real- time PCR assays (from Seegene Technology) can reliably detect SARS-CoV-2 in patient samples and identify known variants of interest and concern. Results from the PCR assays were comparable to those from the
"gold standard" spike gene Sanger sequencing method. Researchers were also
able to successfully streamline testing and reduce cost and turnaround
time by processing samples without extracting RNA for testing. Their
findings appear in The Journal of Molecular Diagnostics,published by
Elsevier.


========================================================================== "Real-time PCR (RT-PCR) methodology for variant detection is accessible,
rapid, simpler, and accurate compared to traditional sequencing,"
said lead investigator Ping Ren, PhD, Department of Pathology,
University of Texas Medical Branch, Galveston, TX, USA. "Combining
an extraction-free processing method with RT-PCR technology can help laboratories without sequencing capabilities track circulating variants
and investigate variant-dependent effects on treatment efficacy and
disease severity." The I, II, and IV assays are designed to detect
genetic mutations associated with the alpha, beta, delta, and epsilon
variants of SARS-CoV-2. At the time of the study, the omicron variant
had not yet emerged. RNA was extracted from each sample for testing by
the Novaplex RT-PCR assays and Sanger sequencing. The samples were also directly tested without extraction of RNA by the Novaplex assays.

Of the 156 samples processed with RNA extraction, the RT-PCR assays
identified 109 variants. The results were 100% in agreement with the
Sanger sequencing test. The RNA extraction-free method was 91.7% as
sensitive as the traditional RNA extraction method. In samples with a
lower viral load, the extraction-free RT-PCR assays did not detect some mutations, presumably because of lower nucleic acid concentrations in
the original samples.

"A major limiting factor for molecular SARS-CoV-2 assays is the shortage
of RNA extraction reagents," explained co-lead author Marisa C. Nielsen,
PhD, Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA. "Conventional extraction remains a time-consuming
aspect of molecular diagnosis of SARS-CoV-2. Recent CDC guidance
recommends sequencing only for cases with a cycle threshold (Ct) value
lower than 28, which indicates a higher viral load, because sequencing
is less reliable in samples with lower viral loads." "Although lower sensitivity was observed with the extraction-free method, it still
represents a viable alternative," Dr. Nielsen added. "Spike sequencing
is still necessary for detecting new variants." RT-PCR assays can be
tailored to include additional representative genes as different variants emerge and allow for more accessible variant detection and monitoring to
inform public health and treatment decisions. While not included in this
study, assays are now available to identify omicron-specific mutations.

"Determining the SARS-CoV-2 variant in individual patient samples
can help guide treatment since some variants are more resistant to
current treatment regimens," Dr. Ren observed. "However, the potential
impact extends beyond individual patients and into the public health
realm. It is important to track variant spread as part of public health surveillance because of variant- dependent transmission, disease severity,
and treatment decisions.


========================================================================== Story Source: Materials provided by Elsevier. Note: Content may be edited
for style and length.


========================================================================== Journal Reference:
1. Marisa C. Nielsen, Rafael R.G. Machado, Brooke M. Mitchell, Allan J.

McConnell, Nehad I. Saada, Scott C. Weaver, Ping Ren. 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. The Journal of
Molecular Diagnostics, 2022; DOI: 10.1016/j.jmoldx.2022.02.001 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/03/220331151438.htm

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