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.