The fecal viral flora of wild rodents

PLoS Pathogens

Volumn 7, Issue 9, 2011, Pages

  Phan, Tung G ^a,b   Kapusinszky, Beatrix ^a,b,c   Wang, Chunlin ^d   Rose, Robert K ^e   Lipton, Howard L ^f   Delwart, Eric L ^a,b  

^a BLOOD SYSTEMS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL CENTER FOR EPIDEMIOLOGY   (Hungary)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e OLD DOMINION UNIVERSITY   (United States)

^f UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA;

ADENO ASSOCIATED VIRUS; ADENOVIRUS; ARTICLE; ASTROVIRUS; BROMOVIRUS; CIRCOVIRIDAE; CORONAVIRUS; FECES MICROFLORA; GEMINIVIRUS; IRIDOVIRUS; KOBUVIRUS; NANOVIRIDAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PARVOVIRUS; PHYCODNAVIRIDAE; PHYLOGENY; PICORNAVIRUS; POLYDNAVIRIDAE; RODENT; SEQUENCE ANALYSIS; TOMBUSVIRUS; TYMOVIRIDAE; VIRUS CHARACTERIZATION; VIRUS GENOME; VIRUS PARTICLE; VIRUS REPLICATION; ZOONOSIS; ANIMAL; CLASSIFICATION; FECES; GENETICS; INSECT VIRUS; ISOLATION AND PURIFICATION; METAGENOMICS; PLANT VIRUS; UNITED STATES; VIROLOGY; VIRUS; WILD ANIMAL;

ADENOVIRIDAE; AICHI VIRUS; ASTROVIRIDAE; BROMOVIRIDAE; CIRCOVIRIDAE; CORONAVIRIDAE; GEMINIVIRIDAE; HEXAPODA; IRIDOVIRIDAE; MAMMALIA; MURIDAE; MURINAE; NANOVIRIDAE; PAPILLOMAVIRIDAE; PARTITIVIRIDAE; PARVOVIRIDAE; PHYCODNAVIRIDAE; PICORNAVIRIDAE; POLYDNAVIRIDAE; RATTUS; RODENTIA; TOMBUSVIRIDAE; TYMOVIRIDAE;

ANIMALS; ANIMALS, WILD; CALIFORNIA; FECES; GENOME, VIRAL; INSECT VIRUSES; METAGENOMICS; PLANT VIRUSES; RODENTIA; VIRGINIA; VIRUSES;

EID: 80053449137     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1002218     Document Type: Article

References (149)

1. Huchon D, Madsen O, Sibbald MJ, Ament K, Stanhope MJ, et al. (2002) Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol Evol 19: 1053-1065.
2. Meerburg BG, Singleton GR, Kijlstra A, (2009) Rodent-borne diseases and their risks for public health. Crit Rev Microbiol 35: 221-270.
3. Charrel RN, de Lamballerie X, (2010) Zoonotic aspects of arenavirus infections. Vet Microbiol 140: 213-220.
4. Cutler SJ, Fooks AR, van der Poel WH, (2010) Public health threat of new, reemerging, and neglected zoonoses in the industrialized world. Emerg Infect Dis 16: 1-7.
5. Klein SL, Calisher CH, (2007) Emergence and persistence of hantaviruses. Curr Top Microbiol Immunol 315: 217-252.
6. LeDuc JW, (1987) Epidemiology of Hantaan and related viruses. Lab Anim Sci 37: 413-418.
7. Mills JN, Childs JE, (1998) Ecologic studies of rodent reservoirs: their relevance for human health. Emerg Infect Dis 4: 529-537.
8. Zeier M, Handermann M, Bahr U, Rensch B, Muller S, et al. (2005) New ecological aspects of hantavirus infection: a change of a paradigm and a challenge of prevention--a review. Virus Genes 30: 157-180.
9. Bengis RG, Leighton FA, Fischer JR, Artois M, Morner T, et al. (2004) The role of wildlife in emerging and re-emerging zoonoses. Rev Sci Tech 23: 497-511.
