RNA-Seq of SARS-CoV-2
RNA extraction from decontaminated nasopharyngeal swabs (NP swabs) was carried out. DNA complementary to the RNA (cDNA) was generated by reverse transcriptase with random hexamers. Target (SARS-CoV-2 viral genome) amplification was carried out by using two separate PCR reactions that were then pooled together. Library preparation was done by using the pooled, amplified fragments and amplicons were tagged with adapter sequences. The adapter-tagged amplicons underwent a second round of PCR amplification using a PCR master mix and unique index adapters. After amplification, indexed libraries are pooled and cleaned using purification beads. Sequencing was accomplished by clustering pooled libraries onto a flow cell and sequencing by applying sequencing by synthesis (SBS) chemistry on the NovaSeq 6000 Sequencing System using the NovaSeq Xp S4 flow cell workflow.