RNA was extracted from municipal wastewater influent and reverse-transcribed to cDNA. Sequencing libraries were constructed using the SureSelect XT Low Input Kit (Agilent Technologies, CA, USA). Libraries were enriched by hybrid capture using a custom capture panel targeting the complete SARS-CoV-2 genome (NC_045512.2). Sequencing was performed on a DNBSEQ-G400RS instrument (MGI, Shenzhen, China) with 2 x 100-bp paired-end reads.