title: Genomic sequencing of SARS-CoV-2: Wastewater
design: RNA extracted from wastewater samples is converted to cDNA using LunaScript RT SuperMix (NEB). Tiled amplicons will be generated by multiplex PCR using the Q5 Hot Start High-Fidelity 2X Master Mix (NEB) with the artic V4 primers (https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4) then prepared for sequencing using the PlexWell 384 Library Prep Kit (SeqWell) following manufacturers instructions, or generated and prepared for sequencing using the Normalase SARS-CoV-2 Amplicon Panel (Swift Biosciences) following manufacturers instructions. Pooled libraries will be sequenced on a NextSeq500/550 (Illumina) at 2x150 targeting a total read count >= 430k paired end reads per sample.