19Laboratories are currently witnessing extraordinary demand globally for sampling devices, 20 reagents, consumables, and diagnostic instruments needed for timely diagnosis of SARS-CoV-2 21 infection. To meet diagnostic needs as the pandemic grows, the US Food and Drug 22 Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use 23 Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed 24 the first manufacturer-independent evaluation of the fully automated sample-to-result two-25 target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which 26 received US FDA EUA on March 12, 2020. The comparator was a standardized 3-hour SARS-CoV-27 2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a 28 two-target RT-PCR, which our laboratory has routinely used since January 2020 (Corman VM et 29 al. EuroSurveill 25(3):2000045). Cobas and the comparator showed overall agreement of 98.1% 30 and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized 31 retrospective samples. Immediate prospective head-to-head comparative evaluation followed 32 on 502 samples, and the diagnostic approaches showed overall percent agreement of 99.6% 33 and a kappa value of 0.98. A good correlation (r² = 0.96) between cycle threshold values for 34 SARS-CoV-2 specific targets obtained by cobas and the comparator was observed. Our results 35 showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal 36 swab samples collected in the UTM-RT system. Under the extraordinary circumstances that 37 laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 hours 38 and in the midst of the COVID-19 pandemic if carefully planned and executed. 39 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 3 40 Keywords: SARS-CoV-2, COVID-19, cobas, cobas 6800 41 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 58 12), followed by the launch of a range of commercial SARS-CoV-2 PCR-based assays in the last 3 59 months. Despite the fact that the US Food and Drug Administration (FDA) granted several 60 commercial SARS-CoV-2 amplification assays Emergency Use Authorization (EUA), as of March 61 29, 2020 no manufacturer-independent evaluation data for any commercial SARS-CoV-2 assay 62 with US FDA EUA is available in peer-reviewed literature. 63 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 5 Here we present the results of the first manufacturer-independent evaluation of the fully 64 automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular 65 Systems, Branchburg, NJ, USA), which received US FDA EUA on March 12, 2020. The 66 performance of cobas was first evaluated on a well-characterized in-house validation panel 67 consisting of 217 samples. The comparator was a standardized 3-hour SARS-CoV-2 detection 68 protocol, consisting of RNA extraction using an automated por...