RNA from fresh samples was reverse-transcribed using a single-step RT-qPCR (GoTaq 1-Step RT-qPCR; Promega, Fitchburg, WI, USA) on a CFX96 instrument (Bio-Rad, Hercules, CA, USA) using TaqMan probes specifically designed to target two regions of the nucleocapsid (N) gene of SARS-CoV-2 (2019-nCoV CDC qPCR Probe Assay emergency kit; IDT, Coralville, IA, USA), together with primers and probes for the human RNase P gene.
On FFPE samples, SARS-CoV-2 detection was performed using the CE-IVD Logix Smart COVID-19 kit (Co-Diagnostics, Salt Lake City, UT, USA), as previously described [20 (link)]. To avoid false-negative results, each sample was retested using SARS-CoV-2 RNA digital droplet PCR (ddPCR; QX200, Bio-Rad, Hercules, CA, USA) with CDC-approved primers and probes (Integrated DNA Technologies, Coralville, IA, USA), as previously described [21 (link)].
On FFPE samples, SARS-CoV-2 detection was performed using the CE-IVD Logix Smart COVID-19 kit (Co-Diagnostics, Salt Lake City, UT, USA), as previously described [20 (link)]. To avoid false-negative results, each sample was retested using SARS-CoV-2 RNA digital droplet PCR (ddPCR; QX200, Bio-Rad, Hercules, CA, USA) with CDC-approved primers and probes (Integrated DNA Technologies, Coralville, IA, USA), as previously described [21 (link)].
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