10. Chomel BB, Belotto A, Meslin FX, (2007) Wildlife, exotic pets, and emerging zoonoses. Emerg Infect Dis 13: 6-11.
11. Enria DA, Pinheiro F, (2000) Rodent-borne emerging viral zoonosis. Hemorrhagic fevers and hantavirus infections in South America. Infect Dis Clin North Am 14: 167-184, x.
12. Mackenzie RB, (1972) Public health importance of rodents in South America. Bull World Health Organ 47: 161-169.
13. Nichol ST, Spiropoulou CF, Morzunov S, Rollin PE, Ksiazek TG, et al. (1993) Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness. Science 262: 914-917.
14. Khan AS, Spiropoulou CF, Morzunov S, Zaki SR, Kohn MA, et al. (1995) Fatal illness associated with a new hantavirus in Louisiana. J Med Virol 46: 281-286.
15. Khan AS, Khabbaz RF, Armstrong LR, Holman RC, Bauer SP, et al. (1996) Hantavirus pulmonary syndrome: the first 100 US cases. J Infect Dis 173: 1297-1303.
16. Monroe MC, Morzunov SP, Johnson AM, Bowen MD, Artsob H, et al. (1999) Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America. Emerg Infect Dis 5: 75-86.
17. Turell MJ, Korch GW, Rossi CA, Sesline D, Enge BA, et al. (1995) Short report: prevalence of hantavirus infection in rodents associated with two fatal human infections in California. Am J Trop Med Hyg 52: 180-182.
18. Goldsmith CS, Elliott LH, Peters CJ, Zaki SR, (1995) Ultrastructural characteristics of Sin Nombre virus, causative agent of hantavirus pulmonary syndrome. Arch Virol 140: 2107-2122.
19. Rivers MN, Alexander JL, Rohde RE, Pierce JR Jr, (2009) Hantavirus pulmonary syndrome in Texas: 1993-2006. South Med J 102: 36-41.
20. Rowe JE, St Jeor SC, Riolo J, Otteson EW, Monroe MC, et al. (1995) Coexistence of several novel hantaviruses in rodents indigenous to North America. Virology 213: 122-130.
21. Schwarz TF, Zaki SR, Morzunov S, Peters CJ, Nichol ST, (1995) Detection and sequence confirmation of Sin Nombre virus RNA in paraffin-embedded human tissues using one-step RT-PCR. J Virol Methods 51: 349-356.
22. Torres-Perez F, Wilson L, Collinge SK, Harmon H, Ray C,et al. Sin Nombre virus infection in field workers, Colorado, USA. Emerg Infect Dis 16: 308-310.
23. White DJ, Means RG, Birkhead GS, Bosler EM, Grady LJ, et al. (1996) Human and rodent hantavirus infection in New York State: public health significance of an emerging infectious disease. Arch Intern Med 156: 722-726.
24. Lonner BN, Douglass RJ, Kuenzi AJ, Hughes K, (2008) Seroprevalence against Sin Nombre virus in resident and dispersing deer mice. Vector Borne Zoonotic Dis 8: 433-441.
25. Pettersson L, Boman J, Juto P, Evander M, Ahlm C, (2008) Outbreak of Puumala virus infection, Sweden. Emerg Infect Dis 14: 808-810.
26. Hjelle B, Jenison SA, Goade DE, Green WB, Feddersen RM, et al. (1995) Hantaviruses: clinical, microbiologic, and epidemiologic aspects. Crit Rev Clin Lab Sci 32: 469-508.
27. Hjertqvist M, Klein SL, Ahlm C, Klingstrom J, (2010) Mortality rate patterns for hemorrhagic fever with renal syndrome caused by Puumala virus. Emerg Infect Dis 16: 1584-1586.
28. Makary P, Kanerva M, Ollgren J, Virtanen MJ, Vapalahti O, et al. (2010) Disease burden of Puumala virus infections, 1995-2008. Epidemiol Infect 138: 1484-1492.
29. Oncul O, Atalay Y, Onem Y, Turhan V, Acar A, et al. (2011) Hantavirus infection in Istanbul, Turkey. Emerg Infect Dis 17: 303-304.
