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To determine the extent to which Ae. albopic...", "publicationTitle": "", "publisher": "", "place": "", "date": "", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.3201/eid2307.161633", "citationKey": "", "url": "https://wwwnc.cdc.gov/eid/article/23/7/16-1633_article", "accessDate": "2019-05-19T22:10:05Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en-us", "libraryCatalog": "wwwnc.cdc.gov", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "CXB2W2EQ" ], "relations": {}, "dateAdded": "2019-05-19T22:10:05Z", "dateModified": "2019-05-19T22:10:05Z" } }, { "key": "88TZRYBR", "version": 1218, "library": { "type": "group", "id": 344915, "name": "twig", "links": { "alternate": { "href": "https://www.zotero.org/groups/twig", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/344915/items/88TZRYBR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/twig/items/88TZRYBR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 35740, "username": "jshoyer", "name": "J. Steen Hoyer", "links": { "alternate": { "href": "https://www.zotero.org/jshoyer", "type": "text/html" } } }, "creatorSummary": "Ehrbar et al.", "parsedDate": "2017-07-01", "numChildren": 2 }, "data": { "key": "88TZRYBR", "version": 1218, "itemType": "journalArticle", "title": "High levels of local inter- and intra-host genetic variation of West Nile virus and evidence of fine-scale evolutionary pressures", "creators": [ { "creatorType": "author", "firstName": "Dylan J.", "lastName": "Ehrbar" }, { "creatorType": "author", "firstName": "Kiet A.", "lastName": "Ngo" }, { "creatorType": "author", "firstName": "Scott R.", "lastName": "Campbell" }, { "creatorType": "author", "firstName": "Laura D.", "lastName": "Kramer" }, { "creatorType": "author", "firstName": "Alexander T.", "lastName": "Ciota" } ], "abstractNote": "West Nile virus (WNV; Flaviviridae, Flavivirus) has been endemic in New York State (NYS) since its 1999 introduction, yet prevalence in Culex mosquitoes varies substantially over small spatial and temporal scales. It is unclear if viral genetics plays a role in this variability, as genetic and phenotypic characterization on local scales has generally been lacking. In addition, intrahost diversity of circulating strains have not been fully characterized despite the documented role of minority variants in viral fitness and virulence. In an effort to characterize WNV variability within epidemiologically relevant scales, we performed phylogenetic analyses on NYS isolates from 1999 to 2012. In addition, we performed full-genome, deep-sequencing and genetic analyses on 15 WNV strains isolated in 2012 from Cx. pipiens in an endemic focus of Suffolk County, NY. Our results indicate continued evolution and seasonal maintenance in NYS, yet also widespread mixing and high levels of genetic diversity within geographic foci and individual seasons. Well supported local clusters with shared amino acid differences were identified and suggest local evolutionary pressures and the potential for phenotypic variability. Intrahost diversity of focal isolates was also high, with polymorphism at levels >1.0% identified in approximately 10% of the WNV genome. Although most minority mutations were unique, mutational hotspots shared among local isolates were identified, particularly in C, NS1 and NS2A genes. The most polymorphic region, positions 3198–3388 of the NS1 gene, was comprised predominately of non-synonymous mutations, suggesting a selective advantage for amino acid diversity in this region.", "publicationTitle": "Infection, Genetics and Evolution", "publisher": "", "place": "", "date": "July 1, 2017", "volume": "51", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "219-226", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Infection, Genetics and Evolution", "DOI": "10.1016/j.meegid.2017.04.010", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1567134817301235", "accessDate": "2019-05-19T22:10:02Z", "PMID": "", "PMCID": "", "ISSN": "1567-1348", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Arbovirus evolution", "type": 1 }, { "tag": "Intrahost diversity", "type": 1 }, { "tag": "West Nile virus", "type": 1 } ], "collections": [ "CXB2W2EQ" ], "relations": {}, "dateAdded": "2019-05-19T22:10:02Z", "dateModified": "2019-05-19T22:10:02Z" } }, { "key": "EDPI4M5P", "version": 1214, "library": { "type": "group", "id": 344915, "name": "twig", "links": { "alternate": { "href": "https://www.zotero.org/groups/twig", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/344915/items/EDPI4M5P", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/twig/items/EDPI4M5P", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/344915/items/NWFJWIFD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 35740, "username": "jshoyer", "name": "J. 