Wastewater SARS-CoV-2 genome sequencing
The libraries were prepared manually with extracted RNA used as initial input for first strand complementary DNA synthesis (cDNA). Amplicon-based library preparation was performed using the Illumina COVIDSeq Test (96 reactions) (ref. 20049393) with spiked ARTIC v4.1 Primer Pools (ref. 20665135 and spiked oligos detailed in Guidelines for detecting the SARS-CoV-2 Omicron variant using the Illumina COVIDSeq Test (RUO Version) Technical Report). Amplicons were then prepared for tagmentation and adapter ligation, followed by their enrichment and cleanup. The libraries were then sequenced on a Novaseq 6000 by using Reagent Kit (300 cycles of sequencing) High Output Flow Cell and reagent cartridge with 2 X150 bp paired-end, dual-indexed reads.