Amplicon sequencing of SARS-CoV-2 from nasal swab
SARS-CoV-2 viral RNA was extracted from mid-turbinate nasal swabs and reverse transcribed using LunaScript RT SuperMix (NEB). The resulting cDNA was amplified in two separate PCR pools using the VarSkip VSS2A primer mixes 1 and 2, which were subsequently combined for Illumina sequencing at the NIH Intramural Sequencing Center (NISC).