Microbe hunting

Microbiology and Molecular Biology Reviews

Volumn 74, Issue 3, 2010, Pages 363-377

  Lipkin, W Ian ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; MEASLES MUMPS RUBELLA VACCINE; PLECONARIL; RIBOSOME RNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMYOTROPHIC LATERAL SCLEROSIS; AUTISM; BIPOLAR DISORDER; BORNA DISEASE VIRUS; CAMPYLOBACTER JEJUNI; CHRONIC FATIGUE SYNDROME; DANDENONG VIRUS; DNA SEQUENCE; GENETIC ENGINEERING; GLIOBLASTOMA; GUILLAIN BARRE SYNDROME; HIV ASSOCIATED DEMENTIA; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOFLUORESCENCE; INFLUENZA VIRUS; INFLUENZA VIRUS A H1N1; LABORATORY; LOOP MEDIATED ISOTHERMAL AMPLIFICATION; LYMPHOCYTIC CHORIOMENINGITIS VIRUS; MAJOR DEPRESSION; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MICROARRAY ANALYSIS; MICROBIAL DIVERSITY; MICROBIOLOGICAL EXAMINATION; MICROORGANISM; MOTOR NEURON DISEASE; MULTIPLE SCLEROSIS; NIPAH VIRUS; NONHUMAN; NORTH AMERICA; PATHOGENESIS; PLASMODIUM FALCIPARUM; POLYMERASE CHAIN REACTION; PROPHYLAXIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SARS CORONAVIRUS; SCHIZOPHRENIA; SIN NOMBRE VIRUS; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE; VIGNETTE; WART VIRUS; WEST NILE FLAVIVIRUS;

BACTERIA; BACTERIAL INFECTIONS; BACTERIAL PROTEINS; COMMUNICABLE DISEASES; HUMANS; METABOLOMICS; PROTEOMICS;

EID: 77957985271     PISSN: 10922172     EISSN: 10985557     Source Type: Journal    
DOI: 10.1128/MMBR.00007-10     Document Type: Review

References (149)

1. Aas, J. A., B. J. Paster, L. N. Stokes, I. Olsen, and F. E. Dewhirst. 2005. Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43:5721-5732.
2. Allos, B. 1997. Association between Campylobacter infection and Guillain-Barré syndrome. J. Infect. Dis. 176:125-128.
3. Arden, K. E., P. McErlean, M. D. Nissen, T. P. Sloots, and I. M. Mackay. 2006. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J. Med. Virol. 78:1232-1240.
4. Armour, C., J. Castle, R. Chen, T. Babak, P. Loerch, S. Jackson, J. Shah, J. Dey, C. Rohl, and J. Johnson. 2009. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat. Methods 6:647-649.
5. Ashwood, P., A. Anthony, A. Pellicer, F. Torrente, J. Walker-Smith, and A. Wakefield. 2003. Intestinal lymphocyte populations in children with regressive autism: evidence for extensive mucosal immunopathology. J. Clin. Immunol. 23:504-517.
6. Ashwood, P., A. Anthony, F. Torrente, and A. Wakefield. 2004. Spontaneous mucosal lymphocyte cytokine profiles in children with autism and gastrointestinal symptoms: mucosal immune activation and reduced counter regulatory interleukin-10. J. Clin. Immunol. 24:664-673.
7. Ashwood, P., and A. Wakefield. 2006. Immune activation of peripheral blood and mucosal CD3+ lymphocyte cytokine profiles in children with autism and gastrointestinal symptoms. J. Neuroimmunol. 173:126-134.
8. Asnis, D. S., R. Conetta, A. A. Teixeira, G. Waldman, and B. A. Sampson. 2000. The West Nile virus outbreak of 1999 in New York: the Flushing Hospital experience. Clin. Infect. Dis. 30:413-418.
9. Barrette, R. W., S. A. Metwally, J. M. Rowland, L. Xu, S. R. Zaki, S. T. Nichol, P. E. Rollin, J. S. Towner, W. J. Shieh, B. Batten, T. K. Sealy, C. Carrillo, K. E. Moran, A. J. Bracht, G. A. Mayr, M. Sirios-Cruz, D. P. Catbagan, E. A. Lautner, T. G. Ksiazek, W. R. White, and M. T. McIntosh. 2009. Discovery of swine as a host for the Reston ebolavirus. Science 325:204-206.
10. Berger, M. M., N. Kopp, C. Vital, B. Redl, M. Aymard, and B. Lina. 2000. Detection and cellular localization of enterovirus RNA sequences in spinal cord of patients with ALS. Neurology 54:20-25.
