Amplicon sequencing of SARS-CoV-2: WA1 and WA1-655Y, 24h human-like pneumocyte cells, 70-30, Replicate 3
Whole-genome amplification with custom designed tiling primers (Quick et al., 2017) and the Artic Consortium protocol (https://artic.network/ncov-2019), with modifications. Briefly, cDNA synthesis was performed with random hexamers and ProtoScript II (New England Biolabs, E6560). The RT reaction was incubated for 30 minutes at 48C, followed by enzyme inactivation at 85C for 5 minutes. Targeted amplification was performed as previously described (Gonzalez-Reiche et al., 2020). Next, amplicons were visualized on a 2% agarose gel and cleaned with Ampure XT beads. Amplicon libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina,  FC-131-1096),