{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T09:24:34Z","timestamp":1791192274241,"version":"4.1.0"},"reference-count":28,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2005,5,17]],"date-time":"2005-05-17T00:00:00Z","timestamp":1116288000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100010918","name":"Montclair State University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100010918","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Comp Funct Genom"],"published-print":{"date-parts":[[2005,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non\u2010structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus. Copyright \u00a9 2005 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/cfg.478","type":"journal-article","created":{"date-parts":[[2005,5,17]],"date-time":"2005-05-17T13:46:54Z","timestamp":1116337614000},"page":"217-227","source":"Crossref","is-referenced-by-count":19,"title":["A phylogenomic study of the genus Alphavirus employing whole genome comparison"],"prefix":"10.1155","volume":"6","author":[{"given":"Aim\u00e9e J.","family":"Luers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra D.","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John V.","family":"Smalley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James J.","family":"Campanella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2005,5,17]]},"reference":[{"key":"e_1_2_6_2_1","first-page":"215","article-title":"Observation of virus\u2010like particles in rainbow\u2010trout Onchornychus mykiss infected with sleeping disease virulent material","volume":"14","author":"Boucher P","year":"1994","journal-title":"Bull Eur Assoc Fish Pathol"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2761.1996.tb00708.x"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.1980.29.1428"},{"key":"e_1_2_6_5_1","volume-title":"Arbovirus Serogroups: Definition and Geographic Distribution.","author":"Calisher C","year":"1988"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.1988.38.447"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-29"},{"key":"e_1_2_6_8_1","doi-asserted-by":"crossref","unstructured":"ChenX KwongS LiM.2000.A compression algorithm for DNA sequences based on approximate matching. 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