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The Cycle Threshold (Ct) value of SARS-CoV-2 RT-PCRs is used as an indicator of viral load. Using a collection of 45 fresh nasopharyngeal samples collected on universal transport media, we compare the Ct value obtained with 2 RT-PCR assays, the Alinity M SARS-CoV-2, and the Alinity M RESP-4-Plex (Abbott Molecular, Des Plaines, Illinois, United States) processed on an Alinity M device. The assays are highly correlated; however, the Ct values were a median of 4.54 lower with the Alinity M RESP-4-Plex. This difference could be attributed to earlier detection of positivity by the Alinity M software rather than a difference in RT-PCR performances. The Ct-value of SARS-CoV-2 RT-PCRs should be interpreted with caution, taking into account the clinical context and pre-analytical and analytical findings.