{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T15:04:44Z","timestamp":1779721484231,"version":"3.53.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":126,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ifremer Scientific Direction"},{"name":"VEO European Project","award":["H2020 SCI-2019-874735"],"award-info":[{"award-number":["H2020 SCI-2019-874735"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Investigating potential zoonotic viruses in animal reservoirs is crucial to anticipate viral emergence. Seals can represent large populations of coastal mammals with unknown consequences on the microbiological quality of their surrounding environment. To assess this, we conducted a metaviromics analysis of feces collected from two species of seals in the North-Western Atlantic (Saint-Pierre et Miquelon archipelago). We focused on the Caliciviridae family, which regroups several genera with viruses infecting humans and other mammals, including marine mammals, but none identified in seals (Phocidae). Among the assembled sequences identified as Caliciviridae, there were four known genera (norovirus, sapovirus, vesivirus, and salovirus) and unknown, distantly related viruses. Complete or nearly-complete genomes could be assembled for each genus. Norovirus and sapovirus sequences from seals were diverse and likely represent several new genogroups or genotypes. Seal vesivirus formed a monophyletic group, representing a potential new species related to the canine vesivirus. Salovirus, which are fish viruses, were likely diet-derived, like the distant sequences which exhibited the hallmarks of caliciviruses and were more closely related to fish and reptile viruses. In conclusion, seals are a reservoir for a large diversity of Caliciviridae, some related to norovirus or sapovirus genotypes known to infect humans, and their impact on the quality of coastal water or shellfish should be further assessed. This study expands the knowledge on Caliciviridae genetic diversity and circulation in marine mammals.<\/jats:p>","DOI":"10.1093\/ve\/veag029","type":"journal-article","created":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T11:40:53Z","timestamp":1778067653000},"source":"Crossref","is-referenced-by-count":0,"title":["Metaviromics reveals a high diversity of viruses belonging to the\n                    <i>Caliciviridae<\/i>\n                    family in seal feces"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2625-1575","authenticated-orcid":false,"given":"Marion","family":"Desdouits","sequence":"first","affiliation":[{"name":"Ifremer, MASAE , rue de l'\u00eele d'Yeu, 44311 Nantes cedex 03 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Schaeffer","sequence":"additional","affiliation":[{"name":"Ifremer, MASAE , rue de l'\u00eele d'Yeu, 44311 Nantes cedex 03 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9cile","family":"Le Mennec","sequence":"additional","affiliation":[{"name":"Ifremer, MASAE , rue de l'\u00eele d'Yeu, 44311 Nantes cedex 03 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mich\u00e8le","family":"Gourmelon","sequence":"additional","affiliation":[{"name":"Ifremer, DYNECO , 1625 route de Sainte-Anne, CS 10070, 29280 Plouzan\u00e9 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7oise S","family":"Le Guyader","sequence":"additional","affiliation":[{"name":"Ifremer, MASAE , rue de l'\u00eele d'Yeu, 44311 Nantes cedex 03 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"2026052510370234200_ref1","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/S0140-6736(18)31128-0","article-title":"Viral gastroenteritis","volume":"392","author":"B\u00e1nyai","year":"2018","journal-title":"Lancet"},{"key":"2026052510370234200_ref2","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1111\/j.1365-2907.2011.00193.x","article-title":"Pinniped taxonomy: review of currently recognized species and subspecies, and evidence used for their description","volume":"42","author":"Berta","year":"2012","journal-title":"Mammal Rev"},{"key":"2026052510370234200_ref3","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.770385","article-title":"Human and animal RNA virus diversity detected by metagenomics in Cameroonian clams","volume":"12","author":"Bonny","year":"2021","journal-title":"Front Microbiol"},{"key":"2026052510370234200_ref4","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2026052510370234200_ref5","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.marpol.2010.10.011","article-title":"Perceptions and costs of seal impacts on Atlantic salmon fisheries in the Moray Firth, Scotland: implications for the adaptive co-management of seal-fishery conflict","volume":"35","author":"Butler","year":"2011","journal-title":"Mar Policy"},{"key":"2026052510370234200_ref6","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2026052510370234200_ref7","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1099\/jgv.0.001318","article-title":"Updated classification of norovirus genogroups and genotypes","volume":"100","author":"Chhabra","year":"2019","journal-title":"J Gen Virol"},{"key":"2026052510370234200_ref8","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/s41586-018-0852-1","article-title":"Calicivirus VP2 forms a portal-like assembly following receptor engagement","volume":"565","author":"Conley","year":"2019","journal-title":"Nature"},{"key":"2026052510370234200_ref9","doi-asserted-by":"publisher","first-page":"286","DOI":"10.3390\/v11030286","article-title":"Caliciviridae