design: RNA was extracted either using methods developed in TGen North Clinical Laboratory or using Thermo Fisher's MagMax Viral Pathogen II kit (A48383R) and a Kingfisher liquid handler. DNase treatment was performed on the extracted RNA using Zymo's DNase I kit (Zymo, E1010). RNA was converted to cDNA using Thermofisher's Superscript IV (18090050). Target amplification was performed via the ARTIC protocol using the v3 primer set, and sequencing adapters were added using either Illumina's DNA prep kit (20018705) or Seqwell's plexWell kit (PW384). Libraries were sequenced on an Illumina NextSeq 550 with v2, paired-end chemistry.