A localized small-scale external quality assessment (EQA) for PCR testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the molecular laboratories

The aim of this study was to estimate the PCR results for SARS-CoV-2 testing in 32 participating laboratories in a localized small-scale external quality assessment (EQA) scheme. EQA samples were distributed to the participants and detected immediately on the day of delivery. Qualitative results were submitted to the EQA provider, including negative or positive results along with cycle threshold (Ct) values for different target genes. Although the variability of Ct values differed among the laboratories in the EQA, a total of 32 (100 %) participants reported correct qualitative results. The study showed that the mean loads of N or E gene were higher than those of ORF1ab in SARS-CoV-2 RNA samples. Regardless of the analyzed gene target, the mean Ct values for weak positive and positive samples varied by fewer than 1.74 and 1.91 cycles, respectively. Less than 12 % of reported Ct values for ORF1ab and N genes deviated by more than ±4 cycles (maximum: −9.92 cycles), while none deviated by more than ±4 cycles for the E gene. The current EQA program can provide a robust practical basis for follow-up planning to conduct evaluations for SARS-CoV-2 PCR testing and other novel emerging pathogens in the future.