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Chapter 14 : Microbial Genomics and Pathogen Discovery

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Abstract:

This chapter discusses the concepts of microbial genomics and pathogen discovery. The discussion begins with an overview of traditional efforts, followed by a brief description of the evolution of sequencing technologies. Finally, the chapter illustrates how the two fields began to intersect in the first few years of the 21st century. The discoveries of Hepatitis C virus (HCV) and Human herpesvirus 8 (HHV-8), also called Kaposi's sarcoma-associated herpesvirus (KSHV), represented two breakthroughs in the application of candidate-independent molecular methods for pathogen discovery. The onset of the 21st century has seen the convergence of the fields of pathogen discovery and microbial genomics. The PhyloChip, a high-density 16S rRNA microarray containing 300,000 probes, was used to examine the microbial diversity in three environmental samples, including urban aerosol, subsurface soil, and subsurface water. This study demonstrated that the array could reveal broader diversity than classical cloning and sequencing of the same sample. The challenge facing the scientific community for the remainder of this century is to develop commensurate approaches to defining the biological relevance of this multitude of novel microbes to human disease.

Citation: Gaynor A, Wang D. 2011. Microbial Genomics and Pathogen Discovery, p 199-209. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch14

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Severe Acute Respiratory Syndrome
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Restriction Fragment Length Polymorphism
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FIGURE 1

Major landmarks in pathogen discovery and microbial genomics. RDA, representational difference analysis; RAP-PCR, random arbitrarily primed PCR; VIDISCA, virus discovery cDNA-AFLP (amplified restriction fragment length polymorphism).

Citation: Gaynor A, Wang D. 2011. Microbial Genomics and Pathogen Discovery, p 199-209. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch14
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1. Allander, T.,, K. Andreasson,, S. Gupta,, A. Bjerkner,, G. Bogdanovic,, M. A. A. Persson,, T. Dalianis,, T. Ramqvist,, and B. Andersson. 2007. Identification of a third human polyomavirus. J. Virol. 81:41304136.
2. Allander, T.,, S. U. Emerson,, R. E. Engle,, R. H. Purcell,, and J. Bukh. 2001. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc. Natl. Acad. Sci. USA 98:1160911614.
3. Allander, T.,, M. T. Tammi,, M. Eriksson,, A. Bjerkner,, A. Tiveljung-Lindell,, and B. Andersson. 2005. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl. Acad. Sci. USA 102:1289112896.
3a. Allred, A. F.,, G. Wu,, T. Wulan,, K. F. Fischer,, M. R. Holbrook,, R. B. Tesh,, and D. Wang. 2010. VIPR: a probabilistic algorithm for analysis of microbial detection bioarrays. BMC Bioinformatics 11:384.
4. Al-Sunaidi, M.,, C. H. Williams,, P. J. Hughes,, D. P. Schnurr,, and G. Stanway. 2007. Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains. J. Virol. 81:10131021.
5. Arthur, J. L.,, G. D. Higgins,, G. P. Davidson,, R. C. Givney,, and R. M. Ratcliff. 2009. A novel bocavirus associated with acute gastroenteritis in Australian children. PLoS Pathog. 5:e1000391.
6. 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 325:204206.
7. Baumgarte, S.,, L. K. de Souza Luna,, K. Grywna,, M. Panning,, J. F. Drexler,, C. Karsten,, H. I. Huppertz,, and C. Drosten. 2008. Prevalence, types, and RNA concentrations of human parechoviruses, including a sixth parechovirus type, in stool samples from patients with acute enteritis. J. Clin. Microbiol. 46:242248.
8. Benschop, K. S.,, J. Schinkel,, M. E. Luken,, P. J. van den Broek,, M. F. Beersma,, N. Menelik,, H. W. vanEijk,, H. L. Zaaijer,, C. M. Van den Broucke-Grauls,, M. G. Beld,, and K. C. Wolthers. 2006. Fourth human parechovirus serotype. Emerg. Infect. Dis. 12:15721575.
9. Breitbart, M.,, and F. Rohwer. 2005. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. BioTechniques 39:729736.
10. Briese, T.,, J. T. Paweska,, L. K. McMullan,, S. K. Hutchison,, C. Street,, G. Palacios,, M. L. Khristova,, J. Weyer,, R. Swanepoel,, M. Egholm,, S. T. Nichol,, and W. I. Lipkin. 2009. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 5:e1000455.
