The virome in mammalian physiology and disease

Cell

Volumn 157, Issue 1, 2014, Pages 142-150

  Virgin, Herbert W ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAMMA INTERFERON;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; BACTERIOPHAGE; CURVULARIA; CYTOKINE PRODUCTION; DNA VIRUS; EUKARYOTE; HEAT TOLERANCE; IDIOPATHIC DISEASE; IMMUNOCOMPETENT CELL; IMMUNOPHENOTYPING; IMMUNOSURVEILLANCE; INFLAMMATION; LISTERIA MONOCYTOGENES; MAMMAL; METAGENOME; MUCOSAL IMMUNITY; NATURAL KILLER CELL; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; REVIEW; RNA VIRUS; SYMBIOSIS; VIROME; VIRUS; VIRUS CELL INTERACTION; VIRUS IMMUNITY; VIRUS TRANSMISSION; VIRUS VIRULENCE; YERSINIA PESTIS; EUKARYOTIC CELL; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HOST CELL; HOST RESISTANCE; MAMMALIAN GENETICS; MAMMALIAN VIROME; MICROBIOME; VIRUS GENOME; VIRUS REPLICATION;

MAMMALIA;

ANIMALS; BACTERIA; BACTERIOPHAGES; HOST-PATHOGEN INTERACTIONS; HUMANS; MAMMALS; MICROBIOTA; VIRUSES;

EID: 84897127283     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.02.032     Document Type: Review

References (75)

