Item talk:Q309765
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{
"USGS Publications Warehouse": { "@context": "https://schema.org", "@type": "Article", "additionalType": "Journal Article", "name": "Discovery and genomic characterization of a novel hepadnavirus from asymptomatic anadromous alewife (Alosa pseudoharengus)", "identifier": [ { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse IndexID", "value": "70255715", "url": "https://pubs.usgs.gov/publication/70255715" }, { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse Internal ID", "value": 70255715 }, { "@type": "PropertyValue", "propertyID": "DOI", "value": "10.3390/v16060824", "url": "https://doi.org/10.3390/v16060824" } ], "journal": { "@type": "Periodical", "name": "Viruses", "volumeNumber": "16", "issueNumber": "6" }, "inLanguage": "en", "isPartOf": [ { "@type": "CreativeWorkSeries", "name": "Viruses" } ], "datePublished": "2024", "dateModified": "2024-07-02", "abstract": "The alewife (Alosa pseudoharengus)\u00a0is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015\u20132018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family:\u00a0Hepadnaviridae; genus:\u00a0Metahepadnavirus). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in this species, alewives are migratory interjurisdictional fishes of management concern. 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"https://www.usgs.gov/centers/western-fisheries-research-center" } ] }, { "@type": "Person", "name": "Phelps, Nicolas B.D.", "givenName": "Nicolas B.D.", "familyName": "Phelps", "affiliation": [ { "@type": "Organization", "name": "University of Minnesota" } ] }, { "@type": "Person", "name": "Mor, Sunil", "givenName": "Sunil", "familyName": "Mor", "affiliation": [ { "@type": "Organization", "name": "South Dakota State University" } ] }, { "@type": "Person", "name": "Ng, Terry", "givenName": "Terry", "familyName": "Ng", "affiliation": [ { "@type": "Organization", "name": "Centers for Disease Control and Prevention" } ] }, { "@type": "Person", "name": "Iwanowicz, Luke", "givenName": "Luke", "familyName": "Iwanowicz", "identifier": { "@type": "PropertyValue", "propertyID": "ORCID", "value": "0000-0002-1197-6178", "url": "https://orcid.org/0000-0002-1197-6178" }, "affiliation": [ { "@type": "Organization", "name": "USDA" } ] } ], "funder": [ { "@type": "Organization", "name": "Western Fisheries Research Center", "url": "https://www.usgs.gov/centers/western-fisheries-research-center" }, { "@type": "Organization", "name": "Eastern Ecological Science Center", "url": "https://www.usgs.gov/centers/eesc" } ], "spatialCoverage": [ { "@type": "Place", "additionalType": "country", "name": "United States", "url": "https://geonames.org/4074035" }, { "@type": "Place", "additionalType": "state", "name": "New Jersey" }, { "@type": "Place", "geo": [ { "@type": "GeoShape", "additionalProperty": { "@type": "PropertyValue", "name": "GeoJSON", "value": { "type": "FeatureCollection", "features": [ { "type": "Feature", "properties": {}, "geometry": { "coordinates": [ [ [ -75.45013476920779, 41.012795334894605 ], [ -75.45013476920779, 39.47832891534992 ], [ -73.8900761754575, 39.47832891534992 ], [ -73.8900761754575, 41.012795334894605 ], [ -75.45013476920779, 41.012795334894605 ] ] ], "type": "Polygon" } } ] } } }, { "@type": "GeoCoordinates", "latitude": 40.245562125122255, 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