11. Bik, E. M., P. B. Eckburg, S. R. Gill, K. E. Nelson, E. A. Purdom, F. Francois, G. Perez-Perez, M. J. Blaser, and D. A. Relman. 2006. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U. S. A. 103:732-737.
12. Blomqvist, S., C. Savolainen-Kopra, A. Paananen, T. Hovi, and M. Roivainen. 2009. Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses. J. Gen. Virol. 90:1371-1381.
13. Bode, L., D. Dietrich, R. Stoyloff, H. Emrich, and H. Ludwig. 1997. Amantadine and human Borna disease virus in vitro and in vivo in an infected patient with bipolar depression. Lancet 349:178-179. (Pubitemid 27039203)
14. Bosch, F. X., M. M. Manos, N. Munoz, M. Sherman, A. M. Jansen, J. Peto, M. H. Schiffman, V. Moreno, R. Kurman, and K. V. Shah. 1995. Prevalence of human papillomavirus in cervical cancer: a worldwide perspective. J. Natl. Cancer Inst. 87:796-802.
15. Bowen, E., G. Lloyd, W. Harris, G. Platt, A. Baskerville, and E. Vella. 1977. Viral hemorrhagic fever in southern Sudan and northern Zaire: preliminary studies on the aetiological agent. Lancet 309:571-573. (Pubitemid 8048854)
16. Braun, E., T. Zimmerman, T. B. Hur, E. Reinhartz, Y. Fellig, A. Panet, and I. Steiner. 2006. Neurotropism of herpes simplex virus type 1 in brain organ cultures. J. Gen. Virol. 87:2827-2837.
17. Briese, T., W. G. Glass, and W. I. Lipkin. 2000. Detection of West Nile virus sequences in cerebrospinal fluid. Lancet 355:1614-1615.
18. Briese, T., M. Hornig, and W. Lipkin. 1999. Bornavirus immunopathogenesis in rodents: models for human neurological diseases. J. Neurovirol. 5:604-612. (Pubitemid 30032086)
19. Briese, T., X. Y. Jia, C. Huang, L. J. Grady, and W. I. Lipkin. 1999. Identification of a Kunjin/West Nile-like flavivirus in brains of patients with New York encephalitis. Lancet 354:1261-1262.
20. Briese, T., G. Palacios, M. Kokoris, O. Jabado, Z. Liu, N. Renwick, V. Kapoor, I. Casas, F. Pozo, R. Limberger, P. Perez-Brena, J. Ju, and W. I. Lipkin. 2005. Diagnostic system for rapid and sensitive differential detection of pathogens. Emerg. Infect. Dis. 11:310-313.
21. Briese, T., N. Renwick, M. Venter, R. Jarman, D. Ghosh, S. Kn̂dgen, S. Shrestha, A. Hoegh, I. Casas, E. Adjogoua, et al. 2008. Global distribution of novel rhinovirus genotype. Emerg. Infect. Dis. 14:944-947.
22. Bristol, N. 2008. William H Stewart. Lancet 372:110.
23. Brown, A. S., M. D. Begg, S. Gravenstein, C. A. Schaefer, R. J. Wyatt, M. Bresnahan, V. P. Babulas, and E. S. Susser. 2004. Serologic evidence of prenatal influenza in the etiology of schizophrenia. Arch. Gen. Psychiatry 61:774-780.
24. Brüggemann, H., S. Bäumer, W. F. Fricke, A. Wiezer, H. Liesegang, I. Decker, C. Herzberg, R. MartÌnez-Arias, R. Merkl, A. Henne, and G. Gottschalk. 2003. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc. Natl. Acad. Sci. U. S. A. 100:1316-1321.
25. Brunstein, J., and E. Thomas. 2006. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2. Diagn. Mol. Pathol. 15:169-173.
26. Buchwald, B., R. Ahangari, A. Weishaupt, and K. Toyka. 2002. Intravenous immunoglobulins neutralize blocking antibodies in Guillain-Barre syndrome. Ann. Neurol. 51:673-680.
27. Cai, Z., Z. L. Pan, Y. Pang, O. B. Evans, and P. G. Rhodes. 2000. Cytokine induction in fetal rat brains and brain injury in neonatal rats after maternal lipopolysaccharide administration. Pediatr. Res. 47:64-72.
28. Casas, I., A. Tenorio, J. Echevarria, P. Klapper, and G. Cleator. 1997. Detection of enteroviral RNA and specific DNA of herpesviruses by multiplex genome amplification. J. Virol. Methods 66:39-50. (Pubitemid 27293925)
29. Casrouge, A., S. Zhang, C. Eidenschenk, E. Jouanguy, A. Puel, K. Yang, A. Alcais, C. Picard, N. Mahfoufi, N. Nicolas, et al. 2006. Herpes simplex virus encephalitis in human UNC-93B deficiency. Science 314:308-312.
