Will our increasing understanding of virus-host interactions translate into a new generation of antiviral therapeutics or steer us toward an expensive journey to nowhere?
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Narrative review on century of respiratory pandemics from Spanish flu to COVID-19 and impact of nanotechnology on COVID-19 diagnosis and immune system boosting
Virology Journal Open Access 24 October 2022
-
A global lipid map defines a network essential for Zika virus replication
Nature Communications Open Access 21 July 2020
-
Human enterovirus 71 protein interaction network prompts antiviral drug repositioning
Scientific Reports Open Access 21 February 2017
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout



References
Noble, D. The Music of Life: Biology Beyond the Genome (Oxford University Press, New York, 2006).
Salerno, D. et al. Direct inhibition of CDK9 blocks HIV-1 replication without preventing T-cell activation in primary human peripheral blood lymphocytes. Gene 405, 65–78 (2007).
Schang, L.M. First demonstration of the effectiveness of inhibitors of cellular protein kinases in antiviral therapy. Expert Rev. Anti Infect. Ther. 4, 953–956 (2006).
de Angelis, D.S., Freire, W.S., Pannuti, C.S., Succi, R.C. & Machado, D.M. CCR5 genotypes and progression to HIV disease in perinatally infected children. Braz. J. Infect. Dis. 11, 196–198 (2007).
Wheeler, J., McHale, M., Jackson, V. & Penny, M. Assessing theoretical risk and benefit suggested by genetic association studies of CCR5: experience in a drug development programme for maraviroc. Antivir. Ther. 12, 233–245 (2007).
Tan, S.L., He, Y., Huang, Y. & Gale, M. Jr. Strategies for hepatitis C therapeutic intervention: now and next. Curr. Opin. Pharmacol. 4, 465–470 (2004).
Horsmans, Y. et al. Isatoribine, an agonist of TLR7, reduces plasma virus concentration in chronic hepatitis C infection. Hepatology 42, 724–731 (2005).
Lee, J. et al. Activation of anti-hepatitis C virus responses via Toll-like receptor 7. Proc. Natl. Acad. Sci. USA 103, 1828–1833 (2006).
Vanwolleghem, T. et al. Ultra-rapid cardiotoxicity of the hepatitis C virus protease inhibitor BILN 2061 in the urokinase-type plasminogen activator mouse. Gastroenterology 133, 1144–1155 (2007).
ViroPharma Inc. Potential Safety Issue Identified in Ongoing Phase 2 Clinical Study of HCV-796 (press release) (ViroPharma Inc., Exton, Pennsylvania, USA, 2007).
Davidov, E., Holland, J., Marple, E. & Naylor, S. Advancing drug discovery through systems biology. Drug Discov. Today 8, 175–183 (2003).
Butcher, E.C., Berg, E.L. & Kunkel, E.J. Systems biology in drug discovery. Nat. Biotechnol. 22, 1253–1259 (2004).
Gibbs, R.A. et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222–234 (2007).
Wallace, J.C. et al. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. BMC Genomics 8, 28 (2007).
Tumpey, T.M. et al. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 310, 77–80 (2005).
Kobasa, D. et al. Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 445, 319–323 (2007).
Walters, K.A. et al. Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis. Virol. J. 3, 37–44 (2006).
Kash, J.C. et al. Global suppression of the host antiviral response by Ebola- and Marburgviruses: increased antagonism of the type 1 interferon response is associated with enhanced virulence. J. Virol. 80, 3009–3020 (2006).
Fredericksen, B.L., Smith, M., Katze, M.G., Shi, P.Y. & Gale, M. Jr. The host response to West Nile Virus infection limits viral spread through the activation of the interferon regulatory factor 3 pathway. J. Virol. 78, 7737–7747 (2004).
Baas, T., Taubenberger, J., Chong, P.Y., Chui, P. & Katze, M.G. SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues. J. Interferon Cytokine Res. 26, 309–317 (2006).
Pasieka, T.J. et al. Functional genomics analysis of herpes simplex virus type 1 counteraction of the host innate response. J. Virol. 80, 7600–7612 (2006).
Li, Y., Chan, E.Y. & Katze, M.G. Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus. Virology 366, 137–149 (2007).
Wallace, J.C., Korth, M.J., Diamond, D.L., Proll, S.C. & Katze, M.G. Virology in the 21st century: finding function with functional genomics. Future Virol. 1, 47–53 (2006).
Diamond, D.L. et al. Proteomic profiling of human liver biopsies: hepatitis C virus-induced fibrosis and mitochondrial dysfunction. Hepatology 46, 649–657 (2007).
Bandyopadhyay, S., Kelley, R. & Ideker, T. Discovering regulated networks during HIV-1 latency and reactivation. Pac. Symp. Biocomput. 11, 354–366 (2006).
Uetz, P. et al. Herpesviral protein networks and their interaction with the human proteome. Science 311, 239–242 (2006).
Chan, L.Y., Kosuri, S. & Endy, D. Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005.0018 (2005).
Bartee, E., McCormack, A. & Fruh, K. Quantitative membrane proteomics reveals new cellular targets of viral immune modulators. PLoS Pathog. 2, e107 (2006).
Bentwich, I. Bioinformatically detectable group of novel HIV regulatory genes and uses thereof. US Patent 7,217,807 (2007).
Burnside, J. et al. Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J. Virol. 80, 8778–8786 (2006).
