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Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).
Caza, Mélissa; Hogan, Catherine A; Jassem, Agatha; Prystajecky, Natalie; Hadzic, Amir; Wilmer, Amanda.
  • Caza M; Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada. Electronic address: Melissa.Caza@interiorhealth.ca.
  • Hogan CA; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Jassem A; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Prystajecky N; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Hadzic A; Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Wilmer A; Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
J Clin Virol ; 144: 104996, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1505745
ABSTRACT

BACKGROUND:

High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited.

OBJECTIVE:

This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene.

METHODS:

Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms.

RESULTS:

The clinical study revealed sensitivity of 100% (95% CI 99.27%-100%) and specificity of 100% (95% CI 98.99%-100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%-100%) and specificity of 100% (95% CI 93.73% - 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% - 100%) and specificity of 98.10% (95% CI 96.53% - 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted.

CONCLUSION:

The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Clin Virol Journal subject: Virology Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Clin Virol Journal subject: Virology Year: 2021 Document Type: Article