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Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We te...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654790/ https://www.ncbi.nlm.nih.gov/pubmed/36359961 http://dx.doi.org/10.3390/foods11213348 |
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author | Buytaers, Florence E. Verhaegen, Bavo Gand, Mathieu D’aes, Jolien Vanneste, Kevin Roosens, Nancy H. C. Marchal, Kathleen Denayer, Sarah De Keersmaecker, Sigrid C. J. |
author_facet | Buytaers, Florence E. Verhaegen, Bavo Gand, Mathieu D’aes, Jolien Vanneste, Kevin Roosens, Nancy H. C. Marchal, Kathleen Denayer, Sarah De Keersmaecker, Sigrid C. J. |
author_sort | Buytaers, Florence E. |
collection | PubMed |
description | In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field. |
format | Online Article Text |
id | pubmed-9654790 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96547902022-11-15 Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study Buytaers, Florence E. Verhaegen, Bavo Gand, Mathieu D’aes, Jolien Vanneste, Kevin Roosens, Nancy H. C. Marchal, Kathleen Denayer, Sarah De Keersmaecker, Sigrid C. J. Foods Article In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field. MDPI 2022-10-25 /pmc/articles/PMC9654790/ /pubmed/36359961 http://dx.doi.org/10.3390/foods11213348 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Buytaers, Florence E. Verhaegen, Bavo Gand, Mathieu D’aes, Jolien Vanneste, Kevin Roosens, Nancy H. C. Marchal, Kathleen Denayer, Sarah De Keersmaecker, Sigrid C. J. Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title | Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title_full | Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title_fullStr | Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title_full_unstemmed | Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title_short | Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study |
title_sort | metagenomics to detect and characterize viruses in food samples at genome level? lessons learnt from a norovirus study |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654790/ https://www.ncbi.nlm.nih.gov/pubmed/36359961 http://dx.doi.org/10.3390/foods11213348 |
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