11. Brosius, J.,, M. L. Palmer,, P. J. Kennedy,, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:48014805.
12. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:20122018.
13. Chang, Y.,, E. Cesarman,, M. S. Pessin,, F. Lee,, J. Culpepper,, D. M. Knowles,, and P. S. Moore. 1994. Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi’s sarcoma. Science 266:18651869.
14. 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. 45:23402343.
15. Chiu, C. Y.,, A. L. Greninger,, K. Kanada,, T. Kwok,, K. F. Fischer,, C. Runckel,, J. K. Louie,, C. A. Glaser,, S. Yagi,, D. P. Schnurr,, T. D. Haggerty,, J. Parsonnet,, D. Ganem,, and J. L. Derisi. 2008. Identification of cardioviruses related to Theiler’s murine encephalomyelitis virus in human infections. Proc. Natl. Acad. Sci. USA 105:1412414129.
16. 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:e71e76.
17. Choo, Q. L.,, G. Kuo,, A. J. Weiner,, L. R. Overby,, D. W. Bradley,, and M. Houghton. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359362.
18. Deffrasnes, C.,, M. E. Hamelin,, and G. Boivin. 2007. Human metapneumovirus. Semin. Respir. Crit. Care Med. 28:213221.
19. Delgado, S.,, B. R. Erickson,, R. Agudo,, P. J. Blair,, E. Vallejo,, C. G. Albarino,, J. Vargas,, J. A. Comer,, P. E. Rollin,, T. G. Ksiazek,, J. G. Olson,, and S. T. Nichol. 2008. Chapare virus, a newly discovered arenavirus isolated from a fatal hemorrhagic fever case in Bolivia. PLoS Pathog. 4:e1000047.
20. DeRisi, J. L.,, V. R. Iyer,, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680686.
21. DeSantis, T. Z.,, E. L. Brodie,, J. P. Moberg,, I. X. Zubieta,, Y. M. Piceno,, and G. L. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371383.
22. Dijkman, R.,, M. F. Jebbink,, N. B. El Idrissi,, K. Pyrc,, M. A. Muller,, T. W. Kuijpers,, H. L. Zaaijer,, and L. van der Hoek. 2008. Human coronavirus NL63 and 229E seroconversion in children. J. Clin. Microbiol. 46:23682373.
23. Drexler, J. F.,, K. Grywna,, A. Stöcker,, P. S. Almeida,, T. C. Medrado Ribeiro,, M. Eschbach-Bludau,, N. Petersen,, H. da Costa Ribeiro, Jr., and C. Drosten. 2009. Novel human parechovirus from Brazil. Emerg. Infect. Dis. 15:310313.
24. Drexler, J. F.,, L. K. Luna,, A. Stöcker,, P. S. Almeida,, T. C. Medrado Ribeiro,, N. Petersen,, P. Herzog,, C. Pedroso,, H. I. Huppertz,, H. da Costa Ribeiro, Jr., S. Baumgarte, and C. Drosten. 2008. Circulation of 3 lineages of a novel Saffold cardiovirus in humans. Emerg. Infect. Dis. 14:13981405.
25. Eisen, M. B.,, P. T. Spellman,, P. O. Brown,, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:1486314868.
26. Endo, R.,, N. Ishiguro,, H. Kikuta,, S. Teramoto,, R. Shirkoohi,, X. Ma,, T. Ebihara,, H. Ishiko,, and T. Ariga. 2007. Seroepidemiology of human bocavirus in Hokkaido prefecture, Japan. J. Clin. Microbiol. 45:32183223.
27. Feng, H.,, M. Shuda,, Y. Chang,, and P. S. Moore. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:10961100.
28. Finkbeiner, S. R.,, C. D. Kirkwood,, and D. Wang. 2008. Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. Virol. J. 5:117.
29. Finkbeiner, S. R.,, B. M. Le,, L. R. Holtz,, G. A. Storch,, and D. Wang. 2009. Detection of newly described astrovirus MLB1 in stool samples from children. Emerg. Infect. Dis. 15:441444.
30. Finkbeiner, S. R.,, Y. Li,, S. Ruone,, C. Conrardy,, N. Gregoricus,, D. Toney,, H. W. Virgin,, L. J. Anderson,, J. Vinje,, D. Wang,, and S. Tong. 2009. Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J. Virol. 83:1083610839.
31. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Wholegenome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
32. Fouchier, R. A.,, V. Munster,, A. Wallensten,, T. M. Bestebroer,, S. Herfst,, D. Smith,, G. F. Rimmelzwaan,, B. Olsen,, and A. D. Osterhaus. 2005. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J. Virol. 79:28142822.
33. Fredericks, D. N.,, and D. A. Relman. 1996. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin. Microbiol. Rev. 9:1833.
34. Gaynor, A. M.,, M. D. Nissen,, D. M. Whiley,, I. M. Mackay,, S. B. Lambert,, G. Wu,, D. C. Brennan,, G. A. Storch,, T. P. Sloots,, and D. Wang. 2007. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog. 3:e64.
35. Goffeau, A.,, B. G. Barrell,, H. Bussey,, R. W. Davis,, B. Dujon,, H. Feldmann,, F. Galibert,, J. D. Hoheisel,, C. Jacq,, M. Johnston,, E. J. Louis,, H. W. Mewes,, Y. Murakami,, P. Philippsen,, H. Tettelin,, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546, 563567.
36. Greninger, A. L.,, C. Runckel,, C. Y. Chiu,, T. Haggerty,, J. Parsonnet,, D. Ganem,, and J. L. DeRisi. 2009. The complete genome of klassevirus—a novel picornavirus in pediatric stool. Virol. J. 6:82.
37. Hales, L. M.,, N. J. Knowles,, P. S. Reddy,, L. Xu,, C. Hay,, and P. L. Hallenbeck. 2008. Complete genome sequence analysis of Seneca Valley virus-001, a novel oncolytic picornavirus. J. Gen. Virol. 89:12651275.
38. Holtz, L. R.,, S. R. Finkbeiner,, C. D. Kirkwood,, and D. Wang. 2008. Identification of a novel picornavirus related to cosaviruses in a child with acute diarrhea. Virol. J. 5:159.
39. Holtz, L. R.,, S. R. Finkbeiner,, G. Zhao,, C. D. Kirkwood,, R. Girones,, J. M. Pipas,, and D. Wang. 2009. Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. Virol. J. 6:86.
40. Ito, M.,, T. Yamashita,, H. Tsuzuki,, N. Takeda,, and K. Sakae. 2004. Isolation and identification of a novel human parechovirus. J. Gen. Virol. 85:391398.
41. Jones, M. S.,, A. Kapoor,, V. V. Lukashov,, P. Simmonds,, F. Hecht,, and E. Delwart. 2005. New DNA viruses identified in patients with acute viral infection syndrome. J. Virol. 79:82308236.
42. Jones, M. S.,, V. V. Lukashov,, R. D. Ganac,, and D. P. Schnurr. 2007. Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J. Clin. Microbiol. 45:21442150.
43. Kantola, K.,, L. Hedman,, T. Allander,, T. Jartti,, P. Lehtinen,, O. Ruuskanen,, K. Hedman,, and M. Soderlund-Venermo. 2008. Serodiagnosis of human bocavirus infection. Clin. Infect. Dis. 46:540546.
44. Kapoor, A.,, E. Slikas,, P. Simmonds,, T. Chieochansin,, A. Naeem,, S. Shaukat,, M. M. Alam,, S. Sharif,, M. Angez,, S. Zaidi,, and E. Delwart. 2009. A newly identified bocavirus species in human stool. J. Infect. Dis. 199:196200.
45. Kapoor, A.,, J. Victoria,, P. Simmonds,, E. Slikas,, T. Chieochansin,, A. Naeem,, S. Shaukat,, S. Sharif,, M. M. Alam,, M. Angez,, C. Wang,, R. W. Shafer,, S. Zaidi,, and E. Delwart. 2008. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc. Natl. Acad. Sci. USA 105:2048220487.
46. Kim, S.,, N. Kim,, B. Dong,, D. Boren,, S. A. Lee,, J. Das Gupta,, C. Gaughan,, E. A. Klein,, C. Lee,, R. H. Silverman,, and S. A. Chow. 2008. Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer. J. Virol. 82:99649977.
47. 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. 196:817825.
