Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome

Cell

Volumn 151, Issue 2, 2012, Pages 253-266

  Handley, Scott A ^a   Thackray, Larissa B ^a   Zhao, Guoyan ^a   Presti, Rachel ^a   Miller, Andrew D ^b   Droit, Lindsay ^a   Abbink, Peter ^c   Maxfield, Lori F ^c   Kambal, Amal ^a   Duan, Erning ^a   Stanley, Kelly ^c   Kramer, Joshua ^b   MacRi, Sheila C ^b   Permar, Sallie R ^d   Schmitz, Joern E ^c   Mansfield, Keith ^b   Brenchley, Jason M ^e   Veazey, Ronald S ^f   Stappenbeck, Thaddeus S ^a   Wang, David ^a   Barouch, Dan H ^b,c   Virgin, Herbert W ^a   more..

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^d DUKE UNIVERSITY MEDICAL CENTER   (United States)

^e NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^f TULANE NATIONAL PRIMATE RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADENOVIRUS INFECTION; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BACTERIUM DETECTION; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE COURSE; ENTERIC VIRUS; ENTERITIS; ENTEROBACTERIACEAE; ENTEROPATHY; GENE SEQUENCE; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; PARVOVIRUS; PATHOGENESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; TAXONOMY; VIREMIA; VIRUS CULTURE; VIRUS PATHOGENESIS;

EID: 84867521316     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2012.09.024     Document Type: Article

References (45)

1. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
2. C. Bailey, and K. Mansfield Emerging and reemerging infectious diseases of nonhuman primates in the laboratory setting Vet. Pathol. 47 2010 462 481
3. 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 IV Herpesvirus latency confers symbiotic protection from bacterial infection Nature 447 2007 326 329
4. S.R. Bench, T.E. Hanson, K.E. Williamson, D. Ghosh, M. Radosovich, K. Wang, and K.E. Wommack Metagenomic characterization of Chesapeake Bay virioplankton Appl. Environ. Microbiol. 73 2007 7629 7641
5. S.M. Bloom, V.N. Bijanki, G.M. Nava, L. Sun, N.P. Malvin, D.L. Donermeyer, W.M. Dunne Jr., P.M. Allen, and T.S. Stappenbeck Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease Cell Host Microbe 9 2011 390 403
6. J.M. Brenchley, and D.C. Douek Microbial translocation across the GI tract Annu. Rev. Immunol. 30 2012 149 173
7. J.M. Brenchley, D.A. Price, and D.C. Douek HIV disease: fallout from a mucosal catastrophe? Nat. Immunol. 7 2006 235 239
8. J.M. Brenchley, D.A. Price, T.W. Schacker, T.E. Asher, G. Silvestri, S. Rao, Z. Kazzaz, E. Bornstein, O. Lambotte, and D. Altmann Microbial translocation is a cause of systemic immune activation in chronic HIV infection Nat. Med. 12 2006 1365 1371
9. J.M. Brenchley, G. Silvestri, and D.C. Douek Nonprogressive and progressive primate immunodeficiency lentivirus infections Immunity 32 2010 737 742
10. K. Cadwell, J.Y. Liu, S.L. Brown, H. Miyoshi, J. Loh, J.K. Lennerz, C. Kishi, W. Kc, J.A. Carrero, and S. Hunt A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells Nature 456 2008 259 263
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. E.K. Costello, C.L. Lauber, M. Hamady, N. Fierer, J.I. Gordon, and R. Knight Bacterial community variation in human body habitats across space and time Science 326 2009 1694 1697
13. J.D. Estes, L.D. Harris, N.R. Klatt, B. Tabb, S. Pittaluga, M. Paiardini, G.R. Barclay, J. Smedley, R. Pung, and K.M. Oliveira Damaged intestinal epithelial integrity linked to microbial translocation in pathogenic simian immunodeficiency virus infections PLoS Pathog. 6 2010 e1001052
14. T. Farkas, K. Sestak, C. Wei, and X. Jiang Characterization of a rhesus monkey calicivirus representing a new genus of Caliciviridae J. Virol. 82 2008 5408 5416
15. M.A. Félix, A. Ashe, J. Piffaretti, G. Wu, I. Nuez, T. Bélicard, Y. Jiang, G. Zhao, C.J. Franz, and L.D. Goldstein Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses PLoS Biol. 9 2011 e1000586
16. D.H. Huson, A.F. Auch, J. Qi, and S.C. Schuster MEGAN analysis of metagenomic data Genome Res. 17 2007 377 386
17. D.H. Huson, D.C. Richter, S. Mitra, A.F. Auch, and S.C. Schuster Methods for comparative metagenomics BMC Bioinformatics 10 Suppl 1 2009 S12
18. 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 Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis Science 336 2012 1314 1317
19. A.L. Kau, P.P. Ahern, N.W. Griffin, A.L. Goodman, and J.I. Gordon Human nutrition, the gut microbiome and the immune system Nature 474 2011 327 336
20. P. Legendre, and L. Legendre Numerical Ecology Second English Edition 1998 Elsevier Science B.V. Amsterdam
21. W. Li, and A. Godzik Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 2006 1658 1659
22. J. Loh, G. Zhao, R.M. Presti, L.R. Holtz, S.R. Finkbeiner, L. Droit, Z. Villasana, C. Todd, J.M. Pipas, and B. Calgua Detection of novel sequences related to African swine fever virus in human serum and sewage J. Virol. 83 2009 13019 13025
23. J. Loh, G. Zhao, C.A. Nelson, P. Coder, L. Droit, S.A. Handley, L.S. Johnson, P. Vachharajani, H. Guzman, and R.B. Tesh Identification and sequencing of a novel rodent gammaherpesvirus that establishes acute and latent infection in laboratory mice J. Virol. 85 2011 2642 2656
24. P. McKenna, C. Hoffmann, N. Minkah, P.P. Aye, A. Lackner, Z. Liu, C.A. Lozupone, M. Hamady, R. Knight, and F.D. Bushman The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis PLoS Pathog. 4 2008 e20
25. G.M. Nava, H.J. Friedrichsen, and T.S. Stappenbeck Spatial organization of intestinal microbiota in the mouse ascending colon ISME J. 5 2011 627 638
26. M.S. Oberste, K. Maher, and M.A. Pallansch Molecular phylogeny and proposed classification of the simian picornaviruses J. Virol. 76 2002 1244 1251
27. M.S. Oberste, K. Maher, and M.A. Pallansch Complete genome sequences for nine simian enteroviruses J. Gen. Virol. 88 2007 3360 3372
28. I. Pandrea, T. Gaufin, J.M. Brenchley, R. Gautam, C. Monjure, A. Gautam, C. Coleman, A.A. Lackner, R.M. Ribeiro, D.C. Douek, and C. Apetrei Cutting edge: experimentally induced immune activation in natural hosts of simian immunodeficiency virus induces significant increases in viral replication and CD4+ T cell depletion J. Immunol. 181 2008 6687 6691
29. T.G. Phan, N.P. Vo, I.J. Bonkoungou, A. Kapoor, N. Barro, M. O'Ryan, B. Kapusinszky, C. Wang, and E. Delwart Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus J. Virol. 86 2012 11024 11030
30. R.M. Presti, G. Zhao, W.L. Beatty, K.A. Mihindukulasuriya, A.P. da Rosa, V.L. Popov, R.B. Tesh, H.W. Virgin, and D. Wang Quaranfil, Johnston Atoll, and Lake Chad viruses are novel members of the family Orthomyxoviridae J. Virol. 83 2009 11599 11606
31. N.G. Sandler, and D.C. Douek Microbial translocation in HIV infection: causes, consequences and treatment opportunities Nat. Rev. Microbiol. 10 2012 655 666
32. V.G. Sasseville, and K.G. Mansfield Overview of known non-human primate pathogens with potential to affect colonies used for toxicity testing J. Immunotoxicol. 7 2010 79 92
33. D.L. Sodora, J.S. Allan, C. Apetrei, J.M. Brenchley, D.C. Douek, J.G. Else, J.D. Estes, B.H. Hahn, V.M. Hirsch, and A. Kaur Toward an AIDS vaccine: lessons from natural simian immunodeficiency virus infections of African nonhuman primate hosts Nat. Med. 15 2009 861 865
34. H.W. Virgin, and J.A. Todd Metagenomics and personalized medicine Cell 147 2011 44 56
35. H.W. Virgin, E.J. Wherry, and R. Ahmed Redefining chronic viral infection Cell 138 2009 30 50
36. D. Wang, A. Urisman, Y.T. Liu, M. Springer, T.G. Ksiazek, D.D. Erdman, E.R. Mardis, M. Hickenbotham, V. Magrini, and J. Eldred Viral discovery and sequence recovery using DNA microarrays PLoS Biol. 1 2003 E2
37. Y. Wang, X. Tu, C. Humphrey, H. McClure, X. Jiang, C. Qin, R.I. Glass, and B. Jiang Detection of viral agents in fecal specimens of monkeys with diarrhea J. Med. Primatol. 36 2007 101 107
38. K.E. Wommack, J. Bhavsar, and J. Ravel Metagenomics: read length matters Appl. Environ. Microbiol. 74 2008 1453 1463
39. T. Yatsunenko, F.E. Rey, M.J. Manary, I. Trehan, M.G. Dominguez-Bello, M. Contreras, M. Magris, G. Hidalgo, R.N. Baldassano, and A.P. Anokhin Human gut microbiome viewed across age and geography Nature 486 2012 222 227
40. G. Zhao, L. Droit, R.B. Tesh, V.L. Popov, N.S. Little, C. Upton, H.W. Virgin, and D. Wang The genome of Yoka poxvirus J. Virol. 85 2011 10230 10238
41. Abbink, P., Lemckert, A.A., Ewald, B.A., Lynch, D.M., Denholtz, M., Smits, S., Holterman, L., Damen, I., Vogels, R., Thorner, A.R., et al. (2007). Comparative seroprevalence and immunogenicity of six rare serotype recombinant adenovirus vaccine vectors from subgroups B and D. J. Virol. 81, 4654-4663.
42. Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.
43. Finkbeiner, S.R., Li, Y., Ruone, S., Conrardy, C., Gregoricus, N., Toney, D., Virgin, H.W., Anderson, L.J., Vinjé, J., Wang, D., and Tong, S. (2009). Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J. Virol. 83, 10836-10839.
44. Page, R.D. (1996). TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357-358.
45. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.