Pitfalls in SARS-CoV-2 PCR diagnostics

Abstract

To combat the COVID-19 pandemic, millions of PCR tests are performed worldwide. Any deviation of the diagnostic sensitivity and specificity will reduce the predictive values of the test. Here, we report the occurrence of contaminations of commercial primers/probe sets with the SARS-CoV-2 target sequence of the RT-qPCR as an example for pitfalls during PCR diagnostics affecting diagnostic specificity. In several purchased in-house primers/probe sets, quantification cycle values as low as 17 were measured for negative control samples. However, there were also primers/probe sets that displayed very low-level contaminations, which were detected only during thorough internal validation. Hence, it appears imperative to pre-test each batch of reagents extensively before use in routine diagnosis, to avoid false-positive results and low positive predictive value in low-prevalence situations. As such, contaminations may have happened more widely, and COVID-19 diagnostic results should be re-assessed retrospectively to validate the epidemiological basis for control measures.

Keywords: COVID-19; contamination; coronavirus; diagnostics; pooling; real-time PCR; swab.

FIGURE 1

Real‐time RT‐PCR results generated by using two different batches of the identical in‐house primers and probe (Corman et al., 2020) in combination with two distinct PCR kits. RIC, RNA isolation control; NTC, no template control; PC, positive control; AgPath, AgPath‐ID™ One‐Step RT‐PCR kit (Thermo Fisher Scientific); SSIII, SuperScript III One‐Step RT‐PCR kit (Thermo Fisher Scientific)

FIGURE 2

Real‐time RT‐PCR results of samples that were tested either individually (black dots) or in pools consisting of one SARS‐CoV‐2‐positive and four negative samples (blue dots). RIC, RNA isolation control; NTC, no template control; PC, positive control; AgPath, AgPath‐ID™ One‐Step RT‐PCR kit (Thermo Fisher Scientific)