Establishing farm dust as a useful viral metagenomic surveillance matrix

Kwok, K. T. T. , de Rooij, M. M. T., Messink, A. B., Wouters, I. M., Smit, L. A. M., Cotten, M. , Heederik, D. J. J., Koopmans, M. P. G. and Phan, M. V. T. (2022) Establishing farm dust as a useful viral metagenomic surveillance matrix. Scientific Reports, 12, 16308. (doi: 10.1038/s41598-022-20701-x) (PMID:36175536) (PMCID:PMC9521564)

Abstract

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.

• Item Type: Articles
• Additional Information: This virome study was funded by ZonMW TOP project 91217040 (K.T.T.K., M.M.T.dR., L.A.M.S., D.J.J.H. and M.P.G.K.) and a Marie Sklodowska-Curie Individual Fellowship, supported by Horizon 2020 (grant no. 799417; M.V.T.P.). M.V.T.P and M.C. was additionally supported by the Wellcome Trust and FCDO (grant agreement number 220977/Z/20/Z, awarded to M.C.). Sample collection was supported with internal funds from the Utrecht University (M.M.T.dR., A.B.M., and I.M.W.).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Kwok, Ms Kirsty and Cotten, Professor Matthew
• Authors: Kwok, K. T. T., de Rooij, M. M. T., Messink, A. B., Wouters, I. M., Smit, L. A. M., Cotten, M., Heederik, D. J. J., Koopmans, M. P. G., and Phan, M. V. T.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Scientific Reports
• Publisher: Nature Research
• ISSN: 2045-2322
• ISSN (Online): 2045-2322
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Scientific Reports 12: 16308
• Publisher Policy: Reproduced under a Creative Commons License