We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.
Keywords: COVID-19; SARS-CoV-2; coronavirus; coronavirus disease; genomics; high-throughput nucleotide sequencing; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; whole-genome sequencing; zoonoses.