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| Strubbia, Sofia; Phan, My V. T.; Schaeffer, Julien; Koopmans, Marion; Cotten, Matthew; Le Guyader, Soizick. |
| This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was... |
| Tipo: Text |
Palavras-chave: Human enteric viruses; Norovirus; Sewage; Metagenomic; Virome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00512/62332/66592.pdf |
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| Strubbia, Sofia; Schaeffer, Julien; Oude Munnink, Bas B.; Besnard, Alban; Phan, My V. T.; Nieuwenhuijse, David F.; De Graaf, Miranda; Schapendonk, Claudia M. E.; Wacrenier, Candice; Cotten, Matthew; Koopmans, Marion P. G.; Le Guyader, Soizick. |
| Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in... |
| Tipo: Text |
Palavras-chave: Norovirus; Sewage; Oysters; Metagenomic sequencing; Metavirome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00586/69765/67656.pdf |
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| Desdouits, Marion; De Graaf, Miranda; Strubbia, Sofia; Oude Munnink, Bas B.; Kroneman, Annelies; Le Guyader, Soizick; Koopmans, Marion P. G.. |
| 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 |
| Tipo: Text |
Palavras-chave: Next-generation sequencing; Metagenomics; Foodborne virus; Food virology; Human enteric virus; Norovirus. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00641/75330/75988.pdf |
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| Rince, Alain; Baliere, Charlotte; Hervio-heath, Dominique; Cozien, Joelle; Lozach, Solen; Parnaudeau, Sylvain; Le Guyader, Francoise S.; Le Hello, Simon; Giard, Jean-christophe; Sauvageot, Nicolas; Benachour, Abdellah; Strubbia, Sofia; Gourmelon, Michele. |
| During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. Escherichia coli isolates classified into the phylogenetic groups B2, or D and enterococci from Enterococcus faecalis and E. faecium species were tested for the presence of virulence genes and for antimicrobial susceptibility. Salmonella members were serotyped and the most abundant serovars (Typhimurium and its monophasic variants and Mbandaka) were genetically characterized by high discriminative subtyping methods.... |
| Tipo: Text |
Palavras-chave: Campylobacter; Salmonella; Vibrio; HuNoVs; Fecal bacterial indicators; Shellfish; Water. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00461/57243/59243.pdf |
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| Strubbia, Sofia; Lyons, B. P.; Lee, R. J.. |
| Environmental conditions and xenobiotic exposure can be sources of stress to living organisms. Biological markers are measurable indicator of changes which may happen at any biological level and which can be considered an early warning signal of some biological or environmental state or condition. A structured field study was undertaken to investigate the relationship between three biomarker assays and the spatial and temporal variation of each biomarker in samples of Mytilus edulis. The three biomarkers were the neutral red retention assay, micronucleus assay and comet assay, which indicate damage at different cellular/molecular levels. Three sites in Poole Harbour, an area on the South coast of the UK were sampled on six separate occasions at least three... |
| Tipo: Text |
Palavras-chave: Mytilus edulis; Biomarkers; Stress; Neutral red retention; Comet assay; Micronucleus assay; Poole Harbour. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00481/59274/63447.pdf |
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