1. A. Ablasser, J.L. Schmid-Burgk, I. Hemmerling, G.L. Horvath, T. Schmidt, E. Latz, and V. Hornung Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP Nature 503 2013 530 534
2. M.C. Abt, L.C. Osborne, L.A. Monticelli, T.A. Doering, T. Alenghat, G.F. Sonnenberg, M.A. Paley, M. Antenus, K.L. Williams, and J. Erikson et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity Immunity 37 2012 158 170
3. L.J. Abu-Raddad, P. Patnaik, and J.G. Kublin Dual infection with HIV and malaria fuels the spread of both diseases in sub-Saharan Africa Science 314 2006 1603 1606
4. J.K. Actor, M. Shirai, M.C. Kullberg, R.M. Buller, A. Sher, and J.A. Berzofsky Helminth infection results in decreased virus-specific CD8+ cytotoxic T-cell and Th1 cytokine responses as well as delayed virus clearance Proc. Natl. Acad. Sci. USA 90 1993 948 952
5. F. Angly, B. Rodriguez-Brito, D. Bangor, P. McNairnie, M. Breitbart, P. Salamon, B. Felts, J. Nulton, J. Mahaffy, and F. Rohwer PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information BMC Bioinformatics 6 2005 41
6. X. Bao, and M.J. Roossinck A life history view of mutualistic viral symbioses: quantity or quality for cooperation? Curr. Opin. Microbiol. 16 2013 514 518
7. J.J. Barr, R. Auro, M. Furlan, K.L. Whiteson, M.L. Erb, J. Pogliano, A. Stotland, R. Wolkowicz, A.S. Cutting, and K.S. Doran et al. Bacteriophage adhering to mucus provide a non-host-derived immunity Proc. Natl. Acad. Sci. USA 110 2013 10771 10776
8. E.S. Barton, D.W. White, J.S. Cathelyn, K.A. Brett-McClellan, M. Engle, M.S. Diamond, V.L. Miller, and H.W. Virgin 4th Herpesvirus latency confers symbiotic protection from bacterial infection Nature 447 2007 326 329
9. M. Basic, L.M. Keubler, M. Buettner, M. Achard, G. Breves, B. Schröder, A. Smoczek, A. Jörns, D. Wedekind, and N.H. Zschemisch et al. Norovirus triggered microbiota-driven mucosal inflammation in interleukin 10-deficient mice Inflamm. Bowel Dis. 20 2014 431 443
10. A.A. Bosch, G. Biesbroek, K. Trzcinski, E.A. Sanders, and D. Bogaert Viral and bacterial interactions in the upper respiratory tract PLoS Pathog. 9 2013 e1003057
11. K. Cadwell, K.K. Patel, N.S. Maloney, T.C. Liu, A.C. Ng, C.E. Storer, R.D. Head, R. Xavier, T.S. Stappenbeck, and H.W. Virgin Virus-plus- susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine Cell 141 2010 1135 1145
12. S.P. Canny, G. Goel, T.A. Reese, X. Zhang, R.J. Xavier, and H.W. Virgin Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs J. Virol. 88 2014 730 738
13. P. Colson, L. Fancello, G. Gimenez, F. Armougom, C. Desnues, G. Fournous, N. Yoosuf, M. Million, B. La Scola, and D. Raoult Evidence of the megavirome in humans J. Clin. Virol. 57 2013 191 200
14. R. Contreras-Galindo, M.H. Kaplan, S. He, A.C. Contreras-Galindo, M.J. Gonzalez-Hernandez, F. Kappes, D. Dube, S.M. Chan, D. Robinson, and F. Meng et al. HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses Genome Res. 23 2013 1505 1513
15. A.M. Cuesta, E. Suárez, M. Larsen, K.B. Jensen, L. Sanz, M. Compte, P. Kristensen, and L. Alvarez-Vallina Enhancement of DNA vaccine potency through linkage of antigen to filamentous bacteriophage coat protein III domain I Immunology 117 2006 502 506
16. J.C. de la Torre, and M.B. Oldstone Selective disruption of growth hormone transcription machinery by viral infection Proc. Natl. Acad. Sci. USA 89 1992 9939 9943
17. I. De Vlaminck, K.K. Khush, C. Strehl, B. Kohli, H. Luikart, N.F. Neff, J. Okamoto, T.M. Snyder, D.N. Cornfield, and M.R. Nicolls et al. Temporal response of the human virome to immunosuppression and antiviral therapy Cell 155 2013 1178 1187
18. B.A. Duerkop, and L.V. Hooper Resident viruses and their interactions with the immune system Nat. Immunol. 14 2013 654 659
19. F. Eriksson, P. Tsagozis, K. Lundberg, R. Parsa, S.M. Mangsbo, M.A.A. Persson, R.A. Harris, and P. Pisa Tumor-specific bacteriophages induce tumor destruction through activation of tumor-associated macrophages J. Immunol. 182 2009 3105 3111
20. M.A. Farrar, and R.D. Schreiber The molecular cell biology of interferon-gamma and its receptor Annu. Rev. Immunol. 11 1993 571 611
21. C. Feschotte, and C. Gilbert Endogenous viruses: insights into viral evolution and impact on host biology Nat. Rev. Genet. 13 2012 283 296
22. R.N. Fichorova, Y. Lee, H.S. Yamamoto, Y. Takagi, G.R. Hayes, R.P. Goodman, X. Chepa-Lotrea, O.R. Buck, R. Murray, and T. Kula et al. Endobiont viruses sensed by the human host - beyond conventional antiparasitic therapy PLoS ONE 7 2012 e48418
23. K. Findley, J. Oh, J. Yang, S. Conlan, C. Deming, J.A. Meyer, D. Schoenfeld, E. Nomicos, M. Park, H.H. Kong, J.A. Segre NIH Intramural Sequencing Center Comparative Sequencing Program Topographic diversity of fungal and bacterial communities in human skin Nature 498 2013 367 370
