More and more rapid antigen tests for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) appear in the market with varying performance. The sensitivity of these tests heavily depends on the viral load, extrapolated by the threshold cycle (Ct). It is therefore essential to verify their performance before their inclusion in routine. The Coronavirus Ag Rapid Test Cassette Bio‐Rad, the GSD NovaGen SARS‐CoV‐2 (COVID‐19) Antigen Rapid Test, and the Aegle Coronavirus Ag Rapid Test Cassette were evaluated on 199 samples: 150 fresh samples from the routine and positive in quantitative reverse‐transcription polymerase chain reaction (RT‐qPCR), nine fresh samples negative in RT‐qPCR, and 40 frozen samples, taken before the discovery of SARS‐CoV‐2 but positive for other respiratory viruses. Positive RT‐qPCR samples were categorized according to their Ct: Ct < 20 (18.7%), ≥ 20–< 25 (27.3%), ≥ 25–< 30 (18.7%), ≥ 30–35 (17.3%), and > 35 (18.0%). Sensitivities (95% confidence interval) for Ct below 25 were 95.7% (92.4–98.9), 97.1% (94.4–99.8), and 97.1% (94.4–99.8) for GSD NovaGen, Bio‐Rad, and Aegle, respectively but drastically dropped when Ct exceeded 27. Among samples with previously diagnosed viruses, seven false‐positive results were found with GSD NovaGen only (specificity 85.7%). Equivalent, high sensitivities were observed with the highest viral load samples. The GSD NovaGen assay showed less specificity. Although the three kits tested in this study are inadequate for routine testing in a high throughput laboratory, they can help to quickly identify the most infectious patients and screen their close contacts in an environment where molecular tests are not readily available.
Introduction Following the emergence of SARS-CoV-2 variants of concern (VOCs) worldwide, it is important to monitor local epidemiology to better understand the occurrence of clusters, reinfections, or infection after vaccination. Detecting mutations by specific RT-qPCR is a rapid and affordable alternative to sequencing. However, care must be taken to ensure that the techniques used are up-to-date and adapted to the variants circulating in the studied population. Material and methods All samples tested positive for SARS-CoV-2 were screened for detection of mutations of the spike protein using the Novaplex™ SARS-CoV-2 Variants I Assay from week 11 of 2021. Target sought were deletion H69/V70 and mutations N501Y and E484 K. From week 18 we used in addition the new Novaplex™ SARS-CoV-2 Variants II Assay for samples with no targets found with the Variants I assay or with the mutation E484 K alone, in order to screen the mutations L452R, K417 N/T and W152C. Results Between weeks 11 and 25, 2239 positive samples out of 54317 were tested with the Variants I Assay. Between weeks 18 and 25, 94 samples met the criteria for being tested with the Variants II Assay. Of these, 47 had the L452R mutation without the W152C mutation, typical in the B.1.617 variant. At week 25, this profile was found in 45.5% of the samples and was the most frequent. Conclusion According to our observations, variant B.1.617 has become predominant in our institution and most probably in our region. In the absence of the use of the Variants II Assay, they would have been considered wild.
The occurrence of the COVID‐19 second‐wave outbreak in Europe has pushed laboratories performing molecular SARS‐CoV‐2 tests to increase their throughput and decrease the result rendering time. In this evaluation, we tested for the first time a new, extraction‐free, protocol with the Allplex SARS‐CoV‐2 Assay RT‐qPCR kit on a Nimbus platform. Ninety‐one samples, of which 71 previously tested positive with RT‐qPCR with extraction were immediately analyzed without extraction, using only a dilution and thermal shock protocol. The positive and negative percentage agreements were respectively 97.2% (95% confidence interval [CI]: 0.90–0.99) and 95.0% (95% CI: 0.76–0.99). The two false negatives observed were very weakly positive with the comparison method. Moderate variations in Ct of the targeted genes were observed (median ± 95% CI): E gene, +2.49 ± 0.44; N gene, +0.98 ± 0.54; RdRP/S genes, +2.64 ± 0.48. On the other hand, the number of tests performed within 24 h raised from 86.4% to 97.8%, the turn‐around time decreased from 19:18 to 09:03 (p < .0001), and the number of tests that can be performed per day doubled since this technique was introduced routinely in our laboratory.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.