other than noroviruses","volume":"11","author":"Desselberger","year":"2019","journal-title":"Viruses"},{"key":"2026052510370234200_ref10","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/s41586-022-04895-8","article-title":"Enteric viruses replicate in salivary glands and infect through saliva","volume":"607","author":"Ghosh","year":"2022","journal-title":"Nature"},{"key":"2026052510370234200_ref11","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1484094","article-title":"Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker","volume":"15","author":"Godino Sanchez","year":"2024","journal-title":"Front Microbiol"},{"key":"2026052510370234200_ref12","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1038\/nrmicro.2016.48","article-title":"Human norovirus transmission and evolution in a changing world","volume":"14","author":"Graaf","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"2026052510370234200_ref13","doi-asserted-by":"publisher","first-page":"87","DOI":"10.3201\/eid2301.161081","article-title":"Norovirus infection in harbor porpoises","volume-title":"Emerging Infectious Diseases","author":"de Graaf","year":"2017"},{"key":"2026052510370234200_ref14","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2024.1461135","article-title":"Viral metagenomic survey of Caspian seals","volume":"11","author":"Karamendin","year":"2024","journal-title":"Front Vet Sci"},{"key":"2026052510370234200_ref15","doi-asserted-by":"publisher","first-page":"e2202871119","DOI":"10.1073\/pnas.2202871119","article-title":"Pandemic origins and a One Health approach to preparedness and prevention: solutions based on SARS-CoV-2 and other RNA viruses","volume":"119","author":"Keusch","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026052510370234200_ref16","doi-asserted-by":"publisher","first-page":"e0151921","DOI":"10.1371\/journal.pone.0151921","article-title":"Metagenomic survey of viral diversity obtained from feces of Subantarctic and South American fur seals","volume":"11","author":"Kluge","year":"2016","journal-title":"PLoS One"},{"key":"2026052510370234200_ref17","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.jcv.2011.03.006","article-title":"An automated genotyping tool for enteroviruses and noroviruses","volume":"51","author":"Kroneman","year":"2011","journal-title":"J Clin Virol"},{"key":"2026052510370234200_ref17a","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gappedread alignment with Bowtie 2","volume":"9","author":"","year":"2012","journal-title":"Nature Methods"},{"key":"2026052510370234200_ref18","doi-asserted-by":"publisher","first-page":"13","DOI":"10.2174\/1874839201105010013","article-title":"Changes in seal habitat use of nearshore waters around Newfoundland and southern Labrador: implications for potential predation on Salmon","volume":"5","author":"Lenky","year":"2011","journal-title":"AACE Clin Case Rep"},{"key":"2026052510370234200_ref19","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2026052510370234200_ref20","doi-asserted-by":"publisher","first-page":"vez005","DOI":"10.1093\/ve\/vez005","article-title":"The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus","volume":"5","author":"Mahar","year":"2019","journal-title":"Virus Evol"},{"key":"2026052510370234200_ref21","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-23114-y","article-title":"Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals","volume":"12","author":"Mart\u00ednez-Puchol","year":"2022","journal-title":"Sci Rep"},{"key":"2026052510370234200_ref22","doi-asserted-by":"publisher","first-page":"e107132","DOI":"10.1371\/journal.pone.0107132","article-title":"Characterization of a novel calicivirus causing systemic infection in Atlantic salmon (Salmo salar L.): proposal for a new genus of Caliciviridae","volume":"9","author":"Mikalsen","year":"2014","journal-title":"PLoS One"},{"key":"2026052510370234200_ref23","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/bib\/bbs012","article-title":"Using Tablet for visual exploration of second-generation sequencing data","volume":"14","author":"Milne","year":"2013","journal-title":"Brief Bioinform"},{"key":"2026052510370234200_ref24","doi-asserted-by":"publisher","first-page":"veaa069","DOI":"10.1093\/ve\/veaa069","article-title":"Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR","volume":"7","author":"Mordecai","year":"2021","journal-title":"Virus Evol"},{"key":"2026052510370234200_ref24a","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"","year":"2017","journal-title":"Genome Research"},{"key":"2026052510370234200_ref25","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1128\/CMR.00011-14","article-title":"Comprehensive review of human sapoviruses","volume":"28","author":"Oka","year":"2015","journal-title":"Clin Microbiol Rev"},{"key":"2026052510370234200_ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2024.173220","article-title":"Occurrence of recreational water quality monitoring general fecal indicator bacteria and fecal source identification genetic markers in gray seal scat","volume":"934","author":"Paar","year":"2024","journal-title":"Sci Total Environ"},{"key":"2026052510370234200_ref27","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1007\/s00300-024-03334-w","article-title":"Viral diversity in stool samples