48. Ksiazek, T. G.,, D. Erdman,, C. S. Goldsmith,, S. R. Zaki,, T. Peret,, S. Emery,, S. Tong,, C. Urbani,, J. A. Comer,, W. Lim,, P. E. Rollin,, S. F. Dowell,, A. E. Ling,, C. D. Humphrey,, W. J. Shieh,, J. Guarner,, C. D. Paddock,, P. Rota,, B. Fields,, J. DeRisi,, J. Y. Yang,, N. Cox,, J. M. Hughes,, J. W. LeDuc,, W. J. Bellini,, and L. J. Anderson. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348:19531966.
49. 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-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004– 2005. J. Infect. Dis. 194:13981402.
50. Lander, E. S.,, L. M. Linton,, B. Birren,, C. Nusbaum,, M. C. Zody,, J. Baldwin,, K. Devon,, K. Dewar,, M. Doyle,, W. FitzHugh,, R. Funke,, D. Gage,, K. Harris,, A. Heaford,, J. Howland,, L. Kann,, J. Lehoczky,, R. LeVine,, P. McEwan,, K. McKernan,, J. Meldrim,, J. P. Mesirov,, C. Miranda,, W. Morris,, J. Naylor,, C. Raymond,, M. Rosetti,, R. Santos,, A. Sheridan,, C. Sougnez,, N. Stange-Thomann,, N. Stojanovic,, A. Subramanian,, D. Wyman,, J. Rogers,, J. Sulston,, R. Ainscough,, S. Beck,, D. Bentley,, J. Burton,, C. Clee,, N. Carter,, A. Coulson,, R. Deadman,, P. Deloukas,, A. Dunham,, I. Dunham,, R. Durbin,, L. French,, D. Grafham,, S. Gregory,, T. Hubbard,, S. Humphray,, A. Hunt,, M. Jones,, C. Lloyd,, A. McMurray,, L. Matthews,, S. Mercer,, S. Milne,, J. C. Mullikin,, A. Mungall,, R. Plumb,, M. Ross,, R. Shownkeen,, S. Sims,, R. H. Waterston,, R. K. Wilson,, L. W. Hillier,, J. D. McPherson,, M. A. Marra,, E. R. Mardis,, L. A. Fulton,, A. T. Chinwalla,, K. H. Pepin,, W. R. Gish,, S. L. Chissoe,, M. C. Wendl,, K. D. Delehaunty,, T. L. Miner,, A. Delehaunty,, J. B. Kramer,, L. L. Cook,, R. S. Fulton,, D. L. Johnson,, P. J. Minx,, S. W. Clifton,, T. Hawkins,, E. Branscomb,, P. Predki,, P. Richardson,, S. Wenning,, T. Slezak,, N. Doggett,, J. F. Cheng,, A. Olsen,, S. Lucas,, C. Elkin,, E. Uberbacher,, M. Frazier, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860921.
51. 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. 45:36553664.
52. Lee, W. M.,, C. Kiesner,, T. Pappas,, I. Lee,, K. Grindle,, T. Jartti,, B. Jakiela,, R. F. Lemanske, Jr.,, P. A. Shult,, and J. E. Gern. 2007. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS ONE 2:e966.
53. Ley, R. E.,, F. Backhed,, P. Turnbaugh,, C. A. Lozupone,, R. D. Knight,, and J. I. Gordon. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:1107011075.
54. Ley, R. E.,, P. J. Turnbaugh,, S. Klein,, and J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:10221023.
55. Li, L.,, J. Victoria,, A. Kapoor,, A. Naeem,, S. Shaukat,, S. Sharif,, M. M. Alam,, M. Angez,, S. Z. Zaidi,, and E. Delwart. 2009. Genomic characterization of novel human parechovirus type. Emerg. Infect. Dis. 15:288291.
56. Lin, B.,, A. P. Malanoski,, Z. Wang,, K. M. Blaney,, A. G. Ligler,, R. K. Rowley,, E. H. Hanson,, E. von Rosenvinge,, F. S. Ligler,, A. W. Kusterbeck,, D. Metzgar,, C. P. Barrozo,, K. L. Russell,, C. Tibbetts,, J. M. Schnur,, and D. A. Stenger. 2007. Application of broad-spectrum, sequence-based pathogen identification in an urban population. PLoS ONE 2:e419.
57. Lombardi, V. C.,, F. W. Ruscetti,, J. Das Gupta,, M. A. Pfost,, K. S. Hagen,, D. L. Peterson,, S. K. Ruscetti,, R. K. Bagni,, C. Petrow-Sadowski,, B. Gold,, M. Dean,, R. H. Silverman,, and J. A. Mikovits. 2009. Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science 326:585589.
