Metagenomic analysis of the turkey gut RNA virus community

Virology Journal

Volumn 7, Issue , 2010, Pages

  Day, J Michael ^a   Ballard, Linda L ^b   Duke, Mary V ^b   Scheffler, Brian E ^b   Zsak, Laszlo ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED RNA; VIRUS RNA;

AMINO ACID SUBSTITUTION; ANIMAL TISSUE; ARTICLE; BIRD DISEASE; CALICIVIRUS; GASTROINTESTINAL TRACT; NONHUMAN; NUCLEOTIDE SEQUENCE; PICOBIRNAVIRUS; PICORNAVIRUS; POLYMERASE CHAIN REACTION; POULT ENTERITIS COMPLEX; POULTRY; RNA VIRUS; STUNTING SYNDROME; TURKEY (BIRD); VIRAL GASTROENTERITIS; VIRUS DIAGNOSIS; VIRUS INFECTION; ANIMAL; BIODIVERSITY; CLASSIFICATION; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; ISOLATION AND PURIFICATION; METAGENOME; MOLECULAR GENETICS; UNITED STATES; VIROLOGY;

AVES; CALICIVIRIDAE; RNA VIRUSES;

ANIMALS; BIODIVERSITY; CALICIVIRIDAE; GASTROINTESTINAL TRACT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; MOLECULAR SEQUENCE DATA; PICOBIRNAVIRUS; PICORNAVIRIDAE; RNA VIRUSES; TURKEYS; UNITED STATES;

EID: 78149299038     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-7-313     Document Type: Article

References (44)