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O.", "lastName": "Yerumoh" }, { "creatorType": "author", "firstName": "I.", "lastName": "Odia" }, { "creatorType": "author", "firstName": "C.", "lastName": "Aire" }, { "creatorType": "author", "firstName": "M.", "lastName": "Okonofua" }, { "creatorType": "author", "firstName": "R.", "lastName": "Atafo" }, { "creatorType": "author", "firstName": "E.", "lastName": "Tobin" }, { "creatorType": "author", "firstName": "D.", "lastName": "Asogun" }, { "creatorType": "author", "firstName": "N.", "lastName": "Akpede" }, { "creatorType": "author", "firstName": "P. O.", "lastName": "Okokhere" }, { "creatorType": "author", "firstName": "M. O.", "lastName": "Rafiu" }, { "creatorType": "author", "firstName": "K. O.", "lastName": "Iraoyah" }, { "creatorType": "author", "firstName": "C. O.", "lastName": "Iruolagbe" }, { "creatorType": "author", "firstName": "P.", "lastName": "Akhideno" }, { "creatorType": "author", "firstName": "C.", "lastName": "Erameh" }, { "creatorType": "author", "firstName": "G.", "lastName": "Akpede" }, { "creatorType": "author", "firstName": "E.", "lastName": "Isibor" }, { "creatorType": "author", "firstName": "D.", "lastName": "Naidoo" }, { "creatorType": "author", "firstName": "R.", "lastName": "Hewson" }, { "creatorType": "author", "firstName": "J. A.", "lastName": "Hiscox" }, { "creatorType": "author", "firstName": "R.", "lastName": "Vipond" }, { "creatorType": "author", "firstName": "M. W.", "lastName": "Carroll" }, { "creatorType": "author", "firstName": "C.", "lastName": "Ihekweazu" }, { "creatorType": "author", "firstName": "P.", "lastName": "Formenty" }, { "creatorType": "author", "firstName": "S.", "lastName": "Okogbenin" }, { "creatorType": "author", "firstName": "E.", "lastName": "Ogbaini-Emovon" }, { "creatorType": "author", "firstName": "S.", "lastName": "Günther" }, { "creatorType": "author", "firstName": "S.", "lastName": "Duraffour" } ], "abstractNote": "Mobile detection of Lassa virus\nLassa fever is a hemorrhagic viral disease endemic to West Africa. Usually, each year sees only a smattering of cases reported, but hospitalized patients risk a 15% chance of death. Responding to fears that a 10-fold surge in cases in Nigeria in 2018 signaled an incipient outbreak, Kafetzopoulou et al. performed metagenomic nanopore sequencing directly from samples from 120 patients (see the Perspective by Bhadelia). Results showed no strong evidence of a new strain emerging nor of person-to-person transmission; rather, rodent contamination was the main source. To prevent future escalation of this disease, we need to understand what triggers the irruption of rodents into human dwellings.\nScience, this issue p. 74; see also p. 30\nThe 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.\nMobile nanopore sequencing technology has been successfully used for direct sequencing from hemorrhagic fever patient samples.\nMobile nanopore sequencing technology has been successfully used for direct sequencing from hemorrhagic fever patient samples.", "publicationTitle": "Science", "publisher": "", "place": "", "date": "2019/01/04", "volume": "363", "issue": "6422", "section": "", "partNumber": "", "partTitle": "", "pages": "74-77", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1126/science.aau9343", "citationKey": "", "url": "https://science.sciencemag.org/content/363/6422/74", "accessDate": "2019-05-19T20:34:10Z", "PMID": "30606844", "PMCID": "", "ISSN": "0036-8075, 1095-9203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "science.sciencemag.org", "callNumber": "", "rights": "Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. 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