Abstract
The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
Highlights
We retrospectively examined a multi‐variant panel (n = 72) of SARS‐CoV‐2‐positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild‐type strains circulating in Liguria (Italy) from January to August 2021
Specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS‐CoV‐2 Variants II Assay Allplex, UltraGene Assay SARS‐CoV‐2 452R & 484K & 484Q Mutations V1, COVID‐19 Ultra Variant Catcher, SARS‐CoV‐2 Extended ELITe MGB and Simplexa SARS‐CoV‐2 Variants Direct
Since the onset of the coronavirus disease 2019 (COVID‐19) pandemic, multiple emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) have been identified, but only some of these have a high degree of global public health significance [1,2]
Summary
Since the onset of the coronavirus disease 2019 (COVID‐19) pandemic, multiple emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) have been identified, but only some of these have a high degree of global public health significance [1,2]. VOIs present genetic changes that could affect some virus features, such as transmissibility; disease severity; and immune, diagnostic and therapeutic escapes. The increase in virus transmission observed in multiple countries suggests that these variants could be an emerging risk to global public health [2]. VUMs are variants with important substitutions that affect viral characteristics without any evidence of phenotypic or epidemiological impact. These variants, including those previously designated as VOCs or VOIs, present a minor threat to public health [2]
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