Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA.
Stanford Genome Technology Center, Stanford University, 855 California Ave, Palo Alto, CA 94304, USA.
Viruses. 2010 Sep;2(9):1933-1967. doi: 10.3390/v2091933. Epub 2010 Sep 15.
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.
痘病毒是高度成功的病原体，已知可感染多种宿主。痘病毒科包括天花病毒，天花病毒是天花的病原体，已被根除，不再构成公共卫生威胁，但有可能作为生物恐怖主义威胁重新出现。风险情景包括其他动物痘病毒和痘病毒的基因工程改造。对同源基因集的研究确立了痘病毒科内成员的进化关系。然而，目前尚不清楚过去家族成员之间的变异是如何产生的，这是了解这些病毒如何变异并可能产生未来威胁的一个重要问题。我们使用新开发的痘病毒特异性工具，预测了正痘病毒属中完全测序基因组病毒的准确基因集。我们采用了敏感的序列比较技术和同线性基因图谱比较，建立了所有病毒基因集之间的关系。这些技术使我们能够明确识别在正痘病毒进化过程中发生的基因丢失/获得事件。很明显，对于所有现有的正痘病毒物种，没有一种物种获得了该物种特有的蛋白编码基因。所有现有的物种都包含存在于牛痘病毒成员中的基因，而牛痘病毒株包含任何其他正痘病毒株中存在的所有基因。这些结果支持了一种简化进化理论，即假定祖先病毒核心基因集的大小减少在物种形成中起着关键作用，并将任何新出现的病毒物种限制在特定的环境（宿主或组织）小生境中。
