NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water
Marta Itarte,
Sandra Martínez-Puchol,
Eva Forés,
Ayalkibet Hundesa,
Natàlia Timoneda,
Sílvia Bofill-Mas,
Rosina Girones,
Marta Rusiñol
Affiliations
Marta Itarte
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Sandra Martínez-Puchol
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Eva Forés
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Ayalkibet Hundesa
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Natàlia Timoneda
Department of Marine Biology and Oceanography, Institute of Marine Science, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
Sílvia Bofill-Mas
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Rosina Girones
Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
Marta Rusiñol
Institute of Environmental Assessment & Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC), 08034 Barcelona, Spain
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
