Data mining human adenovirus genomes using comparative genomics and bioinformatics approaches.

摘要

Comparative whole genome and proteome analysis methods provide insight into the natural variation of organisms, specifically closely related ones like adenoviruses. These data are directly from the genome and thus are primary data; its analysis completes a new "gold" standard in the classification of organisms such as viruses. Presented are the use of these methods in adenoviruses and bacteriophages, and the continued development of software tools for use in comparative genomics. Human adenoviruses are responsible for many diseases globally. For example, HAdV-3 causes outbreaks of acute respiratory disease. The prototype strain, which was isolated in 1953, is compared to three recently isolated "modern" HAdV-3 field strains (a US strain and two Chinese strains) using whole genome analysis methods. Over a 50 year period, it is demonstrated that the HAdV-3 strains are well conserved. Whole genome phylogenetic analysis reveals that the Chinese strains are closer to each other than to the US strain. However, there are differences between the HAdV-3 strains.;This approach is also applied to the characterization of HAdV-52, which is a recently discovered strain associated with gastroenteritis. It is claimed to belong to a new HAdV species as well a new serotype. The incomplete published analysis has been complemented and extended with additional whole genome phylogenetic and proteome analysis. These analyses show that it belongs correctly to a new species, along with two additional members, simian adenoviruses, SAdV-1 and SAdV-7.;To complement the comparative analyses, two whole genome analysis tools known as CoreGenes and GeneOrder have been upgraded and refined. These tools are applied to both an analysis of human adenoviruses and proposed re-classification of bacteriophages. Specifically, in one example, the T7, P22, and lambda bacteriophages are analyzed using these tools. The results indicate that P22 and lambda are more closely related to each other than to T7, contrary to the current ICTV accepted classification. All these results show that whole genome and proteome methods are valuable tools that aid in the comparative genomics of viral genomes.