30. Papa A, Christova I, (2011) Genetic detection of dobrava/belgrade virus, bulgaria. Emerg Infect Dis 17: 308-309.
31. Vapalahti O, Mustonen J, Lundkvist A, Henttonen H, Plyusnin A, et al. (2003) Hantavirus infections in Europe. Lancet Infect Dis 3: 653-661.
32. Zhang YZ, Zou Y, Fu ZF, Plyusnin A, Hantavirus infections in humans and animals, ChinaEmerg Infect Dis 16: 1195-1203.
33. Zhang YZ, Zhang FX, Wang JB, Zhao ZW, Li MH, et al. (2009) Hantaviruses in rodents and humans, Inner Mongolia Autonomous Region, China. Emerg Infect Dis 15: 885-891.
34. Zuo SQ, Zhang PH, Jiang JF, Zhan L, Wu XM, et al. (2008) Seoul virus in patients and rodents from Beijing, China. Am J Trop Med Hyg 78: 833-837.
35. Zou Y, Wang JB, Gaowa HS, Yao LS, Hu GW, et al. (2008) Isolation and genetic characterization of hantaviruses carried by Microtus voles in China. J Med Virol 80: 680-688.
36. Korva M, Duh D, Puterle A, Trilar T, Zupanc TA, (2009) First molecular evidence of Tula hantavirus in Microtus voles in Slovenia. Virus Res 144: 318-322.
37. Plyusnin A, Vapalahti O, Lankinen H, Lehvaslaiho H, Apekina N, et al. (1994) Tula virus: a newly detected hantavirus carried by European common voles. J Virol 68: 7833-7839.
38. Song JW, Baek LJ, Song KJ, Skrok A, Markowski J, et al. (2004) Characterization of Tula virus from common voles (microtus arvalis) in Poland: evidence for geographic-specific phylogenetic clustering. Virus Genes 29: 239-247.
39. Song JW, Gligic A, Yanagihara R, (2002) Identification of Tula hantavirus in Pitymys subterraneus captured in the Cacak region of Serbia-Yugoslavia. Int J Infect Dis 6: 31-36.
40. Schultze D, Lundkvist A, Blauenstein U, Heyman P, (2002) Tula virus infection associated with fever and exanthema after a wild rodent bite. Eur J Clin Microbiol Infect Dis 21: 304-306.
41. Lindquist L, Vapalahti O, (2008) Tick-borne encephalitis. Lancet 371: 1861-1871.
42. Mansfield KL, Johnson N, Phipps LP, Stephenson JR, Fooks AR, et al. (2009) Tick-borne encephalitis virus- a review of an emerging zoonosis. J Gen Virol 90: 1781-1794.
43. Bakhvalova VN, Dobrotvorsky AK, Panov VV, Matveeva VA, Tkachev SE, et al. (2006) Natural tick-borne encephalitis virus infection among wild small mammals in the southeastern part of western Siberia, Russia. Vector Borne Zoonotic Dis 6: 32-41.
44. Tonteri E, Jaaskelainen AE, Tikkakoski T, Voutilainen L, Niemimaa J, et al. (2011) Tick-borne encephalitis virus in wild rodents in winter, Finland, 2008-2009. Emerg Infect Dis 17: 72-75.
45. Frame JD, Baldwin JM Jr, Gocke DJ, Troup JM, (1970) Lassa fever, a new virus disease of man from West Africa. I. Clinical description and pathological findings. Am J Trop Med Hyg 19: 670-676.
46. Khan SH, Goba A, Chu M, Roth C, Healing T, et al. (2008) New opportunities for field research on the pathogenesis and treatment of Lassa fever. Antiviral Res 78: 103-115.
47. Klempa B, (2009) Hantaviruses and climate change. Clin Microbiol Infect 15: 518-523.
48. Tersago K, Schreurs A, Linard C, Verhagen R, Van Dongen S, et al. (2008) Population, environmental, and community effects on local bank vole (Myodes glareolus) Puumala virus infection in an area with low human incidence. Vector Borne Zoonotic Dis 8: 235-244.