30. CDC. 2003. Detection of West Nile virus in blood donations-United States, 2003. MMWR Morb. Mortal. Wkly. Rep. 52:769-772.
31. CDC. 2004. Update: West Nile virus screening of blood donations and transfusion-associated transmission-United States, 2003. MMWR Morb. Mortal. Wkly. Rep. 53:281-284.
32. Chess, S., P. Fernandez, and S. Korn. 1978. Behavioral consequences of congenital rubella. J. Pediatr. 93:699-703.
33. Chiu, C. Y., A. A. Alizadeh, S. Rouskin, J. D. Merker, E. Yeh, S. Yagi, D. Schnurr, B. K. Patterson, D. Ganem, and J. L. DeRisi. 2007. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. J. Clin. Microbiol. 45:2340-2343.
34. Chiu, C. Y., S. Rouskin, A. Koshy, A. Urisman, K. Fischer, S. Yagi, D. Schnurr, P. B. Eckburg, L. S. Tompkins, B. G. Blackburn, J. D. Merker, B. K. Patterson, D. Ganem, and J. L. DeRisi. 2006. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin. Infect. Dis. 43:e71-e76.
35. Chizhikov, V., C. Spiropoulou, S. Morzunov, M. Monroe, C. Peters, and S. Nichol. 1995. Complete genetic characterization and analysis of isolation of Sin Nombre virus. J. Virol. 69:8132-8136.
36. Crotty, S., D. Maag, J. Arnold, W. Zhong, J. Lau, Z. Hong, R. Andino, and C. Cameron. 2000. The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen. Nat. Med. 6:1375-1379.
37. Cubitt, B., and J. De la Torre. 1997. Amantadine does not have antiviral activity against Borna disease virus. Arch. Virol. 142:2035-2042.
38. Reference deleted.
39. Davies, W. L., R. R. Grunert, R. F. Haff, J. W. McGahen, E. M. Neumayer, M. Paulshock, J. C. Watts, T. R. Wood, E. C. Hermann, and C. E. Hoffmann. 1964. Antiviral activity of 1-adamantanamine (amantadine). Science 144:862-863.
40. Degryse, E., N. Glansdorff, and A. Pièrard. 1978. A comparative analysis of extreme thermophilic bacteria belonging to the genus Thermus. Arch. Microbiol. 117:189-196.
41. de Kruif, P. 1926. Microbe hunters. Harcourt, Brace Co., New York, NY.
42. De Miranda, J., K. Yaddanapudi, M. Hornig, and W. I. Lipkin. 2009. Astrocytes recognize intracellular polyinosinic-polycytidylic acid via MDA-5. FASEB J. 23:1064-1071.
43. Dominguez, S., T. Briese, G. Palacios, J. Hui, J. Villari, V. Kapoor, R. Tokarz, M. Glodé, M. Anderson, and C. Robinson. 2008. Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade. J. Clin. Virol. 43:219-222.
44. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
45. Eriksson, B., E. Helgstrand, N. G. Johansson, A. Larsson, A. Misiorny, J. O. Noren, L. Philipson, K. Stenberg, G. Stening, S. Stridh, and B. Öberg. 1977. Inhibition of influenza virus ribonucleic acid polymerase by ribavirin triphosphate. Antimicrob. Agents Chemother. 11:946-951.
46. Evans, A. S. 1976. Causation and disease: the Henle-Koch postulates revisited. Yale J. Biol. Med. 49:175-195.
47. Evengard, B., T. Briese, G. Lindh, S. Lee, and W. Lipkin. 1999. Absence of evidence of Borna disease virus infection in Swedish patients with chronic fatigue syndrome. J. Neurovirol. 5:495-499. (Pubitemid 29484178)
48. Fredericks, D. N., and D. A. Relman. 1996. Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin. Microbiol. Rev. 9:18-33.
49. Furlano, R., A. Anthony, R. Day, A. Brown, L. McGarvey, M. Thomson, S. Davies, M. Berelowitz, A. Forbes, and A. Wakefield. 2001. Colonic CD8 and gammadelta T-cell infiltration with epithelial damage in children with autism. J. Pediatr. 138:366-372. (Pubitemid 32207139)
50. Gao, Z., C. H. Tseng, Z. Pei, and M. J. Blaser. 2007. Molecular analysis of human forearm superficial skin bacterial biota. Proc. Natl. Acad. Sci. U. S. A. 104:2927-2932.
51. Glaser, L., G. Conenello, J. Paulson, and P. Palese. 2007. Effective replication of human influenza viruses in mice lacking a major 2,6 sialyltransferase. Virus Res. 126:9-18. (Pubitemid 46726689)
52. Grelak, R. P., R. Clark, J. M. Stump, and V. G. Vernier. 1970. Amantadinedopamine interaction: possible mode of action in Parkinsonism. Science (New York) 169:203-204.
