RNA was extracted from swabs using the QIAamp Viral RNA kit (Qiagen) according to the manufacturer’s instructions. Tissues were homogenized in RLT buffer and RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. For detection of viral RNA, 5 µl RNA was used in a one-step real-time RT-PCR against the N gene which detects genomic and subgenomic RNA17 using the Rotor-Gene probe kit (Qiagen) according to instructions of the manufacturer. In each run, standard dilutions of RNA standards counted by droplet digital PCR were run in parallel, to calculate copy numbers in the samples. A complete list of primers is shown in Supplementary Table 4.

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