49. Davis S, Calvet E, Leirs H, (2005) Fluctuating rodent populations and risk to humans from rodent-borne zoonoses. Vector Borne Zoonotic Dis 5: 305-314.
50. Day JM, Ballard LL, Duke MV, Scheffler BE, Zsak L, (2010) Metagenomic analysis of the turkey gut RNA virus community. Virol J 7: 313.
51. Li L, Victoria JG, Wang C, Jones M, Fellers GM, et al. (2010) Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84: 6955-6965.
52. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, et al. (2009) Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83: 4642-4651.
53. Bernard HU, Burk RD, Chen Z, van Doorslaer K, Hausen H, et al. (2010) Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 401: 70-79.
54. de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H, (2004) Classification of papillomaviruses. Virology 324: 17-27.
55. Gibbs MJ, Smeianov VV, Steele JL, Upcroft P, Efimov BA, (2006) Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. Mol Biol Evol 23: 1097-1100.
56. Rosario K, Duffy S, Breitbart M, (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90: 2418-2424.
57. Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M, (2009) Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11: 2806-2820.
58. Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, et al. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332: 714-717.
59. Faurez F, Dory D, Grasland B, Jestin A, (2009) Replication of porcine circoviruses. Virol J 6: 60.
60. Steinfeldt T, Finsterbusch T, Mankertz A, (2001) Rep and Rep' protein of porcine circovirus type 1 bind to the origin of replication in vitro. Virology 291: 152-160.
61. Steinfeldt T, Finsterbusch T, Mankertz A, (2007) Functional analysis of cis- and trans-acting replication factors of porcine circovirus type 1. J Virol 81: 5696-5704.
62. Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, et al. (2010) Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol 91: 74-86.
63. Yamashita T, Kobayashi S, Sakae K, Nakata S, Chiba S, et al. (1991) Isolation of cytopathic small round viruses with BS-C-1 cells from patients with gastroenteritis. J Infect Dis 164: 954-957.
64. Yamashita T, Sakae K, Ishihara Y, Isomura S, Utagawa E, (1993) Prevalence of newly isolated, cytopathic small round virus (Aichi strain) in Japan. J Clin Microbiol 31: 2938-2943.
65. Yamashita T, Sakae K, Tsuzuki H, Suzuki Y, Ishikawa N, et al. (1998) Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans. J Virol 72: 8408-8412.
66. Greninger AL, Holtz L, Kang G, Ganem D, Wang D, et al. (2010) Serological evidence of human klassevirus infection. Clin Vaccine Immunol 17: 1584-1588.
67. Shan T, Wang C, Cui L, Yu Y, Delwart E, et al. (2010) Picornavirus salivirus/klassevirus in children with diarrhea, China. Emerg Infect Dis 16: 1303-1305.
68. Li L, Victoria J, Kapoor A, Blinkova O, Wang C, et al. (2009) A novel picornavirus associated with gastroenteritis. J Virol 83: 12002-12006.
69. Holtz LR, Finkbeiner SR, Zhao G, Kirkwood CD, Girones R, et al. (2009) Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. Virol J 6: 86.
70. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, et al. (2009) The complete genome of klassevirus- a novel picornavirus in pediatric stool. Virol J 6: 82.
71. Dvorak CM, Hall DJ, Hill M, Riddle M, Pranter A, et al. (2001) Leader protein of encephalomyocarditis virus binds zinc, is phosphorylated during viral infection, and affects the efficiency of genome translation. Virology 290: 261-271.
72. Paul S, Michiels T, (2006) Cardiovirus leader proteins are functionally interchangeable and have evolved to adapt to virus replication fitness. J Gen Virol 87: 1237-1246.
73. Kaikkonen S, Rasanen S, Ramet M, Vesikari T, (2010) Aichi virus infection in children with acute gastroenteritis in Finland. Epidemiol Infect 138: 1166-1171.
74. Pham NT, Khamrin P, Nguyen TA, Kanti DS, Phan TG, et al. (2007) Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam. J Clin Microbiol 45: 2287-2288.