53. Griffiths, D. 2001. Endogenous retroviruses in the human genome sequence. Genome Biol. 2:1017.
54. Gubler, D. J. 1998. Dengue and dengue hemorrhagic fever. Clin. Microbiol. Rev. 11:480-496.
55. Hagiwara, M., H. Sasaki, K. Matsuo, M. Honda, M. Kawase, and H. Nakagawa. 2007. Loop-mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18. J. Med. Virol. 79:605-615.
56. Han, J., D. C. Swan, S. J. Smith, S. H. Lum, S. E. Sefers, E. R. Unger, and Y. W. Tang. 2006. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology. J. Clin. Microbiol. 44:4157-4162.
57. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669-685.
58. Heid, C. A., J. Stevens, K. J. Livak, and P. M. Williams. 1996. Real time quantitative PCR. Genome Res. 6:986-994.
59. Hoban, D. 2003. Antibiotics and collateral damage. Clin. Cornerstone 5:12-20.
60. Hofstadler, S. A., K. A. Sannes-Lowery, and J. C. Hannis. 2005. Analysis of nucleic acids by FTICR MS. Mass Spectrom. Rev. 24:265-285.
61. Honkavuori, K. S., H. L. Shivaprasad, B. L. Williams, P. L. Quan, M. Hornig, C. Street, G. Palacios, S. K. Hutchison, M. Franca, M. Egholm, T. Briese, and W. I. Lipkin. 2008. Novel Borna virus in psittacine birds with proventricular dilatation disease. Emerg. Infect. Dis. 14:1883-1886.
62. Hornig, M., T. Briese, T. Buie, M. Bauman, G. Lauwers, U. Siemetzki, K. Hummel, P. Rota, W. Bellini, and J. O'Leary. 2008. Lack of association between measles virus vaccine and autism with enteropathy: a case-control study. PLoS One 3:e3140.
63. Jabado, O. J., G. Palacios, V. Kapoor, J. Hui, N. Renwick, J. Zhai, T. Briese, and W. I. Lipkin. 2006. Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res. 34:6605-6611.
64. Jayawardena, S., C. Y. Cheung, I. Barr, K. H. Chan, H. Chen, Y. Guan, J. S. Peiris, and L. L. Poon. 2007. Loop-mediated isothermal amplification for influenza A (H5N1) virus. Emerg. Infect. Dis. 13:899-901.
65. Kawashima, H., T. Mori, Y. Kashiwagi, K. Takekuma, A. Hoshika, and A. Wakefield. 2000. Detection and sequencing of measles virus from peripheral mononuclear cells from patients with inflammatory bowel disease and autism. Dig. Dis. Sci. 45:723-729.
66. Khetsuriani, N., X. Lu, W. G. Teague, N. Kazerouni, L. J. Anderson, and D. D. Erdman. 2008. Novel human rhinoviruses and exacerbation of asthma in children. Emerg. Infect. Dis. 14:1793-1796.
67. Kistler, A., P. C. Avila, S. Rouskin, D. Wang, T. Ward, S. Yagi, D. Schnurr, D. Ganem, J. L. DeRisi, and H. A. Boushey. 2007. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J. Infect. Dis. 196:817-825.
68. Kistler, A. L., A. Gancz, S. Clubb, P. Skewes-Cox, K. Fischer, K. Sorber, C. Y. Chiu, A. Lublin, S. Mechani, Y. Farnoushi, et al. 2008. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Virol. J. 5:88.
69. Koch, R. 1891. Ueber bakteriologische Forschung, Verhandl. des X. Interna. Med. Congr., Berlin 1890. August Hirschwald, Berlin, Germany.
70. Koprowski, H., and M. B. Oldstone. 1996. Microbe hunters-then and now. Medi-Ed Press, Bloomington, IL.
71. Lamson, D., N. Renwick, V. Kapoor, Z. Liu, G. Palacios, J. Ju, A. Dean, K. St. George, T. Briese, and W. I. Lipkin. 2006. MassTag polymerase- chainreaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004-2005. J. Infect. Dis. 194:1398-1402.
72. Lanciotti, R. S., J. T. Roehrig, V. Deubel, J. Smith, M. Parker, K. Steele, B. Crise, K. E. Volpe, M. B. Crabtree, J. H. Scherret, R. A. Hall, J. S. MacKenzie, C. B. Cropp, B. Panigrahy, E. Ostlund, B. Schmitt, M. Malkinson, C. Banet, J. Weissman, N. Komar, H. M. Savage, W. Stone, T. McNamara, and D. J. Gubler. 1999. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science 286:2333-2337.
