NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water

Special issue Next-Generation Sequencing and Emerging Technologies for the Identification and Control of Microbial Contaminants in the Food Chain.-- 21 pages, 2 figures, 5 tables, supplementary materials https://www.mdpi.com/article/10.3390/foods10081820/s1.-- Data Availability Statement: The datasets generated during the current study are available in Zenodo under the DOI number https://doi.org/10.5281/zenodo.4722797Fresh 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 samplesThis work was partially funded by a grant from the Spanish Ministry of Economy and Competitiveness (MINECO) AGL2017-86797-C2-1-R. IDEA-CSIC is a Centre of Excellence Severo Ochoa (Spanish Ministry of Science and Innovation (MICINN), Project CEX2018-000794-S)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe