{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T04:06:58Z","timestamp":1792037218508,"version":"4.4.0"},"reference-count":110,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2010,9,15]],"date-time":"2010-09-15T00:00:00Z","timestamp":1284508800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses. Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family. It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats. Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus. Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets. These techniques allowed us to unambiguously identify the gene loss\/gain events that have occurred over the course of orthopoxvirus evolution. It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species. All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain. These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche.<\/jats:p>","DOI":"10.3390\/v2091933","type":"journal-article","created":{"date-parts":[[2010,9,19]],"date-time":"2010-09-19T09:41:46Z","timestamp":1284889306000},"page":"1933-1967","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":223,"title":["Orthopoxvirus Genome Evolution: The Role of Gene Loss"],"prefix":"10.3390","volume":"2","author":[{"given":"Robert Curtis","family":"Hendrickson","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Alabama at Birmingham, BBRB 276\/11, 845 19th St S, Birmingham, AL 35222, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunlin","family":"Wang","sequence":"additional","affiliation":[{"name":"Stanford Genome Technology Center, Stanford University, 855 California Ave, Palo Alto, CA 94304, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eneida L.","family":"Hatcher","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Alabama at Birmingham, BBRB 276\/11, 845 19th St S, Birmingham, AL 35222, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elliot J.","family":"Lefkowitz","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Alabama at Birmingham, BBRB 276\/11, 845 19th St S, Birmingham, AL 35222, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2010,9,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.virusres.2009.05.006","article-title":"Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events","volume":"144","author":"Odom","year":"2009","journal-title":"Virus Res."},{"key":"ref_2","unstructured":"Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. 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