73. Lau, S. K., C. C. Yip, H. W. Tsoi, R. A. Lee, L. Y. So, Y. L. Lau, K. H. Chan, P. C. Woo, and K. Y. Yuen. 2007. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J. Clin. Microbiol. 45:3655-3664.
74. Lee, W., C. Kiesner, T. Pappas, I. Lee, K. Grindle, T. Jartti, B. Jakiela, R. Lemanske, Jr., P. Shult, and J. Gern. 2007. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS One 2:e966.
75. Li, H., M. A. McCormac, R. W. Estes, S. E. Sefers, R. K. Dare, J. D. Chappell, D. D. Erdman, P. F. Wright, and Y. W. Tang. 2007. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections. J. Clin. Microbiol. 45:2105-2109.
76. Lin, B., K. M. Blaney, A. P. Malanoski, A. G. Ligler, J. M. Schnur, D. Metzgar, K. L. Russell, and D. A. Stenger. 2007. Using a resequencing microarray as a multiple respiratory pathogen detection assay. J. Clin. Microbiol. 45:443-452.
77. Lipkin, W. I., and T. Briese. 2007. Bornaviridae, p. 1829-1851. In D. M. Knipe and R. M. Howley (ed.), Virology, 5th ed. Lippincott, Williams & Wilkins, Philadelphia, PA.
78. Lipkin, W. I., G. H. Travis, K. M. Carbone, and M. C. Wilson. 1990. Isolation and characterization of Borna disease agent cDNA clones. Proc. Natl. Acad. Sci. U. S. A. 87:4184-4188.
79. Löwer, R., J. Löwer, and R. Kurth. 1996. The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc. Natl. Acad. Sci. U. S. A. 93:5177-5184.
80. Lucas, S. B., C. S. Peacock, A. Hounnou, K. Brattegaard, K. Koffi, M. Honde, J. Andoh, J. Bell, and K. M. De Cock. 1996. Disease in children infected with HIV in Abidjan, Cote d'Ivoire. BMJ 312:335-338.
81. Mantovani, A., P. Allavena, A. Sica, and F. Balkwill. 2008. Cancer-related inflammation. Nature 454:436-444.
82. Martina, Y., K. T. Marcucci, S. Cherqui, A. Szabo, T. Drysdale, U. Srinivisan, C. A. Wilson, C. Patience, and D. R. Salomon. 2006. Mice transgenic for a human porcine endogenous retrovirus receptor are susceptible to productive viral infection. J. Virol. 80:3135-3146.
83. McCullers, J., and K. Bartmess. 2003. Role of neuraminidase in lethal synergism between influenza virus and Streptococcus pneumoniae. J. Infect. Dis. 187:1000-1009.
84. McErlean, P., L. Shackelton, E. Andrews, D. Webster, S. Lambert, M. Nissen, T. Sloots, and I. Mackay. 2008. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One 3:e1847.
85. McErlean, P., L. A. Shackelton, S. B. Lambert, M. D. Nissen, T. P. Sloots, and I. M. Mackay. 2007. Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis. J. Clin. Virol. 39:67-75.
86. Meyers, C. 1996. Organotypic (raft) epithelial tissue culture system for the differentiation-dependent replication of papillomavirus. Methods Cell Sci. 18:201-210.
87. Miller, E., K. Edwards, G. Weinberg, M. Iwane, M. Griffin, C. Hall, Y. Zhu, P. Szilagyi, L. Morin, and L. Heil. 2009. A novel group of rhinoviruses is associated with asthma hospitalizations. J. Allergy Clin. Immunol. 123:98-104.
88. Mori, M., A. Rothman, I. Kurane, J. Montoya, K. Nolte, J. Norman, D. Waite, F. Koster, and F. Ennis. 1999. High levels of cytokine-producing cells in the lung tissues of patients with fatal hantavirus pulmonary syndrome. J. Infect. Dis. 179:295-302.
89. Nakaya, T., H. Takahashi, Y. Nakamura, S. Asahi, M. Tobiume, H. Kuratsune, T. Kitani, K. Yamanishi, and K. Ikuta. 1996. Demonstration of Borna disease virus RNA in peripheral blood mononuclear cells derived from Japanese patients with chronic fatigue syndrome. FEBS Lett. 378:145-149. (Pubitemid 26015562)
90. Nakaya, T., H. Takahashi, Y. Nakamura, H. Kuratsune, T. Kitani, T. Machii, K. Yamanishi, and K. Ikuta. 1999. Borna disease virus infection in two family clusters of patients with chronic fatigue syndrome. Microbiol. Immunol. 43:679-689.
