Seq of SARS-CoV-2 from NP swab RNA
For each sample, 13 microliters of extracted RNA was reverse transcribed using the Maxima H-minus ds cDNA kits (ThermoFisher Scientific) and the libraries were enriched using a Nextera Flex for Enrichment Library Preparation kit with a Respiratory Virus Oligo Set v1, with samples being pooled in 12-plex enrichment reactions. The resulting pools were quantified and grouped in sets of no more than 48 samples and run on a NextSeq 550 using a 150cyc High Output Flow Cell. We used BreSeq (v.0.34.1) to map reads to Wuhan-Hu-1 SARS-CoV-2 (NC_045512) or 2019-nCoV WIV04 (GISAID accession number EPI_ISL_402124; NCBI Genbank accession number MN996528) and call the consensus sequence. All predicted mutations were reported for isolates exceeding mean 40x coverage.