Deep metatranscriptomic sequencing data of wastewater from Los Angeles, USA, 2023–2024

Wastewater monitoring for pathogen detection has greatly advanced over the course of the COVID-19 pandemic. While most wastewater surveillance programs only target specific pathogens using qPCR or amplicon sequencing, untargeted wastewater metatranscriptomic sequencing (W-MTS) offers broader detection capabilities. However, there is a lack of data allowing the comparison of W-MTS with more established detection methods. Here we present a dataset consisting of 13.1 terabases (43B read pairs) of untargeted Illumina W-MTS data, generated from 20 wastewater samples, with 1.4B to 2.8B 150 bp read pairs per sample. Wastewater samples were collected between December 2023 and April 2024 at the Hyperion Water Reclamation Plant (HWRP), Los Angeles, USA, serving a population of approximately 4 million residents. The resulting dataset, one of the largest W-MTS collections to date, contains bacterial, archaeal, eukaryotic, and viral taxa-including human-infecting viruses-and many sequences of unknown origin. Uploaded to the NCBI Sequence Read Archive, we expect this data to spur additional research into the viability of pathogen-agnostic wastewater epidemiology and pathogen early detection.