ABSTRACT
The circulation of certain SARS-CoV-2 variants may have a great impact on the epidemiological status of a geographical area; therefore, it is important that their presence is monitored. Currently, the gold standard method used to identify newly emerged variants is sequencing of either genes or whole genomes. However, since this method is relatively expensive and has a long turnaround time, other rapid strategies should also be employed. The current study aimed to evaluate the performance of the Simplexa® SARS-CoV-2 Variants Direct assay, which is a RT-PCR that determines the variant present in a nasopharyngeal swab sample in approximately two hours. Totally, 527 positive samples for SARS-CoV-2 were analyzed from January until December 2022 and next-generation sequencing (NGS) was used as the reference method. The assay showed high sensitivity, ranging from 94.12 % to 100 %, depending on the variant. The assay also showed high specificity, reaching 100 % for Delta and BA.1 variants, and 99.74 % and 98.67 % for BA.2 and BA.4/BA.5 variants, respectively. Moreover, the assay was able to identify the correct variant category in the presence of any subvariant in the sample. We conclude that the assay can be used to facilitate faster monitoring of circulating SARS-CoV-2 variants, however sequencing cannot be completely replaced, since new variants always emerge, and constant updates are needed, so that the user is able to interpret the melting curve patterns.
ABSTRACT
The SARS-CoV-2 pandemic led to an urgent need for rapid diagnostic testing in order to inform timely patients' management. This study aimed to assess the performance of the STANDARD™ M10 SARS-CoV-2 assay as a diagnostic tool for COVID-19. A total of 400 nasopharyngeal or oropharyngeal swabs were tested against a reference real-time RT-PCR, including 200 positive samples spanning the full range of observed Ct values. The sensitivity of the STANDARD™ M10 SARS-CoV-2 assay was 98.00% (95% CI 94.96% to 99.45%, 196/200), while the specificity was also estimated at 97.50% (95% CI 94.26% to 99.18%, 195/200). The assay proved highly efficient for the detection of SARS-CoV-2, even in samples with low viral load (Ct>25), presenting lower Ct values compared to the reference method. We concluded that the STANDARD™ M10 SARS-CoV-2 assay has a similar performance compared to the reference method and other molecular point-of-care assays and can be a valuable tool for rapid and accurate diagnosis.