of fur seals from Antarctica using metagenomic shotgun","volume":"48","author":"Prado","year":"2025","journal-title":"Polar Biol"},{"key":"2026052510370234200_ref28","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1007\/s00705-023-05733-6","article-title":"A novel vesivirus (family Caliciviridae) in European badgers (Meles meles) in Hungary, 2020\/2021","volume":"168","author":"Reuter","year":"2023","journal-title":"Arch Virol"},{"key":"2026052510370234200_ref29","doi-asserted-by":"publisher","first-page":"3118","DOI":"10.1093\/bioinformatics\/btac287","article-title":"SimPlot++: a Python application for representing sequence similarity and detecting recombination","volume":"38","author":"Samson","year":"2022","journal-title":"Bioinformatics"},{"key":"2026052510370234200_ref30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1161674","article-title":"Looking into sewage: how far can metagenomics help to detect human enteric viruses?","volume":"14","author":"Schaeffer","year":"2023","journal-title":"Front Microbiol"},{"key":"2026052510370234200_ref31","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/nature20167","article-title":"Redefining the invertebrate RNA virosphere","volume":"540","author":"Shi","year":"2016","journal-title":"Nature"},{"key":"2026052510370234200_ref32","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1038\/s41579-025-01243-1","article-title":"Viral emergence and pandemic preparedness in a One Health framework","volume":"24","author":"Sikkema","year":"2026","journal-title":"Nat Rev Microbiol"},{"key":"2026052510370234200_ref33","doi-asserted-by":"publisher","first-page":"13","DOI":"10.3201\/eid0401.980103","article-title":"Calicivirus emergence from ocean reservoirs: zoonotic and interspecies movements","volume":"4","author":"Smith","year":"1998","journal-title":"Emerg Infect Dis"},{"key":"2026052510370234200_ref34","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00031-17","article-title":"Identification of human junctional adhesion molecule 1 as a functional receptor for the Hom-1 calicivirus on human cells","volume":"8","author":"Sosnovtsev","year":"2017","journal-title":"mBio"},{"key":"2026052510370234200_ref35","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1007\/s12560-019-09402-3","article-title":"Characterization of norovirus and other human enteric viruses in sewage and stool samples through next-generation sequencing","volume":"11","author":"Strubbia","year":"2019","journal-title":"Food Environ Virol"},{"key":"2026052510370234200_ref36","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1099\/jgv.0.001071","article-title":"Two novel noroviruses and a novel norovirus genogroup in California sea lions","volume":"99","author":"Teng","year":"2018","journal-title":"J Gen Virol"},{"key":"2026052510370234200_ref37","doi-asserted-by":"publisher","first-page":"478","DOI":"10.3390\/v11050478","article-title":"Animals as reservoir for human norovirus","volume":"11","author":"Villabruna","year":"2019","journal-title":"Viruses"},{"key":"2026052510370234200_ref38","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01492-20","article-title":"Human noroviruses attach to intestinal tissue of a broad range of animal species","volume":"95","author":"Villabruna","year":"2020","journal-title":"J Virol [Preprint]"},{"key":"2026052510370234200_ref39","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1099\/jgv.0.001332","article-title":"ICTV virus taxonomy profile: Caliciviridae","volume":"100","author":"Vinj\u00e9","year":"2019","journal-title":"J Gen Virol"},{"key":"2026052510370234200_ref40","doi-asserted-by":"publisher","first-page":"5263","DOI":"10.1111\/mec.14918","article-title":"Virus\u2013virus interactions and host ecology are associated with RNA virome structure in wild birds","volume":"27","author":"Wille","year":"2018","journal-title":"Mol Ecol"},{"key":"2026052510370234200_ref41","doi-asserted-by":"publisher","first-page":"1642","DOI":"10.1080\/22221751.2019.1686335","article-title":"Structural basis of host ligand specificity change of GII porcine noroviruses from their closely related GII human noroviruses from their closely related GII human noroviruses","volume-title":"Emerging Microbes & Infections","author":"Yang","year":"2019"},{"key":"2026052510370234200_ref42","doi-asserted-by":"publisher","first-page":"6404","DOI":"10.1128\/AEM.00671-10","article-title":"Bovine norovirus: Carbohydrate ligand, environmental contamination, and potential cross-species transmission via oysters","volume":"76","author":"Zakhour","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"2026052510370234200_ref43","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1186\/s12864-024-11048-w","article-title":"A dual typing system establishment and global diversity analysis for sapoviruses","volume":"25","author":"Zhao","year":"2024","journal-title":"BMC Genomics"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veag029\/68244825\/veag029.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag029\/68244825\/veag029.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag029\/68244825\/veag029.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T14:37:10Z","timestamp":1779719830000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veag029\/8672018"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veag029","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"veag029"}}