Limited SARS-CoV-2 diversity within hosts and following passage in cell culture

Gage Kahl Moreno; Katarina M Braun; Peter J Halfmann; Trent M Prall; Kasen K Riemersma; Amelia K Haj; Joseph Lalli; Kelsey R Florek; Thomas C Friedrich; Yoshihiro Kawaoka; David H O'Connor

Brea, CA, USA) and eluted in 48µL of water. PCR products were quantified using Qubit dsDNA 332 high-sensitivity kit (Invitrogen, USA) and were diluted to a final concentration of 0.2 ng/µl (1 ng 333 in 5 µl volume). Each sample was then made compatible for deep sequencing using the Nextera 334 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint fragmented and tagged with short oligonucleotide adapters, followed by 14 cycles of PCR for 336 template indexing. Samples were purified using two consecutive AMPure bead cleanups (0.5x 337 and 0.7x) and were quantified once more using Qubit dsDNA high-sensitivity kit (Invitrogen, 338 USA). The average sample fragment length and purity was determined using Agilent High were pooled with seven other samples (not included in this manuscript) and were denatured to a 346 final concentration of 14pM with a PhiX-derived control library accounting for 1% of total DNA 347 and was loaded onto a 600-cycle v3 flowcell. Average quality metrics were recorded, reads 348 were demultiplexed, and FASTQ files were generated on Illumina's BaseSpace platform. 349