Novel opportunities for NGS-based one health surveillance of foodborne viruses

Marion Desdouits; Miranda de Graaf; Sofia Strubbia; Bas B Oude Munnink; Annelies Kroneman; Françoise S Le Guyader; Marion P G Koopmans

doi:10.1186/s42522-020-00015-6

Novel opportunities for NGS-based one health surveillance of foodborne viruses

One Health Outlook. 2020 Jun 22:2:14. doi: 10.1186/s42522-020-00015-6. eCollection 2020.

Authors

Marion Desdouits¹, Miranda de Graaf², Sofia Strubbia¹, Bas B Oude Munnink², Annelies Kroneman³, Françoise S Le Guyader¹, Marion P G Koopmans²

Affiliations

¹ IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France.
² Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.
³ Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.

Abstract

Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.

Keywords: Food virology; Foodborne virus; Human enteric virus; Metagenomics; Next-generation sequencing; Norovirus.

Publication types

Review