Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection-Results Questioning Previous Observations

Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation

Although infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) does not appear to be as serious a threat to public health as it was in 2020-2021, the increased transmissibility of multiple Omicron descendants may constitute a continuous challenge for health care systems, and reliable detection of new variants is still imperative. This study evaluates the performance of three SARS-CoV-2 diagnostic tests: Novel Coronavirus (2019-nCoV) Real Time Multiplex RT-PCR Kit (Liferiver); Vitassay qPCR SARS-CoV-2 (Vitaassay) and TaqPath COVID‑19 CE-IVD RT-PCR Kit (Thermo Fisher Scientific). The analytical sensitivity of the assays as well as their specificity were determined with the use of synthetic nucleic acid standards and clinical samples. All assays appeared to be 100% specific for SARS-CoV-2 RNA in general and the Omicron variant in particular. The LOD determined during this validation was 10 viral RNA copies/reaction for Liferiver and TaqPath and 100 viral RNA copies for Vitassay. We cannot exclude that the LOD for the Vitassay might be lower and close to the manufacturer's declared value of ≥ 20 genome copies/reaction, as we obtained 90% positive results for 10 viral RNA copies/reaction. Mean Ct values at the concentration of 10 viral RNA copies/reaction for the Liferiver, Vitassay and TaqPath kits (35, 37 and 33, respectively) were significantly lower than the cutoff values declared by the manufacturers (≤ 41, ≤ 40 and ≤ 37, respectively). We suggest reporting outcomes based on LOD and cutoff Ct values determined during internal validation rather than those declared by the assays' producers.

Comparison of Abbott ID NOW COVID-19 Rapid Molecular Assay to Allplex 2019-nCoV and VIASURE SARS-CoV-2 Detection in Nasal Swabs

BACKGROUND: Readily available, accurate, and rapid diagnostic technologies are of high priority to contain emerging and re-emerging pandemics and to properly allocate personal protective equipment usage and preventing nosocomial spread with subsequent community transmission. Detection of positive 2019-nCoV nucleic acids by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR)-based assays remains the gold standard for COVID-19 diagnostics. However, these assays take an average over 3–5 h to generate results and the PCR tests require certified laboratories, expensive equipment, and trained technicians to operate. Therefore, there is an urgent need for rapid point of care molecular tests that can be readily used in a healthcare setting that generates reliable results within few hours. Those tests should provide reliable results in the setting to facilitate the diagnosis and rapid decision-making. AIM: The present study aimed to evaluate the diagnostic performance of Abbott ID NOW SARS-CoV-2 compared to two gold standard assays (Allplex 2019- nCoV and VIASURE SARS-CoV-2) and to detect the relation between viral load and the sensitivity of ID NOW SARS-CoV-2 assay. METHODS: A total of 86 and 42 nasopharyngeal swabs collected from patients attending the Reference Laboratory of Egyptian University Hospitals during the period from January 2022 to May 2022, were tested by our reference methods of RT-PCR for COVID-19 detection; VIASURE kit and Allplex kits, respectively. Corresponding dry nasal swabs were collected from the same patients for ID NOW SARS-CoV-2 ribonucleic acid (RNA) detection assay. RESULTS: As regards the results of the 86 nasopharyngeal swabs tested by both VIASURE kit and ID NOW, there was a good agreement between both methods (95%) (kappa = 0.924), where the ID NOW method was not able to detect three COVID-19-positive samples (3/86, 5.1%). ID NOW exhibited specificity and sensitivity of 100% and 94.9%, respectively. As for comparing results of ID NOW with Allplex kit, the results of the 42 nasopharyngeal swabs tested by both tests revealed good agreement between both methods (kappa = 0.908). In comparison with Allplex kit, ID NOW exhibited specificity and sensitivity of 90% and 100%, respectively. Regarding the relation between the viral load detected by VIASURE kit and results of the ID NOW test, we found that ID NOW showed a sensitivity of 82.35% in samples with low viral load (CT > 30), while for samples with intermediate (CT: 20–30) and high (CT < 20) viral loads, sensitivity was 100%. CONCLUSION: ID NOW assay in our study exhibited a high diagnostic performance when evaluated with the gold standard RT-PCR methods. Our study further substantiates the high sensitivity of ID NOW in the presence of intermediate and high viral loads detected by molecular RT-PCR SARS-CoV-2 testing. Its analytical performances, combined with the very short 13 min reactional time and the friendly device-guided handling procedure, constitute an additional advantage of ID NOW COVID-19 for setting up a rapid diagnosis within the clinical laboratories and for timely identification of outbreaks allowing for aggressive contact tracing and containment.