SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence

Abstract

Introduction RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets. Methods 260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed. Results In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target. Conclusion We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.

Starting from scratch: Step-by-step development of diagnostic tests for SARS-CoV-2 detection by RT-LAMP

“…In this regard, we observed a discrepancy between CDC and Berlin positive results (59% and 34%, respectively) using RNA extracted from saliva samples ( Table 1 ). According to a previous study, four WHO approved RT-PCR diagnostic protocols for SARS-CoV-2 (including those used in our study) showed discordant results in almost 30% of cases evaluated [ 74 ]. Additionally, Berlin RdRp-SARSr primers-probe set has been reported to show low sensitivity compared with other primers-probe sets [ 75 ].…”

Sensing of COVID-19 spike protein in nasopharyngeal samples using a portable surface plasmon resonance diagnostic system

“…It has to be kept in mind that there is considerable variability in Ct values of a given concentration when using different primers and probes and the IP4 assay used here gives relatively high Ct values compared to some other techniques. 43 The most diluted solution (Figure 4a) has in our case a Ct The sensor was tested in addition for its selectivity in discriminating between SARS-CoV-2…”

Analytical performance of rapid nucleic acid detection assays and routine RT-qPCR assays for detection of SARS-CoV-2 in Shanghai, China in 2022

“…Overall, ORF1ab was more likely to go undetected, leading to discrepancies in the results of 2 targets of the same assay ( Table 1 ). Similarly, Gdoura et al reported that 94.9% of the discrepancy in the results of the DaAn assay were caused by a single positive amplification of the N when detecting the Alpha variant [23] . On the contrary, Wang et al identified more mutations to the targets of probes and/or primers based on the N versus the E and RdRp sequences of the ORF1ab fragment [24] .…”