Virogenomics: the Virus-host Interaction Revisited

Overview

Journal Curr Opin Microbiol

Specialty Microbiology

Date 2008 Sep 30

PMID 18822388

Citations 5

Authors

Arno C Andeweg

Bart L Haagmans

Albert Dme Osterhaus

Affiliations

Soon will be listed here.

Abstract

Genomics tools allow us to assess gene expression 'genome wide' providing an unprecedented view on the host-side of the virus-host interaction. The success of the application of these tools crucially depends on our ability to reduce the total information load while increasing the information density of the data collected. In addition to the advanced data analysis algorithms, gene annotation-pathway databases, and theoretical models, specifically designed sets of complementary experiments are crucial in translating the collected genomics data into palatable knowledge. A better understanding of the molecular basis of virus-host interactions will support the rational design of improved and novel intervention strategies for viral infections.

Citing Articles

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References

Lucchesi W, Brady G, Dittrich-Breiholz O, Kracht M, Russ R, Farrell P . Differential gene regulation by Epstein-Barr virus type 1 and type 2 EBNA2. J Virol. 2008; 82(15):7456-66. PMC: 2493322. DOI: 10.1128/JVI.00223-08. View

Piqueras B, Connolly J, Freitas H, Palucka A, Banchereau J . Upon viral exposure, myeloid and plasmacytoid dendritic cells produce 3 waves of distinct chemokines to recruit immune effectors. Blood. 2005; 107(7):2613-8. PMC: 1895384. DOI: 10.1182/blood-2005-07-2965. View

Martinez I, Lombardia L, Garcia-Barreno B, Dominguez O, Melero J . Distinct gene subsets are induced at different time points after human respiratory syncytial virus infection of A549 cells. J Gen Virol. 2007; 88(Pt 2):570-581. DOI: 10.1099/vir.0.82187-0. View

Cheung C, Poon L, Ng I, Luk W, Sia S, Wu M . Cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis. J Virol. 2005; 79(12):7819-26. PMC: 1143636. DOI: 10.1128/JVI.79.12.7819-7826.2005. View

Cogburn L, Porter T, Duclos M, Simon J, Burgess S, Zhu J . Functional genomics of the chicken--a model organism. Poult Sci. 2007; 86(10):2059-94. DOI: 10.1093/ps/86.10.2059. View

Jenner R, Young R . Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol. 2005; 3(4):281-94. DOI: 10.1038/nrmicro1126. View

Geiss G, Bumgarner R, An M, Agy M, van t Wout A, Hammersmark E . Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology. 1999; 266(1):8-16. DOI: 10.1006/viro.1999.0044. View

Elco C, Guenther J, Williams B, Sen G . Analysis of genes induced by Sendai virus infection of mutant cell lines reveals essential roles of interferon regulatory factor 3, NF-kappaB, and interferon but not toll-like receptor 3. J Virol. 2005; 79(7):3920-9. PMC: 1061568. DOI: 10.1128/JVI.79.7.3920-3929.2005. View

Huang Q, Liu D, Majewski P, Schulte L, Korn J, Young R . The plasticity of dendritic cell responses to pathogens and their components. Science. 2001; 294(5543):870-5. DOI: 10.1126/science.294.5543.870. View

10.

Sherman B, Huang D, Tan Q, Guo Y, Bour S, Liu D . DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics. 2007; 8:426. PMC: 2186358. DOI: 10.1186/1471-2105-8-426. View

11.

Tang B, Chan K, Cheng V, Woo P, Lau S, Lam C . Comparative host gene transcription by microarray analysis early after infection of the Huh7 cell line by severe acute respiratory syndrome coronavirus and human coronavirus 229E. J Virol. 2005; 79(10):6180-93. PMC: 1091719. DOI: 10.1128/JVI.79.10.6180-6193.2005. View

12.

Adamo M, Zapata M, Frey T . Analysis of gene expression in fetal and adult cells infected with rubella virus. Virology. 2007; 370(1):1-11. PMC: 2694049. DOI: 10.1016/j.virol.2007.08.003. View

13.

Sato H, Honma R, Yoneda M, Miura R, Tsukiyama-Kohara K, Ikeda F . Measles virus induces cell-type specific changes in gene expression. Virology. 2008; 375(2):321-30. DOI: 10.1016/j.virol.2008.02.015. View

14.

Tian B, Zhang Y, Luxon B, Garofalo R, Casola A, Sinha M . Identification of NF-kappaB-dependent gene networks in respiratory syncytial virus-infected cells. J Virol. 2002; 76(13):6800-14. PMC: 136270. DOI: 10.1128/jvi.76.13.6800-6814.2002. View

15.

Aich P, Wilson H, Kaushik R, Potter A, Babiuk L, Griebel P . Comparative analysis of innate immune responses following infection of newborn calves with bovine rotavirus and bovine coronavirus. J Gen Virol. 2007; 88(Pt 10):2749-2761. DOI: 10.1099/vir.0.82861-0. View

16.

Mossman K, Macgregor P, Rozmus J, Goryachev A, Edwards A, SMILEY J . Herpes simplex virus triggers and then disarms a host antiviral response. J Virol. 2001; 75(2):750-8. PMC: 113971. DOI: 10.1128/JVI.75.2.750-758.2001. View

17.

Sundstrom M, Chatterji U, Schaffer L, de Rozieres S, Elder J . Feline immunodeficiency virus OrfA alters gene expression of splicing factors and proteasome-ubiquitination proteins. Virology. 2007; 371(2):394-404. PMC: 2255568. DOI: 10.1016/j.virol.2007.09.039. View

18.

Geiss G, An M, Bumgarner R, Hammersmark E, Cunningham D, Katze M . Global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events. J Virol. 2001; 75(9):4321-31. PMC: 114177. DOI: 10.1128/JVI.75.9.4321-4331.2001. View

19.

Augenlicht L, Wahrman M, HALSEY H, Anderson L, Taylor J, Lipkin M . Expression of cloned sequences in biopsies of human colonic tissue and in colonic carcinoma cells induced to differentiate in vitro. Cancer Res. 1987; 47(22):6017-21. View

20.

Kulesh D, Clive D, Zarlenga D, GREENE J . Identification of interferon-modulated proliferation-related cDNA sequences. Proc Natl Acad Sci U S A. 1987; 84(23):8453-7. PMC: 299562. DOI: 10.1073/pnas.84.23.8453. View