75. Sdiri-Loulizi K, Hassine M, Gharbi-Khelifi H, Sakly N, Chouchane S, et al. (2009) Detection and genomic characterization of Aichi viruses in stool samples from children in Monastir, Tunisia. J Clin Microbiol 47: 2275-2278.
76. Pereira HG, Flewett TH, Candeias JA, Barth OM, (1988) A virus with a bisegmented double-stranded RNA genome in rat (Oryzomys nigripes) intestines. J Gen Virol 69 (Pt11): 2749-2754.
77. Chandra R, (1997) Picobirnavirus, a novel group of undescribed viruses of mammals and birds: a minireview. Acta Virol 41: 59-62.
78. van Leeuwen M, Williams MM, Koraka P, Simon JH, Smits SL, et al. (2010) Human picobirnaviruses identified by molecular screening of diarrhea samples. J Clin Microbiol 48: 1787-1794.
79. Giordano MO, Martinez LC, Rinaldi D, Espul C, Martinez N, et al. (1999) Diarrhea and enteric emerging viruses in HIV-infected patients. AIDS Res Hum Retroviruses 15: 1427-1432.
80. Giordano MO, Martinez LC, Rinaldi D, Guinard S, Naretto E, et al. (1998) Detection of picobirnavirus in HIV-infected patients with diarrhea in Argentina. J Acquir Immune Defic Syndr Hum Retrovirol 18: 380-383.
81. Fregolente MC, Gatti MS, (2009) Nomenclature proposal for picobirnavirus. Arch Virol 154: 1953-1954.
82. Ganesh B, Nataraju SM, Rajendran K, Ramamurthy T, Kanungo S, et al. (2010) Detection of closely related Picobirnaviruses among diarrhoeic children in Kolkata: evidence of zoonoses? Infect Genet Evol 10: 511-516.
83. Walter JE, Mitchell DK, (2003) Astrovirus infection in children. Curr Opin Infect Dis 16: 247-253.
84. Vilarino ML, Le Guyader FS, Polo D, Schaeffer J, Krol J, et al. (2009) Assessment of human enteric viruses in cultured and wild bivalve molluscs. Int Microbiol 12: 145-151.
85. Chu DK, Chin AW, Smith GJ, Chan KH, Guan Y, et al. (2010) Detection of novel astroviruses in urban brown rats and previously known astroviruses in humans. J Gen Virol 91: 2457-2462.
86. Jeong AY, Jeong HS, Jo MY, Jung SY, Lee MS, et al. (2011) Molecular epidemiology and genetic diversity of human astrovirus in South Korea from 2002 to 2007. Clin Microbiol Infect 17: 404-408.
87. Reuter G, Pankovics P, Boros A, (2011) Identification of a novel astrovirus in a domestic pig in Hungary. Arch Virol 156: 125-128.
88. Rivera R, Nollens HH, Venn-Watson S, Gulland FM, Wellehan JF Jr, (2010) Characterization of phylogenetically diverse astroviruses of marine mammals. J Gen Virol 91: 166-173.
89. Kapoor A, Li L, Victoria J, Oderinde B, Mason C, et al. (2009) Multiple novel astrovirus species in human stool. J Gen Virol 90: 2965-2972.
90. Finkbeiner SR, Holtz LR, Jiang Y, Rajendran P, Franz CJ, et al. (2009) Human stool contains a previously unrecognized diversity of novel astroviruses. Virol J 6: 161.
91. Finkbeiner SR, Li Y, Ruone S, Conrardy C, Gregoricus N, et al. (2009) Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J Virol 83: 10836-10839.
92. Martella V, Lorusso E, Decaro N, Elia G, Radogna A, et al. (2008) Detection and molecular characterization of a canine norovirus. Emerg Infect Dis 14: 1306-1308.
93. Woo PC, Lau SK, Huang Y, Lam CS, Poon RW, et al. (2010) Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae. J Gen Virol 91: 2433-2448.
94. Srivastava A, Lusby EW, Berns KI, (1983) Nucleotide sequence and organization of the adeno-associated virus 2 genome. J Virol 45: 555-564.
