design: RNA was extracted from bronchoalveolar lavage fluid pool using NucleoSpin Virus (CL) from Macherey-Nagel or Quick-DNA/RNA Miniprep Plus Kit (CML) from Zymo-Research and retrotranscribed in cDNA. Librairies were prepared using both the Ligation Sequencing Kit (SQK-LSK109) and the Native Barcoding Expansion kit (EXP-NBD104) from Oxford Nanopore Technologies and sequenced on a Mk1C MinION sequencer.