SARS-CoV-2 Surveillance sequencing
Respiratory and saliva clinical specimens known to be positive for SARS-CoV-2 are extracted using a modified bead-based purification protocol. DNase treatment is performed, and resulting RNA samples are qualified via qPCR of the N gene. Samples with a Ct of less than or equal to 34 are converted to cDNA using NEB LunaScript RT reagent. Samples are amplified using ARTIC V4.1 primers, including internal optimization of concentration based on low coverage regions. Library preparation is performed using the PlexWell384 library prep kit. Libraries are sequenced on a NextSeq 500 with a target of greater than or equal to 0.1 gigabases of data per sample.