91. Nash, D., F. Mostashari, A. Fine, J. Miller, D. O'Leary, K. Murray, A. Huang, A. Rosenberg, A. Greenberg, M. Sherman, et al. 2001. The outbreak of West Nile virus infection in the New York City area in 1999. N. Engl. J. Med. 344:1807-1814.
92. Nichol, S. T., C. F. Spiropoulou, S. Morzunov, P. E. Rollin, T. G. Ksiazek, H. Feldmann, A. Sanchez, J. Childs, S. Zaki, and C. J. Peters. 1993. Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness. Science 262:914-917.
93. Nicholson, W., N. Munakata, G. Horneck, H. Melosh, and P. Setlow. 2000. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol. Mol. Biol. Rev. 64:548-572.
94. Nix, W. A., M. M. Berger, M. S. Oberste, B. R. Brooks, D. M. McKenna-Yasek, R. H. Brown, Jr., R. P. Roos, and M. A. Pallansch. 2004. Failure to detect enterovirus in the spinal cord of ALS patients using a sensitive RT-PCR method. Neurology 62:1372-1377.
95. Notomi, T., H. Okayama, H. Masubuchi, T. Yonekawa, K. Watanabe, N. Amino, and T. Hase. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28:e63.
96. Oakley, B., T. Fiedler, J. Marrazzo, and D. Fredricks. 2008. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl. Environ. Microbiol. 74:4898-4909.
97. Oguma, K., Y. Fujinaga, and K. Inoue. 1995. Structure and function of Clostridium botulinum toxins. Microbiol. Immunol. 39:161-168.
98. O'Leary, J., V. Uhlmann, and A. Wakefield. 2000. Measles virus and autism. Lancet 356:772.
99. Palacios, G., T. Briese, V. Kapoor, O. Jabado, Z. Liu, M. Venter, J. Zhai, N. Renwick, A. Grolla, T. W. Geisbert, C. Drosten, J. Towner, J. Ju, J. Paweska, S. T. Nichol, R. Swanepoel, H. Feldmann, P. B. Jahrling, and W. I. Lipkin. 2006. MassTag polymerase chain reaction for differential diagnosis of viral hemorrhagic fever. Emerg. Infect. Dis. 12:692-695.
100. Palacios, G., J. Druce, L. Du, T. Tran, C. Birch, T. Briese, S. Conlan, P. Quan, J. Hui, J. Marshall, J. Simons, M. Egholm, C. Paddock, W. Shieh, C. Goldsmith, S. Zaki, M. Catton, and W. Lipkin. 2008. A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 358:991-998.
101. Palacios, G., M. Hornig, D. Cisterna, N. Savji, A. Bussetti, V. Kapoor, J. Hui, R. Tokarz, T. Briese, E. Baumeister, and W. I. Lipkin. 2009. Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza. PLoS One 4:e8640.
102. Reference deleted.
103. Palacios, G., P. L. Quan, O. J. Jabado, S. Conlan, D. L. Hirschberg, Y. Liu, J. Zhai, N. Renwick, J. Hui, H. Hegyi, A. Grolla, J. E. Strong, J. S. Towner, T. W. Geisbert, P. B. Jahrling, C. Buchen-Osmond, H. Ellerbrok, M. P. Sanchez-Seco, Y. Lussier, P. Formenty, M. S. Nichol, H. Feldmann, T. Briese, and W. I. Lipkin. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg. Infect. Dis. 13:73-81.
104. Paster, B. J., S. K. Boches, J. L. Galvin, R. E. Ericson, C. N. Lau, V. A. Levanos, A. Sahasrabudhe, and F. E. Dewhirst. 2001. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183:3770-3783.
105. Paton, N., Y. Leo, S. Zaki, A. Auchus, K. Lee, A. Ling, S. Chew, B. Ang, P. Rollin, T. Umapathi, I. Sng, C. C. Lee, E. Lim, and T. G. Ksiazek. 1999. Outbreak of Nipah-virus infection among abattoir workers in Singapore. Lancet 354:1253-1256.
106. Patterson, J., and R. Fernandez-Larsson. 1990. Molecular mechanisms of action of ribavirin. Rev. Infect. Dis. 12:1139-1146.
107. Pei, Z., E. J. Bini, L. Yang, M. Zhou, F. Francois, and M. J. Blaser. 2004. Bacterial biota in the human distal esophagus. Proc. Natl. Acad. Sci. U. S. A. 101:4250-4255.
108. Pichichero, M. E. 1998. Group A beta-hemolytic streptococcal infections. Pediatr. Rev. 19:291-302.
109. Relman, D. A., T. M. Schmidt, R. P. MacDermott, and S. Falkow. 1992. Identification of the uncultured bacillus of Whipple's disease. N. Engl. J. Med. 327:293-301.
