Comparison of SARS-CoV-2 Detection by Rapid Antigen and by Three Commercial RT-qPCR Tests: A Study from Martin University Hospital in Slovakia

Abstract

The global pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is having a tremendous impact on the global economy, health care systems and the lives of almost all people in the world. The Central European country of Slovakia reached one of the highest daily mortality rates per 100,000 inhabitants in the first 3 months of 2021, despite implementing strong prophylactic measures, lockdowns and repeated nationwide antigen testing. The present study reports a comparison of the performance of the Standard Q COVID-19 antigen test (SD Biosensor) with three commercial RT-qPCR kits (vDetect COVID-19-MultiplexDX, gb SARS-CoV-2 Multiplex-GENERI BIOTECH Ltd. and Genvinset COVID-19 [E]-BDR Diagnostics) in the detection of infected individuals among employees of the Martin University Hospital in Slovakia. Health care providers, such as doctors and nurses, are classified as “critical infrastructure”, and there is no doubt about the huge impact that incorrect results could have on patients. Out of 1231 samples, 14 were evaluated as positive for SARS-CoV-2 antigen presence, and all of them were confirmed by RT-qPCR kit 1 and kit 2. As another 26 samples had a signal in the E gene, these 40 samples were re-isolated and subsequently re-analysed using the three kits, which detected the virus in 22, 23 and 12 cases, respectively. The results point to a divergence not only between antigen and RT-qPCR tests, but also within the “gold standard” RT-qPCR testing. Performance analysis of the diagnostic antigen test showed the positive predictive value (PPV) to be 100% and negative predictive value (NPV) to be 98.10%, indicating that 1.90% of individuals with a negative result were, in fact, positive. If these data are extrapolated to the national level, where the mean daily number of antigen tests was 250,000 in April 2021, it points to over 4700 people per day being misinterpreted and posing a risk of virus shedding. While mean Ct values of the samples that were both antigen and RT-qPCR positive were about 20 (kit 1: 20.47 and 20.16 for Sarbeco E and RdRP, kit 2: 19.37 and 19.99 for Sarbeco E and RdRP and kit 3: 17.47 for ORF1b/RdRP), mean Ct values of the samples that were antigen-negative but RT-qPCR-positive were about 30 (kit 1: 30.67 and 30.00 for Sarbeco E and RdRP, kit 2: 29.86 and 31.01 for Sarbeco E and RdRP and kit 3: 27.47 for ORF1b/RdRP). It confirms the advantage of antigen test in detecting the most infectious individuals with a higher viral load. However, the reporting of Ct values is still a matter of ongoing debates and should not be conducted without normalisation to standardised controls of known concentration.

Duplex One-Step RT-qPCR Assays for Simultaneous Detection of Genomic and Subgenomic RNAs of SARS-CoV-2 Variants

“…Nidovirals, such as SARS-CoV-2, use discontinuous transcription of parts of their positive-sense RNA genomes to create a nested set of negative-sense sgRNAs that, in turn, serve as templates for transcription of mRNAs to encode virus structural and accessory proteins [ 10 , 42 ]. Assays available for detection of SARS-CoV-2 nucleic acids predominantly target genomic nucleic acids in either single or multiplex formats [ 15 , 17 , 18 , 21 , 44 , 45 , 46 ]. The main limitation of specifically detecting sgRNAs by RT-qPCR is unintended amplification of other shorter sgRNAs generated in the series of discontinuous transcripts.…”

Accuracy of rapid point-of-care antigen-based diagnostics for SARS-CoV-2: an updated systematic review and meta-analysis with meta regression analyzing influencing factors

“…However, 2 studies with IFU-conforming testing procedure on NP or AN/MT sample, still showed a low sensitivity. This quite likely results from the on average low viral load in 1 study [49], and the asymptomatic study population in the other [175]. On the contrary, compared to the other studies unusual high sensitivity was found in studies where average viral load was high [45, 84, 144, 145] or participants were mainly within the first week of symptom onset [42, 54, 135].…”

A virus preservation solution that inactivates the virus while maintaining the virus particle intact

“…Rapid and accurate diagnosis is crucial for successful outbreak containment. During the current COVID-19 public health emergency, the gold standard for the diagnosis of COVID-19 infection is the detection of viral RNA ( 14 , 15 ). Using homogeneous reaction through plasma technology, we developed a new virus preservation solution, focusing on the selection of high-efficiency anticoagulants, natural preservatives, low-toxicity cell membrane protectors, and osmotic pressure stabilizers.…”

“…This result further showed that viruses treated with our virus preservation solution had intact virus particles, making it easier to extract the nucleic acid of low copy number viruses and reducing false negatives. B (14,15). Using homogeneous reaction through plasma technology, we developed a new virus preservation solution, focusing on the selection of high-efficiency anticoagulants, natural preservatives, low-toxicity cell membrane protectors, and osmotic pressure stabilizers.…”