95. Olivier V, Blanchard P, Chaouch S, Lallemand P, Schurr F, et al. (2008) Molecular characterisation and phylogenetic analysis of Chronic bee paralysis virus, a honey bee virus. Virus Res 132: 59-68.
96. Habayeb MS, Ekengren SK, Hultmark D, (2006) Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family. J Gen Virol 87: 3045-3051.
97. Hartley CJ, Greenwood DR, Gilbert RJ, Masoumi A, Gordon KH, et al. (2005) Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure. J Virol 79: 13385-13398.
98. Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, et al. (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci U S A 107: 8387-8392.
99. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223.
100. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99: 14250-14255.
101. Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, et al. (2009) Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 5: e1000455.
102. Lipkin WI, Palacios G, Briese T, (2009) Diagnostics and discovery in viral hemorrhagic fevers. Ann N Y Acad Sci 1171 (Suppl 1): E6-11.
103. Culley AI, Lang AS, Suttle CA, (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424: 1054-1057.
104. Culley AI, Lang AS, Suttle CA, (2006) Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-1798.
105. Kennedy J, Marchesi JR, Dobson AD, (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7: 27.
106. Quan PL, Wagner TA, Briese T, Torgerson TR, Hornig M, et al. (2010) Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Emerg Infect Dis 16: 918-925.
107. Simon C, Daniel R, (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77: 1153-1161.
108. Svraka S, Rosario K, Duizer E, van der Avoort H, Breitbart M, et al. (2010) Metagenomic sequencing for virus identification in a public-health setting. J Gen Virol 91: 2846-2856.
109. Tang P, Chiu C, (2010) Metagenomics for the discovery of novel human viruses. Future Microbiol 5: 177-189.
110. Towner JS, Sealy TK, Khristova ML, Albarino CG, Conlan S, et al. (2008) Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 4: e1000212.
111. Delwart EL, (2007) Viral metagenomics. Rev Med Virol 17: 115-131.
112. Cann AJ, Fandrich SE, Heaphy S, (2005) Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30: 151-156.
113. Donaldson EF, Haskew AN, Gates JE, Huynh J, Moore CJ, et al. (2010) Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. J Virol 84: 13004-13018.
114. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, et al. (2008) Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4: e1000011.
115. Blinkova O, Rosario K, Li L, Kapoor A, Slikas B, et al. (2009) Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States. J Clin Microbiol 47: 3507-3513.
116. Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, et al. (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84: 1674-1682.
117. Li L, Shan T, Oderinde SB, Masroor AM, Kunz T, et al. (2011) Possible cross-species transmission of circoviruses and cycloviruses in farm animals. J Gen Virol 92: 768-772.
118. Ng TF, Manire C, Borrowman K, Langer T, Ehrhart L, et al. (2009) Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol 83: 2500-2509.
119. Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, et al. (2011) Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol 92: 1302-1308.
120. Le Guyader FS, Le Saux JC, Ambert-Balay K, Krol J, Serais O, et al. (2008) Aichi virus, norovirus, astrovirus, enterovirus, and rotavirus involved in clinical cases from a French oyster-related gastroenteritis outbreak. J Clin Microbiol 46: 4011-4017.
121. Reuter G, Boros A, Pankovics P, (2011) Kobuviruses- a comprehensive review. Rev Med Virol 21: 32-41.
122. Li L, Pesavento P, Shan T, Leutenegger CM, Wang C, et al. (2011) Viruses in diarrhetic dogs include novel kobuviruses and sapoviruses. J Gen Virol [Epub ahead of print].
123. Honkavuori KS, Shivaprasad HL, Briese T, Street C, Hirschberg DL, et al. (2011) Novel picornavirus in Turkey poults with hepatitis, california, USA. Emerg Infect Dis 17: 480-487.
124. Jones MS, Lukashov VV, Ganac RD, Schnurr DP, (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: 2144-2150.
125. Blinkova O, Kapoor A, Victoria J, Jones M, Wolfe N, et al. (2009) Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J Virol 83: 4631-4641.
126. Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, et al. (2008) Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Proc Natl Acad Sci U S A 105: 14124-14129.