110. Ren, R. B., F. Costantini, E. J. Gorgacz, J. J. Lee, and V. R. Racaniello. 1990. Transgenic mice expressing a human poliovirus receptor: a new model for poliomyelitis. Cell 63:353-362.
111. Renwick, N., B. Schweiger, V. Kapoor, Z. Liu, J. Villari, R. Bullmann, R. Miething, T. Briese, and W. Lipkin. 2007. A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany. J. Infect. Dis. 196:1754-1760.
112. Rivers, T. 1937. Viruses and Koch's postulates. J. Bacteriol. 33:1-12.
113. Rothschild, L., and R. Mancinelli. 2001. Life in extreme environments. Nature 409:1092-1101.
114. Rott, R., S. Herzog, B. Fleischer, A. Winokur, J. Amsterdam, W. Dyson, and H. Koprowski. 1985. Detection of serum antibodies to Borna disease virus in patients with psychiatric disorders. Science 228:755-756.
115. Sampath, R., T. A. Hall, C. Massire, F. Li, L. B. Blyn, M. W. Eshoo, S. A. Hofstadler, and D. J. Ecker. 2007. Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann. N. Y. Acad. Sci. 1102:109-120.
116. Saunders, N., and A. Jeffries. 2000. The growing utility of microbial genome sequences. Genome Biol. 1:reports 410.1-reports 410.3.
117. Savage, D. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107-133.
118. Savolainen-Kopra, C., S. Blomqvist, T. Kilpi, M. Roivainen, and T. Hovi. 2009. Novel species of human rhinoviruses in acute otitis media. Pediatr. Infect. Dis. J. 28:59-61.
119. Schneemann, A., P. Schneider, R. Lamb, and W. Lipkin. 1995. The remarkable coding strategy of Borna disease virus: a new member of the nonsegmented negative strand RNA viruses. Virology 210:1-8.
120. Scott, M., D. Foster, C. Mirenda, D. Serban, F. Coufal, M. Wälchli, M. Torchia, D. Groth, et al. 1989. Transgenic mice expressing hamster prion protein produce species-specific scrapie infectivity and amyloid plaques. Cell 59:847-857.
121. Segelke, B., M. Knapp, S. Kadkhodayan, R. Balhorn, and B. Rupp. 2004. Crystal structure of Clostridium botulinum neurotoxin protease in a product-bound state: evidence for noncanonical zinc protease activity. Proc. Natl. Acad. Sci. U. S. A. 101:6888-6893.
122. Shirato, K., H. Nishimura, M. Saijo, M. Okamoto, M. Noda, M. Tashiro, and F. Taguchi. 2007. Diagnosis of human respiratory syncytial virus infection using reverse transcription loop-mediated isothermal amplification. J. Virol. Methods 139:78-84.
123. Steele, K. E., M. J. Linn, R. J. Schoepp, N. Komar, T. W. Geisbert, R. M. Manduca, P. P. Calle, B. L. Raphael, T. L. Clippinger, T. Larsen, J. Smith, R. S. Lanciotti, N. A. Panella, and T. S. McNamara. 2000. Pathology of fatal West Nile virus infections in native and exotic birds during the 1999 outbreak in New York City, New York. Vet. Pathol. 37:208-224.
124. Stephen, E. L., D. E. Jones, C. J. Peters, G. A. Eddy, P. S. Loizeaux, and P. B. Jarling. 1980. Ribavirin treatment of toga-, arena- and bunyavirus infections in subhuman primates and other laboratory animal species, p. 169-183. In R. A. Smith and R. A. Kirkpatrick (ed.), Ribavirin: a broad spectrum antiviral agent. Academic Press Inc., New York, NY.
125. Straub, T. M., K. H. zu Bentrup, P. Orosz-Coghlan, A. Dohnalkova, B. K. Mayer, R. A. Bartholomew, C. O. Valdez, C. J. Bruckner-Lea, C. P. Gerba, M. Abbaszadegan, and C. A. Nickerson. 2007. In vitro cell culture infectivity assay for human noroviruses. Emerg. Infect. Dis. 13:396-403.
126. Suttle, C. 2005. Viruses in the sea. Nature 437:356-361.
127. Templeton, K. E., S. A. Scheltinga, M. F. Beersma, A. C. Kroes, and E. C. Claas. 2004. Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4. J. Clin. Microbiol. 42:1564-1569.
128. Toltzis, P., K. O'Connell, and J. Patterson. 1988. Effect of phosphorylated ribavirin on vesicular stomatitis virus transcription. Antimicrob. Agents Chemother. 32:492-497.
129. Tumpey, T., C. Basler, P. Aguilar, H. Zeng, A. Solorzano, D. Swayne, N. Cox, J. Katz, J. Taubenberger, and P. Palese. 2005. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 310:77-80.