24. S.R. Finkbeiner, A.F. Allred, P.I. Tarr, E.J. Klein, C.D. Kirkwood, and D. Wang Metagenomic analysis of human diarrhea: viral detection and discovery PLoS Pathog. 4 2008 e1000011
25. E.F. Foxman, and A. Iwasaki Genome-virome interactions: examining the role of common viral infections in complex disease Nat. Rev. Microbiol. 9 2011 254 264
26. T. Fülöp, A. Larbi, and G. Pawelec Human T cell aging and the impact of persistent viral infections Front Immunol 4 2013 271
27. E.E. Gill, and F.S. Brinkman The proportional lack of archaeal pathogens: Do viruses/phages hold the key? Bioessays 33 2011 248 254
28. S.A. Handley, L.B. Thackray, G. Zhao, R. Presti, A.D. Miller, L. Droit, P. Abbink, L.F. Maxfield, A. Kambal, and E. Duan et al. Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome Cell 151 2012 253 266
29. A. Haque, N. Rachinel, M.R. Quddus, S. Haque, L.H. Kasper, and E. Usherwood Co-infection of malaria and gamma-herpesvirus: exacerbated lung inflammation or cross-protection depends on the stage of viral infection Clin. Exp. Immunol. 138 2004 396 404
30. E.C. Holmes The evolution of endogenous viral elements Cell Host Microbe 10 2011 368 377
31. T. Ichinohe, I.K. Pang, Y. Kumamoto, D.R. Peaper, J.H. Ho, T.S. Murray, and A. Iwasaki Microbiota regulates immune defense against respiratory tract influenza A virus infection Proc. Natl. Acad. Sci. USA 108 2011 5354 5359
32. I.D. Iliev, V.A. Funari, K.D. Taylor, Q. Nguyen, C.N. Reyes, S.P. Strom, J. Brown, C.A. Becker, P.R. Fleshner, and M. Dubinsky et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis Science 336 2012 1314 1317
33. A. Ives, C. Ronet, F. Prevel, G. Ruzzante, S. Fuertes-Marraco, F. Schutz, H. Zangger, M. Revaz-Breton, L.F. Lye, and S.M. Hickerson et al. Leishmania RNA virus controls the severity of mucocutaneous leishmaniasis Science 331 2011 775 778
34. S.M. Kamal, J.W. Rasenack, L. Bianchi, A. Al Tawil, K. El Sayed Khalifa, T. Peter, H. Mansour, W. Ezzat, and M. Koziel Acute hepatitis C without and with schistosomiasis: correlation with hepatitis C-specific CD4(+) T-cell and cytokine response Gastroenterology 121 2001 646 656
35. M. Kane, L.K. Case, K. Kopaskie, A. Kozlova, C. MacDearmid, A.V. Chervonsky, and T.V. Golovkina Successful transmission of a retrovirus depends on the commensal microbiota Science 334 2011 245 249
36. S.K. Kuss, G.T. Best, C.A. Etheredge, A.J. Pruijssers, J.M. Frierson, L.V. Hooper, T.S. Dermody, and J.K. Pfeiffer Intestinal microbiota promote enteric virus replication and systemic pathogenesis Science 334 2011 249 252
37. D.A. Leib, T.E. Harrison, K.M. Laslo, M.A. Machalek, N.J. Moorman, and H.W. Virgin Interferons regulate the phenotype of wild-type and mutant herpes simplex viruses in vivo J. Exp. Med. 189 1999 663 672
38. D.A. Leib, M.A. Machalek, B.R. Williams, R.H. Silverman, and H.W. Virgin Specific phenotypic restoration of an attenuated virus by knockout of a host resistance gene Proc. Natl. Acad. Sci. USA 97 2000 6097 6101
39. L. Li, T. Shan, C. Wang, C. Côté, J. Kolman, D. Onions, F.M. Gulland, and E. Delwart The fecal viral flora of California sea lions J. Virol. 85 2011 9909 9917
40. L. Li, X. Deng, P. Linsuwanon, D. Bangsberg, M.B. Bwana, P. Hunt, J.N. Martin, S.G. Deeks, and E. Delwart AIDS alters the commensal plasma virome J. Virol. 87 2013 10912 10915
41. F. Lysholm, A. Wetterbom, C. Lindau, H. Darban, A. Bjerkner, K. Fahlander, A.M. Lindberg, B. Persson, T. Allander, and B. Andersson Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing PLoS ONE 7 2012 e30875
42. L.M. Márquez, R.S. Redman, R.J. Rodriguez, and M.J. Roossinck A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance Science 315 2007 513 515
43. S. Minot, S. Grunberg, G.D. Wu, J.D. Lewis, and F.D. Bushman Hypervariable loci in the human gut virome Proc. Natl. Acad. Sci. USA 109 2012 3962 3966
44. J.L. Mokili, F. Rohwer, and B.E. Dutilh Metagenomics and future perspectives in virus discovery Curr. Opin. Virol. 2 2012 63 77
45. K. Mori, T. Kubo, Y. Kibayashi, T. Ohkuma, and A. Kaji Anti-vaccinia virus effect of M13 bacteriophage DNA Antiviral Res. 31 1996 79 86
46. M.R. Morsy, J. Oswald, J. He, Y. Tang, and M.J. Roossinck Teasing apart a three-way symbiosis: transcriptome analyses of Curvularia protuberata in response to viral infection and heat stress Biochem. Biophys. Res. Commun. 401 2010 225 230
47. Y. Nguyen, B.A. McGuffie, V.E. Anderson, and J.B. Weinberg Gammaherpesvirus modulation of mouse adenovirus type 1 pathogenesis Virology 380 2008 182 190
