tARC-seq of SARS-CoV-2 isolates and Pfizer-BioNTech COVID-19 vaccine samples. Raw sequence reads

SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) for both replication and gene expression. RdRp errors introduce genetic variants that fuel viral evolution, however the nature, frequency and mechanism of errors in SARS-CoV-2 remain unknown. We have developed a targeted Accurate RNA Consensus sequencing method (tARC-seq) that can detect de novo RNA variants while removing technical artifacts. Ancestral (WT) SARS-CoV-2 was passaged in Vero cells and analyzed by tARC-seq, along with the Alpha and Delta variants. tARC-seq was similarly applied to Pfizer-BioNTech COVID-19 vaccine samples to measure the extent and spectrum of variants in an mRNA vaccine.