130. Tyagi, S., and F. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
131. Uhlmann, V., C. M. Martin, O. Sheils, L. Pilkington, I. Silva, A. Killalea, S. B. Murch, J. Walker-Smith, M. Thomson, A. J. Wakefield, and J. J. O'Leary. 2002. Potential viral pathogenic mechanism for new variant inflammatory bowel disease. Mol. Pathol. 55:84.
132. VandeWoude, S., J. A. Richt, M. C. Zink, R. Rott, O. Narayan, and J. E. Clements. 1990. A Borna virus cDNA encoding a protein recognized by antibodies in humans with behavioral diseases. Science 250:1278-1281.
133. Van Ert, M., S. Hofstadler, Y. Jiang, J. Busch, D. Wagner, J. Drader, D. Ecker, J. Hannis, L. Huynh, and J. Schupp. 2004. Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 37:642-644, 646, 648.
134. Von Pirquet, Ñ. 1908. Das Verhalten der kutanen Tuberkulin-Reaktion warend der Masern. Dtsch. Med. Wochenschr. 34:1297-1300.
135. Wakefield, A. 2002. Enterocolitis, autism and measles virus. Mol. Psychiatr. 7:44-46.
136. Wakefield, A., A. Anthony, S. Murch, M. Thomson, S. Montgomery, S. Davies, J. O'Leary, M. Berelowitz, and J. Walker-Smith. 2000. Enterocolitis in children with developmental disorders. Am. J. Gastroenterol. 95:2285-2295.
137. Wakefield, A., P. Ashwood, K. Limb, and A. Anthony. 2005. The significance of ileo-colonic lymphoid nodular hyperplasia in children with autistic spectrum disorder. Eur. J. Gastroenterol. Hepatol. 17:827-836.
138. Wakefield, A., S. Murch, A. Anthony, J. Linnell, D. Casson, M. Malik, M. Berelowitz, A. Dhillon, M. Thomson, and P. Harvey. 1998. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet 351:637-641.
139. Walker, M., R. Schlaberg, A. Hays, R. Bowser, and W. Lipkin. 2001. Absence of echovirus sequences in brain and spinal cord of amyotrophic lateral sclerosis patients. Ann. Neurol. 49:249-253.
140. Wang, D., L. Coscoy, M. Zylberberg, P. C. Avila, H. A. Boushey, D. Ganem, and J. L. DeRisi. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U. S. A. 99:15687-15692.
141. Weinberg, R. 1995. The retinoblastoma protein and cell cycle control. Cell 81:323-330.
142. Witsø, E., G. Palacios, K. Rønningen, O. Cinek, D. Janowitz, M. Rewers, B. Grinde, and W. Lipkin. 2007. Asymptomatic circulation of HEV71 in Norway. Virus Res. 123:19-29.
143. Wong, C. W., T. J. Albert, V. B. Vega, J. E. Norton, D. J. Cutler, T. A. Richmond, L. W. Stanton, E. T. Liu, and L. D. Miller. 2004. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res. 14:398-405.
144. Wray, S., B. Gilbert, and V. Knight. 1985. Effect of ribavirin triphosphate on primer generation and elongation during influenza virus transcription in vitro. Antiviral Res. 5:39-48.
145. Xiang, Z., R. Gonzalez, Z. Xie, Y. Xiao, L. Chen, Y. Li, C. Liu, Y. Hu, Y. Yao, and S. Qian. 2008. Human rhinovirus group C infection in children with lower respiratory tract infection. Emerg. Infect. Dis. 14:1665-1667.
146. Yuki, N., K. Susuki, M. Koga, Y. Nishimoto, M. Odaka, K. Hirata, K. Taguchi, T. Miyatake, K. Furukawa, and T. Kobata. 2004. Carbohydrate mimicry between human ganglioside GM1 and Campylobacter jejuni lipooligosaccharide causes Guillain-Barré syndrome. Proc. Natl. Acad. Sci. U. S. A. 101:11404-11409.
147. Zhang, H., J. DiBaise, A. Zuccolo, D. Kudrna, M. Braidotti, Y. Yu, P. Parameswaran, M. Crowell, R. Wing, and B. Rittmann. 2009. Human gut microbiota in obesity and after gastric bypass. Proc. Natl. Acad. Sci. U. S. A. 106:2365-2370.
148. zu Bentrup, H. 2006. Three-dimensional organotypic models of human colonic epithelium to study the early stages of enteric salmonellosis. Microbes Infect. 8:1813-1825.
149. zur Hausen, H. 2002. Papillomaviruses and cancer: from basic studies to clinical application. Nat. Rev. Cancer 2:342-350.