Sequencing SARS-CoV-2 from Antigen Tests
Paragon Genomics CleanPlex FLEX SARS-CoV-2 Panel (Cat. 918014) for Illumina platforms was used to prepare sequencing libraries (starting concentration of 10-50 ng RNA per sample). As a positive control, sequencing libraries were also prepped for VR-1986D, Genomic RNA from SARS-Related Coronavirus 2, Isolate USA-WA1/2020. Library quality and concentration was assessed via fragment analysis using Advanced Analytics High Sensitivity NGS Fragment Analysis Kit (Cat. DNF-474-0500). Library quality ratio scores (QRS) were determined by dividing the fragment analysis 250-350 bp peak concentration (ng/L) by 50-190 bp peak concentration (ng/L): excellent (QRS >10), Good (QRS 1.0  10), Fair (QRS <1 and >0.5), Poor (QRS < 0.5). Libraries with QRS > 1.0 were denatured and diluted to a final loading concentration of 10 pM following the Illumina MiSeq System Denature and Dilute Libraries Guide (Document # 15039740 v10), and then sequenced on the MiSeq system at 2 x 151 bp using the MiSeq v3, (600 cycle) kit (Illumina, Cat. MS-102-3003).