58. Mardis, E. R. 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9:387402.
59. 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. 39:6775.
60. Nguyen, N. L.,, B. M. Le,, and D. Wang. 2009. Serologic evidence of frequent human infection with WU and KI polyomaviruses. Emerg Infect Dis. 15:11991205.
61. 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 262:914917.
62. 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. 13:7381.
63. Palmer, C.,, E. M. Bik,, D. B. DiGiulio,, D. A. Relman,, and P. O. Brown. 2007. Development of the human infant intestinal microbiota. PLoS Biol. 5:e177.
64. Quan, P. L.,, G. Palacios,, O. J. Jabado,, S. Conlan,, D. L. Hirschberg,, F. Pozo,, P. J. Jack,, D. Cisterna,, N. Renwick,, J. Hui,, A. Drysdale,, R. Amos-Ritchie,, E. Baumeister,, V. Savy,, K. M. Lager,, J. A. Richt,, D. B. Boyle,, A. Garcia- Sastre,, I. Casas,, P. Perez-Brena,, T. Briese,, and W. I. Lipkin. 2007. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J. Clin. Microbiol. 45:23592364.
65. Raoult, D.,, S. Audic,, C. Robert,, C. Abergel,, P. Renesto,, H. Ogata,, B. La Scola,, M. Suzan,, and J. M. Claverie. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306:13441350.
66. Rehrauer, H.,, S. Schonmann,, L. Eberl,, and R. Schlapbach. 2008. PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics 24:i83i89.
67. Relman, D. A.,, J. S. Loutit,, T. M. Schmidt,, S. Falkow,, and L. S. Tompkins. 1990. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N. Engl. J. Med. 323:15731580.
68. 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. 327:293301.
69. Rota, P. A.,, M. S. Oberste,, S. S. Monroe,, W. A. Nix,, R. Campagnoli,, J. P. Icenogle,, S. Penaranda,, B. Bankamp,, K. Maher,, M. H. Chen,, S. Tong,, A. Tamin,, L. Lowe,, M. Frace,, J. L. DeRisi,, Q. Chen,, D. Wang,, D. D. Erdman,, T. C. Peret,, C. Burns,, T. G. Ksiazek,, P. E. Rollin,, A. Sanchez,, S. Liffick,, B. Holloway,, J. Limor,, K. McCaustland,, M. Olsen-Rasmussen,, R. Fouchier,, S. Gunther,, A. D. Osterhaus,, C. Drosten,, M. A. Pallansch,, L. J. Anderson,, and W. J. Bellini. 2003. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:13941399.
70. Towner, J. S.,, T. K. Sealy,, M. L. Khristova,, C. G. Albarino,, S. Conlan,, S. A. Reeder,, P. L. Quan,, W. I. Lipkin,, R. Downing,, J. W. Tappero,, S. Okware,, J. Lutwama,, B. Bakamutumaho,, J. Kayiwa,, J. A. Comer,, P. E. Rollin,, T. G. Ksiazek,, and S. T. Nichol. 2008. Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog. 4:e1000212.
71. Urisman, A.,, K. F. Fischer,, C. Y. Chiu,, A. L. Kistler,, S. Beck,, D. Wang,, and J. L. DeRisi. 2005. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol. 6:R78.
72. Urisman, A.,, R. J. Molinaro,, N. Fischer,, S. J. Plummer,, G. Casey,, E. A. Klein,, K. Malathi,, C. Magi-Galluzzi,, R. R. Tubbs,, D. Ganem,, R. H. Silverman,, and J. L. DeRisi. 2006. Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog. 2:e25.
73. van den Hoogen, B. G.,, J. C. deJong,, J. Groen,, T. Kuiken,, R. de Groot,, R. A. Fouchier,, and A. D. Osterhaus. 2001. A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat. Med. 7:719724.
74. van der Hoek, L.,, K. Pyrc,, M. F. Jebbink,, W. Vermeulen- Oost,, R. J. Berkhout,, K. C. Wolthers,, P. M. Wertheimvan Dillen,, J. Kaandorp,, J. Spaargaren,, and B. Berkhout. 2004. Identification of a new human coronavirus. Nat. Med. 10:368373.
