Real-life head-to-head comparison of performance of two high-throughput automated assays for detection of SARS-CoV-2 RNA in nasopharyngeal swabs: the Alinity m SARS-CoV-2 and cobas 6800 SARS-CoV-2 assays

Kogoj, Rok; Kmetič, Petra; Valenčak, Anja Oštrbenk; Komloš, Kristina Fujs; Seme, Katja; Sagadin, Martin; Korva, Miša; Poljak, Mario

Abbott’s Alinity m is a recently launched fully integrated, automated molecular analyzer allowing continuous loading of samples and sample-to-result molecular detection of several microorganisms. Manufacturer-independent clinical evaluation of Alinity m SARS-CoV-2 (Alinity) against cobas 6800 SARS-CoV-2 (cobas) as a standard comparator was performed on 2,157 consecutive nasopharyngeal swabs. Valid initial results of Alinity and cobas were obtained from 2,129/2,157 (98.7%) and 2,157/2,157 (100%) samples, respectively. Overall percent agreement of 98.3% (2,092/2,129; 95%CI:97.6–98.7%), positive percent agreement of 100.0% (961/961; 95%CI:99.6–100.0%), negative percent agreement of 96.8% (1,131/1,168; 95%CI:95.7–97.7%), and a high kappa value of 0.965 (95%CI:0.954–0.976) were observed on 2,129 samples with valid results for both assays. There were 37 discordant results and based on discordant analyses, including previous and/or follow-up PCR results, 22 could be considered Alinity analytically true positive with high probability. Due to the lack of additional information and inability of repeated/further testing, the status of the remaining 15 discordant samples remains unresolved. Comparative real-life throughput of both analyzers assessed while testing 564 samples in parallel across two 8-hour shifts and comparative turnaround time assessment measured while processing in parallel the first 94 routine samples received in the laboratory each working day for 5 consecutive days showed similar real-life performance of both analyzers with certain differences, which has potential importance in some laboratory settings.