Exploring virus relationships based on virus-host protein-protein interaction network

BackgroundCurrently, several systems have been proposed to classify viruses and indicate the relationships between different ones, though each system has its limitations because of the complexity of viral origins and their rapid evolution rate. We hereby propose a new method to explore the relationships between different viruses.MethodA new method, which is based on the virus-host protein-protein interaction network, is proposed in this paper to categorize viruses. The distances between 114 human viruses, including 48 HIV-1 and HIV-2 viruses, are estimated according to the protein-protein interaction network between these viruses and humans.Conclusions/significanceThe results demonstrated that our method can disclose not only relationships consistent with the taxonomic results of currently used systems of classification but also the potential relationships that the current virus classification systems have not revealed. Moreover, the method points to a new direction where the functional relationships between viruses and hosts can be used to explore the virus relationships on a systematic level.

[1]  E. Steinhaus.  Nomenclature and classification of insect viruses. , 1949, Bacteriological reviews.

[2]  A. Lwoff,et al.  A system of viruses. , 1962, Cold Spring Harbor symposia on quantitative biology.

[3]  D. Baltimore.  Expression of animal virus genomes. , 1971, Bacteriological reviews.

[4]  D. McGeoch,et al.  Molecular phylogeny of the alphaherpesvirinae subfamily and a proposed evolutionary timescale. , 1994, Journal of molecular biology.

[5]  S. Cook,et al.  Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses. , 1995, Journal of molecular biology.

[6]  M. Woolhouse,et al.  Parasite―host coevolution and geographic patterns of parasite infectivity and host susceptibility , 1996, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[7]  J. Maniloff,et al.  Taxonomy of bacterial viruses: establishment of tailed virus genera and the other Caudovirales , 1998, Archives of Virology.

[8]  M. A. Mayo,et al.  Virus taxonomy--1997. , 1998, The Journal of general virology.

[9]  A. Brunt,et al.  Virus Taxonomy. Seventh Report of the International Committee on Taxomony of Viruses , 1999 .

[10]  L. Liljas.  Virus assembly. , 1999, Current opinion in structural biology.

[11]  Damgaard,et al.  Coevolution of a plant host-pathogen gene-for-gene system in a metapopulation model without cost of resistance or cost of virulence , 1999, Journal of theoretical biology.

[12]  A. Sasaki.  Host-parasite coevolution in a multilocus gene-for-gene system , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[13]  M. Mayo,et al.  Virus nomenclature: consensus versus chaos , 2000, Archives of Virology.

[14]  N. Suzuki.  Virus Taxonomy : Seventh Report of the International Committee for the Taxonomy of Viruses.(共著) , 2000 .

[15]  S. Gandon,et al.  Evolution of parasite virulence against qualitative or quantitative host resistance , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[16]  B. Charlesworth,et al.  Biological and biomedical implications of the co-evolution of pathogens and their hosts , 2002, Nature Genetics.

[17]  A. Lackner,et al.  Classic AIDS in a Sooty Mangabey after an 18-Year Natural Infection , 2004, Journal of Virology.

[18]  C. Buechen-Osmond,et al.  Towards a universal virus database — progress in the ICTVdB , 2005, Archives of Virology.

[19]  M. Mayo,et al.  ICTV in San Francisco: a report from the Plenary Session , 2005, Archives of Virology.

[20]  T. Barrette,et al.  Probabilistic model of the human protein-protein interaction network , 2005, Nature Biotechnology.

[21]  R. D. de Boer,et al.  The Integration Hypothesis: An Evolutionary Pathway to Benign SIV Infection , 2006, PLoS pathogens.

[22]  Matthew D. Dyer,et al.  The Landscape of Human Proteins Interacting with Viruses and Other Pathogens , 2008, PLoS pathogens.

[23]  Guang Li,et al.  AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology , 2007, Nucleic Acids Res..

[24]  K. Williams,et al.  HIV and SIV infection: the role of cellular restriction and immune responses in viral replication and pathogenesis , 2009, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[25]  A. Ireland,et al.  Applying the Gene Ontology in microbial annotation. , 2009, Trends in microbiology.