SARS-CoV-2 parallel sequencing by Illumina and Oxford Nanopore Technologies

Recent studies of SARS-CoV-2 have sequenced clinical samples or primary passaged samples in real time but have yet to look at low level viral diversity. It is critical to evaluate viral diversity below the consensus level as minor variants may impact patterns of virulence and person-to-person transmission efficiency. Additionally, the relative frequencies and functional impact (at the amino acid level) of this variation can be leveraged to make inferences about viral population dynamics and the relative roles of selection and random genetic fluctuations, or genetic drift.To characterize within-host viral diversity of this emerging virus, we obtained for SARS-CoV-2/2019-nCoV/USA-WI-1/2020 samples from Yoshihiro Kawaoka's lab:1. A clinical swab obtained from a confirmed case in Madison, WI.2. Cell culture isolates - all having undergone one passage each:- Vero 76; ATCC CRL-1587- Vero E6, C1008; ATC-1586- Vero STAT-1 KO; ATCC CCL-81-VHG