75. Venter, J. C.,, M. D. Adams,, E. W. Myers,, P. W. Li,, R. J. Mural,, G. G. Sutton,, H. O. Smith,, M. Yandell,, C. A. Evans,, R. A. Holt,, J. D. Gocayne,, P. Amanatides,, R. M. Ballew,, D. H. Huson,, J. R. Wortman,, Q. Zhang,, C. D. Kodira,, X. H. Zheng,, L. Chen,, M. Skupski,, G. Subramanian,, P. D. Thomas,, J. Zhang,, G. L. Gabor Miklos,, C. Nelson,, S. Broder,, A. G. Clark,, J. Nadeau,, V. A. McKusick,, N. Zinder,, A. J. Levine,, R. J. Roberts,, M. Simon,, C. Slayman,, M. Hunkapiller,, R. Bolanos,, A. Delcher,, I. Dew,, D. Fasulo,, M. Flanigan,, L. Florea,, A. Halpern,, S. Hannenhalli,, S. Kravitz,, S. Levy,, C. Mobarry,, K. Reinert,, K. Remington,, J. Abu-Threideh,, E. Beasley,, K. Biddick,, V. Bonazzi,, R. Brandon,, M. Cargill,, I. Chandramouliswaran,, R. Charlab,, K. Chaturvedi,, Z. Deng,, V. Di Francesco,, P. Dunn,, K. Eilbeck,, C. Evangelista,, A. E. Gabrielian,, W. Gan,, W. Ge,, F. Gong,, Z. Gu,, P. Guan,, T. J. Heiman,, M. E. Higgins,, R. R. Ji,, Z. Ke,, K. A. Ketchum,, Z. Lai,, Y. Lei,, Z. Li,, J. Li,, Y. Liang,, X. Lin,, F. Lu,, G. V. Merkulov,, N. Milshina,, H. M. Moore,, A. K. Naik,, V. A. Narayan,, B. Neelam,, D. Nusskern,, D. B. Rusch,, S. Salzberg,, W. Shao,, B. Shue,, J. Sun,, Z. Wang,, A. Wang,, X. Wang,, J. Wang,, M. Wei,, R. Wides,, C. Xiao,, C. Yan, et al. 2001. The sequence of the human genome. Science 291:13041351.
76. Wang, D.,, L. Coscoy,, M. Zylberberg,, P. C. Avila,, H. A. Boushey,, D. Ganem,, and J. L. DeRisi. 2002. Microarraybased detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99:1568715692.
77. Wang, D.,, A. Urisman,, Y. T. Liu,, M. Springer,, T. G. Ksiazek,, D. D. Erdman,, E. R. Mardis,, M. Hickenbotham,, V. Magrini,, J. Eldred,, J. P. Latreille,, R. K. Wilson,, D. Ganem,, and J. L. DeRisi. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1:e2.
78. Watanabe, K.,, M. Oie,, M. Higuchi,, M. Nishikawa,, and M. Fujii. 2007. Isolation and characterization of novel human parechovirus from clinical samples. Emerg. Infect. Dis. 13:889895.
79. Watson, M.,, J. Dukes,, A. B. Abu-Median,, D. P. King,, and P. Britton. 2007. DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data. Genome Biol. 8:R190.
80. Woese, C. R.,, and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:50885090.
81. Wong, C. W.,, C. L. Heng,, L. Wan Yee,, S. W. Soh,, C. B. Kartasasmita,, E. A. Simoes,, M. L. Hibberd,, W. K. Sung,, and L. D. Miller. 2007. Optimization and clinical validation of a pathogen detection microarray. Genome Biol. 8:R93.
82. Woo, P. C.,, S. K. Lau,, C. M. Chu,, K. H. Chan,, H. W. Tsoi,, Y. Huang,, B. H. Wong,, R. W. Poon,, J. J. Cai,, W. K. Luk,, L. L. Poon,, S. S. Wong,, Y. Guan,, J. S. Peiris,, and K. Y. Yuen. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79:884895.
83. Zoll, J.,, S. Erkens Hulshof,, K. Lanke,, F. Verduyn Lunel,, W. J. Melchers,, E. Schoondermark-van deVen,, M. Roivainen,, J. M. Galama,, and F. J. vanKuppeveld. 2009. Saffold virus, a human Theiler’s-like cardiovirus, is ubiquitous and causes infection early in life. PLoS Pathog. 5:e1000416.

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