SARS-CoV-2 whole genome sequencing to explore the impact of remdesivir on SARS-CoV-2 evolution in vivo

We investigated the diversification and diversity of SARS-CoV-2 over time in a cohort of hospitalized patients who were either treated with or without remdesivir. Whole genome sequencing was conducted on 98 paired specimens from 49 patients, collected before and after remdesivir treatment. These specimens, from individuals testing positive for SARS-CoV-2, were sourced from an established biobank at the Center for Pathogen Genomics and Microbial Evolution, Northwestern University Feinberg School of Medicine. cDNA synthesis was performed using the SuperScript IV First-Strand Synthesis Kit (Thermo) with random hexamer primers, as per the manufacturer's instructions. The viral genome cDNA was then amplified in multiplexed PCR reactions to produce approximately 400 base pair amplicons, covering the entire genome. The multiplex primer set, consisting of two non-overlapping primer pools, was designed using Primal Scheme and provided by the Artic Network (v4 and 4.1). The sequencing libraries were prepared from these amplicon pools using the SeqWell plexWell 384 kit (Seqwell PW384A) according to the manufacturer's protocol. These pooled libraries were sequenced on an Illumina MiSeq platform using the V2 500 cycle kit. To generate consensus sequences, reads were trimmed of adapters and low-quality sequences using Trimmomatic v0.36, and then aligned to the reference genome sequence of SARS-CoV-2 (accession MN908947.3) using bwa v0.7.15.