127. Arden KE, Mackay IM, (2010) Newly identified human rhinoviruses: molecular methods heat up the cold viruses. Rev Med Virol 20: 156-176.
128. Bhattacharya R, Sahoo GC, Nayak MK, Saha DR, Sur D, et al. (2006) Molecular epidemiology of human picobirnaviruses among children of a slum community in Kolkata, India. Infect Genet Evol 6: 453-458.
129. Buzinaro MG, Freitas PP, Kisiellius JJ, Ueda M, Jerez JA, (2003) Identification of a bisegmented double-stranded RNA virus (picobirnavirus) in calf faeces. Vet J 166: 185-187.
130. Giordano MO, Martinez LC, Masachessi G, Barril PA, Ferreyra LJ, et al. (2011) Evidence of closely related picobirnavirus strains circulating in humans and pigs in Argentina. J Infect 62: 45-51.
131. Masachessi G, Martinez LC, Giordano MO, Barril PA, Isa BM, et al. (2007) Picobirnavirus (PBV) natural hosts in captivity and virus excretion pattern in infected animals. Arch Virol 152: 989-998.
132. Fregolente MC, de Castro-Dias E, Martins SS, Spilki FR, Allegretti SM, et al. (2009) Molecular characterization of picobirnaviruses from new hosts. Virus Res 143: 134-136.
133. Zhu HC, Chu DK, Liu W, Dong BQ, Zhang SY, et al. (2009) Detection of diverse astroviruses from bats in China. J Gen Virol 90: 883-887.
134. Chu DK, Poon LL, Guan Y, Peiris JS, (2008) Novel astroviruses in insectivorous bats. J Virol 82: 9107-9114.
135. Brown KE, (2010) The expanding range of parvoviruses which infect humans. Rev Med Virol 20: 231-244.
136. Olson EJ, Haskell SR, Frank RK, Lehmkuhl HD, Hobbs LA, et al. (2004) Isolation of an adenovirus and an adeno-associated virus from goat kids with enteritis. J Vet Diagn Invest 16: 461-464.
137. Henckaerts E, Linden RM, (2010) Adeno-associated virus: a key to the human genome? Future Virol 5: 555-574.
138. Banyai K, Esona MD, Liu A, Wang Y, Tu X, et al. (2010) Molecular detection of novel adenoviruses in fecal specimens of captive monkeys with diarrhea in China. Vet Microbiol 142: 416-419.
139. Kunz AN, Ottolini M, (2010) The role of adenovirus in respiratory tract infections. Curr Infect Dis Rep 12: 81-87.
140. Tong S, Singh J, Ruone S, Humphrey C, Yip CC, et al. (2010) Identification of adenoviruses in fecal specimens from wild chimpanzees (Pan trogylodytes schweinfurthii) in western Tanzania. Am J Trop Med Hyg 82: 967-970.
141. Smith JG, Wiethoff CM, Stewart PL, Nemerow GR, (2010) Adenovirus. Curr Top Microbiol Immunol 343: 195-224.
142. Klempa B, Kruger DH, Auste B, Stanko M, Krawczyk A, et al. (2009) A novel cardiotropic murine adenovirus representing a distinct species of mastadenoviruses. J Virol 83: 5749-5759.
143. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, et al. (2002) Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99: 15687-15692.
144. Palacios G, Quan PL, Jabado OJ, Conlan S, Hirschberg DL, et al. (2007) Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 13: 73-81.
145. Yamashita Y, Ootsuka Y, Kondo R, Oseto M, Doi M, et al. (2010) Molecular characterization of Sapovirus detected in a gastroenteritis outbreak at a wedding hall. J Med Virol 82: 720-726.
146. Katayama K, Shirato-Horikoshi H, Kojima S, Kageyama T, Oka T, et al. (2002) Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses. Virology 299: 225-239.
147. Ishida S, Yoshizumi S, Miyoshi M, Ikeda T, Okui T, et al. (2008) Characterization of sapoviruses detected in Hokkaido, Japan. Jpn J Infect Dis 61: 504-506.
148. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
149. Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.