BAL vs NW
RNA extracted from 50ul of NW and BAL samples using Zymo Viral RNA (Zymo Research). Extracted RNAs were treated with Turbo DNase I (Invitrogen). cDNA was generated using SS III reverse transcriptase (Thermo Fisher) and converted into double stranded cDNA using Sequenase 2.0 (Thermo Fisher). Double stranded cDNA was cleaned up using Zymo DNA clean and concentrator. mNGS libraries were prepped from 2uL of the cDNA using two-fifths Nextera XT volumes with 20 cycles of PCR and 0.8 Ampure XP bead clean-up. Libraries were run on 1X192 bp runs on an Illumina MiSeq.