48. J.M. Norman, S.A. Handley, and H.W. Virgin Kingdom-agnostic metagenomics: the importance of complete characterization of enteric microbial communities Gastroenterology 2014 10.1053/j.gastro.2014.02.001
49. M.R. Patel, M. Emerman, and H.S. Malik Paleovirology - ghosts and gifts of viruses past Curr. Opin. Virol. 1 2011 304 309
50. J.W. Peacock, S.F. Elsawa, C.C. Petty, W.F. Hickey, and K.L. Bost Exacerbation of experimental autoimmune encephalomyelitis in rodents infected with murine gammaherpesvirus-68 Eur. J. Immunol. 33 2003 1849 1858
51. T.G. Phan, B. Kapusinszky, C. Wang, R.K. Rose, H.L. Lipton, and E.L. Delwart The fecal viral flora of wild rodents PLoS Pathog. 7 2011 e1002218
52. N. Popgeorgiev, S. Temmam, D. Raoult, and C. Desnues Describing the silent human virome with an emphasis on giant viruses Intervirology 56 2013 395 412
53. D. Prangishvili The wonderful world of archaeal viruses Annu. Rev. Microbiol. 67 2013 565 585
54. A. Reyes, M. Haynes, N. Hanson, F.E. Angly, A.C. Heath, F. Rohwer, and J.I. Gordon Viruses in the faecal microbiota of monozygotic twins and their mothers Nature 466 2010 334 338
55. A. Reyes, N.P. Semenkovich, K. Whiteson, F. Rohwer, and J.I. Gordon Going viral: next-generation sequencing applied to phage populations in the human gut Nat. Rev. Microbiol. 10 2012 607 617
56. M.J. Roossinck The good viruses: viral mutualistic symbioses Nat. Rev. Microbiol. 9 2011 99 108
57. R. Rosenberg, M.A. Johansson, A.M. Powers, and B.R. Miller Search strategy has influenced the discovery rate of human viruses Proc. Natl. Acad. Sci. USA 110 2013 13961 13964
58. V. Sancho-Shimizu, R. Perez de Diego, E. Jouanguy, S.Y. Zhang, and J.L. Casanova Inborn errors of anti-viral interferon immunity in humans Curr. Opin. Virol. 1 2011 487 496
59. A. Sen, M.E. Rothenberg, G. Mukherjee, N. Feng, T. Kalisky, N. Nair, I.M. Johnstone, M.F. Clarke, and H.B. Greenberg Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution Proc. Natl. Acad. Sci. USA 109 2012 20667 20672
60. T. Shan, L. Li, P. Simmonds, C. Wang, A. Moeser, and E. Delwart The fecal virome of pigs on a high-density farm J. Virol. 85 2011 11697 11708
61. I. Smith, and L.F. Wang Bats and their virome: an important source of emerging viruses capable of infecting humans Curr. Opin. Virol. 3 2013 84 91
62. K.A. Smith, S. Efstathiou, and A. Cooke Murine gammaherpesvirus-68 infection alters self-antigen presentation and type 1 diabetes onset in NOD mice J. Immunol. 179 2007 7325 7333
63. E. Stelekati, and E.J. Wherry Chronic bystander infections and immunity to unrelated antigens Cell Host Microbe 12 2012 458 469
64. N. Sutkowski, G. Chen, G. Calderon, and B.T. Huber Epstein-Barr virus latent membrane protein LMP-2A is sufficient for transactivation of the human endogenous retrovirus HERV-K18 superantigen J. Virol. 78 2004 7852 7860
65. N. Sutkowski, B. Conrad, D.A. Thorley-Lawson, and B.T. Huber Epstein-Barr virus transactivates the human endogenous retrovirus HERV-K18 that encodes a superantigen Immunity 15 2001 579 589
66. J.W. Uhr, J. Dancis, E.C. Franklin, M.S. Finkelstein, and E.W. Lewis The antibody response to bacteriophage phi-X 174 in newborn premature infants J. Clin. Invest. 41 1962 1509 1513
67. A. Valsamakis, Y. Riviere, and M.B. Oldstone Perturbation of differentiated functions in vivo during persistent viral infection. III. Decreased growth hormone mRNA Virology 156 1987 214 220
68. H.W. Virgin, and J.A. Todd Metagenomics and personalized medicine Cell 147 2011 44 56
69. H.W. Virgin, E.J. Wherry, and R. Ahmed Redefining chronic viral infection Cell 138 2009 30 50
70. D.W. White, C.R. Keppel, S.E. Schneider, T.A. Reese, J. Coder, J.E. Payton, T.J. Ley, H.W. Virgin, and T.A. Fehniger Latent herpesvirus infection arms NK cells Blood 115 2010 4377 4383
71. D.W. White, R. Suzanne Beard, and E.S. Barton Immune modulation during latent herpesvirus infection Immunol. Rev. 245 2012 189 208
72. D. Willner, M. Furlan, M. Haynes, R. Schmieder, F.E. Angly, J. Silva, S. Tammadoni, B. Nosrat, D. Conrad, and F. Rohwer Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals PLoS ONE 4 2009 e7370
73. M.E. Woolhouse, R. Howey, E. Gaunt, L. Reilly, M. Chase-Topping, and N. Savill Temporal trends in the discovery of human viruses Proc. Biol. Sci. 275 2008 2111 2115
74. G.R. Young, U. Eksmond, R. Salcedo, L. Alexopoulou, J.P. Stoye, and G. Kassiotis Resurrection of endogenous retroviruses in antibody-deficient mice Nature 491 2012 774 778
75. P. Yu, W. Lübben, H. Slomka, J. Gebler, M. Konert, C. Cai, L. Neubrandt, O. Prazeres da Costa, S. Paul, and S. Dehnert et al. Nucleic acid-sensing Toll-like receptors are essential for the control of endogenous retrovirus viremia and ERV-induced tumors Immunity 37 2012 867 879