Cai, X. et al. Kaposi's sarcoma-associated herpes-virus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. USA 102, 5570–5575 (2005).
Cui, C. et al. Prediction and identification of herpes simplex virus 1-encoded microRNAs. J. Virol. 80, 5499–5508 (2006).
Grey, F. et al. Identification and characterization of human cytomegalovirus-encoded microRNAs. J. Virol. 79, 12095–12099 (2005).
Pfeffer, S. Identification of virally encoded microRNAs. Methods Enzymol. 427, 51–63 (2007).
Sullivan, C.S., Grundhoff, A.T., Tevethia, S., Pipas, J.M. & Ganem, D. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435, 682–686 (2005).
Grundhoff, A., Sullivan, C.S. & Ganem, D. A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpes-viruses. RNA 12, 733–750 (2006).
Chan, E.Y. et al. Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production. J. Virol. 81, 7571–7583 (2007).
Zhu, H., Cong, J.P., Mamtora, G., Gingeras, T. & Shenk, T. Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 95, 14470–14475 (1998).
Moses, A.V. et al. A functional genomics approach to Kaposi's sarcoma. Ann. NY Acad. Sci. 975, 180–191 (2002).
Chun, T.W. et al. Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc. Natl. Acad. Sci. USA 100, 1908–1913 (2003).
Sakamoto, H. et al. Host sphingolipid biosynthesis as a target for hepatitis C virus therapy. Nat. Chem. Biol. 1, 333–337 (2005).
Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436, 78–86 (2005).
Fellay, J. et al. A whole-genome association study of major determinants for host control of HIV-1. Science 317, 944–947 (2007).
Foulkes, A.S. et al. Associations among race/ethnicity, ApoC-III genotypes, and lipids in HIV-1-infected individuals on antiretroviral therapy. PLoS Med. 3, e52 (2006).
Haas, D.W. Human genetic variability and HIV treatment response. Curr. HIV/AIDS Rep. 3, 53–58 (2006).
Dahri, K. & Ensom, M.H. Efavirenz and nevirapine in HIV-1 infection: is there a role for clinical pharmaco-kinetic monitoring? Clin. Pharmacokinet. 46, 109–132 (2007).
Wright, M., Grieve, R., Roberts, J., Main, J., & Thomas, H.C. Health benefits of antiviral therapy for mild chronic hepatitis C: randomised controlled trial and economic evaluation. Health Technol. Assess. 10, 1–113, iii (2006).
Xie, Y. et al. Predictive factors for sustained response to interferon treatment in patients with chronic hepatitis C: a randomized, open, and multi-center controlled trial. Hepatobiliary Pancreat. Dis. Int. 4, 213–219 (2005).
Angulo, M. & Carvajal-Rodriguez, A. Evidence of recombination within human alpha-papillomavirus. Virol. J. 4, 33–40 (2007).
Ding, X.R., Yang, J., Sun, D.C., Lou, S.K. & Wang, S.Q. Whole genome expression profiling of hepatitis B virus-transfected cell line reveals the potential targets of anti-HBV drugs. Pharmacogenomics. J. published online (15 May 2007). doi:10.1038/sj.tpj.6500459
Damm, E.M. & Pelkmans, L. Systems biology of virus entry in mammalian cells. Cell. Microbiol. 8, 1219–1227 (2006).
Silver, P.A. & Way, J.C. Molecular systems biology in drug development. Clin. Pharmacol. Ther. 82, 586–590 (2007).
Giuliano, K.A., Johnston, P.A., Gough, A. & Taylor, D.L. Systems cell biology based on high-content screening. Methods Enzymol. 414, 601–619 (2006).
Piwnica-Worms, D., Schuster, D.P. & Garbow, J.R. Molecular imaging of host-pathogen interactions in intact small animals. Cell. Microbiol. 6, 319–331 (2004).
He, M.L. et al. Inhibition of SARS-associated coronavirus infection and replication by RNA interference. JAMA 290, 2665–2666 (2003).
Neuman de Vegvar, H.E. et al. Microarray profiling of antibody responses against simian-human immunodeficiency virus: postchallenge convergence of reactivities independent of host histocompatibility type and vaccine regimen. J. Virol. 77, 11125–11138 (2003).
Aderem, A. Systems biology: its practice and challenges. Cell 121, 511–513 (2005).
Holmes, E.C. Viral evolution in the genomic age. PLoS Biol. 5, e278 (2007).
Braga-Neto, U.M. & Marques, E.T. Jr. From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput. Biol 2, e81 (2006).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Tan, SL., Ganji, G., Paeper, B. et al. Systems biology and the host response to viral infection. Nat Biotechnol 25, 1383–1389 (2007). https://doi.org/10.1038/nbt1207-1383
Issue date:
DOI: https://doi.org/10.1038/nbt1207-1383
This article is cited by
-
Narrative review on century of respiratory pandemics from Spanish flu to COVID-19 and impact of nanotechnology on COVID-19 diagnosis and immune system boosting
Virology Journal (2022)
-
A global lipid map defines a network essential for Zika virus replication
Nature Communications (2020)
-
Human enterovirus 71 protein interaction network prompts antiviral drug repositioning
Scientific Reports (2017)
-
Identification and characterization of the role of c-terminal Src kinase in dengue virus replication
Scientific Reports (2016)
-
Analysis of sequences of hepatitis C virus NS5A genotype 1 in HIV-coinfected patients with a null response to nitazoxanide or peg-interferon plus ribavirin
Archives of Virology (2013)