title: Longitudinal Sequencing of SARS-CoV-2: ATACCC_B_8
design: cDNA synthesis was then performed using the LunaScript RT SuperMix Kit (NEB) from the RNA extracted for RT-qPCR according to the manufacturers instructions with a total reaction volume of 20 l and extracted sample volume of 5 l. Sequencing libraries were generated using the EasySeq RT-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing kit v4 (Nimagen) according to the manufacturers instructions. Samples were then pooled and purified with AMPure XP (Beckman Coulter) magnetic beads. Suitable quality of libraries was confirmed using a Tapestation (Agilent) and concentrations were measured using the Qubit 1x dsDNA High Sensitivity Assay Kit (Thermofisher Scientific) and Qubit 4 Fluorometer (ThermoFisher Scientific). The final pool was run on a NextSeq 2000 (Illumina) with a total of 322 cycles (151 bp paired reads and 10 bp indices).