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

Type Article
Date 2020-12
Language English
Author(s) Desdouits MarionORCID1, De Graaf Miranda2, Strubbia Sofia1, Oude Munnink Bas B.2, Kroneman Annelies3, Le Guyader Soizick1, Koopmans Marion P. G.2
Affiliation(s) 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
Source One Health Outlook (2524-4655) (Springer Science and Business Media LLC), 2020-12 , Vol. 2 , N. 1 , P. 14 (8p.)
DOI 10.1186/s42522-020-00015-6
Keyword(s) Next-generation sequencing, Metagenomics, Foodborne virus, Food virology, Human enteric virus, Norovirus
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

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