Data for: Sequencing and variant detection of eight abundant plant-infecting tobamoviruses across Southern California wastewater

Tobamoviruses are agriculturally-relevant viruses that cause crop losses and have infected plants in many regions of the world. These viruses are frequently found in municipal wastewater - likely coming from human diet and industrial waste across wastewater catchment areas. As part of a large wastewater-based epidemiology study across Southern California, we analyzed RNA sequence data from 275 influent wastewater samples obtained from eight wastewater treatment plants with a catchment area of approximately 16 million people from July 2020 – August 2021. We assembled over 1,083 high-quality genomes, enumerated viral sequencing reads, and detected thousands of single nucleotide variants from eight common tobamoviruses: Bell Pepper Mottle Virus, Cucumber Green Mottle Mosaic Virus, Pepper Mild Mottle Virus, Tobacco Mild Green Mosaic Virus, Tomato Brown Rugose Fruit Virus, Tomato Mosaic Virus, Tomato Mottle Mosaic Virus, and Tropical Soda Apple Mosaic Virus. We show that single nucleotide variants had amino acid-altering consequences along with synonymous mutations, which represents potential evolution with functional consequences in genomes of these viruses. Our study shows the importance of wastewater sequencing to monitor the genomic diversity of these plant-infecting viruses, and we suggest that our data could be used to continue tracking the genomic variability of such pathogens.