1. Pathogenesis of type 2 turkey astroviruses with variant capsid genes in 2-day-old specific pathogen free poults. MJ Pantin-Jackwood E Spackman JM Day, Avian Pathol 2008 37 193 201 10.1080/03079450801932200 18393099
2. The pathogenesis of turkey origin reoviruses in turkeys and chickens. E Spackman M Pantin-Jackwood J Day H Sellers, Avian Pathology 2005 34 291 296 10.1080/03079450500178501 16147564
3. Enteric viruses detected by molecular methods in commercial chicken and turkey flocks in the United States between 2005 and 2006. M Pantin-Jackwood JM Day MW Jackwood E Spackman, Avian Dis 2008 52 235 244 10.1637/8174-111507-Reg.1 18646452
4. Periodic monitoring of commercial turkeys for enteric viruses indicates continuous presence of astrovirus and rotavirus on the farms. MJ Pantin-Jackwood E Spackman JM Day D Rives, Avian Dis 2007 51 674 680 10.1637/0005-2086(2007) 51[674:PMOCTF]2.0.CO;2 17992925
5. Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: implications for diagnostics. MJ Pantin-Jackwood E Spackman PR Woolcock, Avian Dis 2006 50 397 404 10.1637/7512-020606R.1 17039840
6. Development of a polymerase chain reaction procedure for detection of chicken and turkey parvoviruses. L Zsak KO Strother JM Day, Avian Dis 2009 53 83 88 10.1637/8464-090308-Reg.1 19432008
7. Partial genome sequence analysis of parvoviruses associated with enteric disease in poultry. L Zsak KO Strother J Kisary, Avian Pathol 2008 37 435 441 10.1080/03079450802210648 18622862
8. Genome sequencing in microfabricated high-density picolitre reactors. M Margulies M Egholm W Altman S Attiya J Bader L Bemben J Berka M Braverman YJ Chen Z Chen,,et al Nature 2005 437 376 380 16056220
9. Viral Metagenomics. RA Edwards F Rohwer, Nat Rev Microbiol 2005 3 504 510 10.1038/nrmicro1163 15886693
10. Metagenomic Analyses of an Uncultured Viral Community from Human Feces. M Breitbart I Hewson B Felts J Mahaffy J Nulton P Salamon F Rohwer, J Bacteriol 2003 185 6220 6223 10.1128/JB.185.20.6220-6223.2003 14526037
11. RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses. T Zhang M Breitbart W Lee JQ Run C Wei S Soh M Hibberd E Liu F Rohwer Y Ruan, PLoS Biology 2006 4 3 10.1371/journal.pbio.0040003 16336043
12. Isolation and characterization of Solenopsis invicta virus 3, a new positive-strand RNA virus infecting the red imported fire ant, Solenopis invicta. SM Valles Y Hashimoto, Virology 2009 388 354 361 10.1016/j.virol.2009. 03.028 19403154
13. Metagenomic Analysis of Coastal RNA Virus Communities. A Culley A Lang C Suttle, Science 2006 312 1795 1798 10.1126/science.1127404 16794078
14. Rapid identification of known and new RNA viruses from animal tissues. JG Victoria A Kapoor K Dupuis DP Schnurr EL Delwart, PLoS Pathog 2008 4 1000163 10.1371/journal.ppat.1000163 18818738
15. A metagenomic survey of microbes in honey bee colony collapse disorder. DLCS Cox-Foster EC Holmes G Palacios JD Evans NA Moran PL Quan T Briese M Hornig DM Geiser V Martinson D vanEngelsdorp AL Kalkstein A Drysdale J Hui J Zhai L Cui SK Hutchison JF Simons M Egholm JS Pettis WI Lipkin, Science 2007 318 283 287 10.1126/science.1146498 17823314
16. Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. TFF Ng C Manire K Borrowman T Langer L Ehrhart M Breitbart, J Virol 2009 83 2500 2509 10.1128/JVI.01946-08 19116258
17. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture. O Le Gall P Christian CM Fauquet AMQ King NJ Knowles N Nakashima G Stanway AE Gorbalenya, Archives of Virology 2008 153 715 727 10.1007/s00705-008-0041-x 18293057
18. Electron Microscopic Identification of Viruses Associated with Poult Enteritis in Turkeys Grown in California 1993-2003. PA Woolcock HL Shivaprasad, Avian Diseases 2008 52 209 213 10.1637/8106-090607-Reg.1 18646448
19. Avian Enterovirus-like viruses. JS Guy MS McNulty CS Hayhow, Diseases of Poultry Blackwell Publishing, Saif YM, 12 2008
20. Bovine kobuvirus in Europe. G Reuter L Egyed, Emerging and Infectious Diseases 2009 15 822 823 10.3201/eid1505.081427
21. Bovine kobuviruses from cattle with diarrhea. P Khamrin N Maneekarn S Peerakome S Okitsu M Mizuguchi H Ushijima, Emerging and Infectious Diseases 2008 14 985 986 10.3201/eid1406.070784
22. Candidate new species of Kobuvirus in porcine hosts. G Reuter A Boldizsar I Kiss P Pankovics, Emerging and Infectious Diseases 2008 14 1968 1970 10.3201/eid1412.080797
23. Candidate porcine Kobuvirus, China. J Yu M Jin Q Zhang H Li D Li Z Xu J Li S Cui S Yang N Liu Z Duan, Emerging and Infectious Diseases 2009 15 823 825 10.3201/eid1505.081518
24. Duck Hepatitis. PR Woolcock, Diseases of Poultry Blackwell Publishing, Saif YM, 12 2008
25. Avian Encephalomyelitis. BW Calnek, Diseases of Poultry Blackwell Publishing, Saif YM, 12 2008
26. CM Fauquet MA Mayo J Maniloff U Desselberger LA Ball, Virus Taxonomy: Eighth report of the International Committee on Taxonomy of Viruses Elsevier Academic Press 2005
27. A virus with a bisegmented double-stranded RNA genome in rat (Oryzomys nigripes) intestines. HG Pereira TH Flewett JAN Candeias OM Barth, Journal of General Virologh 1988 69 2749 2754 10.1099/0022-1317-69-11-2749
28. Nomenclature proposal for picobirnavirus. MC Fregolente MS Gatti, Archives of Virology 2009 154 1953 1954 10.1007/s00705-009-0537-z 19882102
29. Picobirnavirus, a novel group of undescribed viruses of mammals and birds: a minireview. R Chandra, Acta Virologica 1997 41 59 62 9199719
30. Molecular characterization of picobirnaviruses from new hosts. MC Fregolente E de Castro-Dias SS Martins FR Spilki SM Allegretti MS Gatti, Virus Research 2009 143 134 136 10.1016/j.virusres.2009.03.006 19463731
31. A novel avian virus with trisegmented double-stranded RNA and further observations on previously described similar viruses with bisegmented genome. JPG Leite SP Monteiro AM Fialho HG Pereira, Virus Research 1990 16 119 126 10.1016/0168-1702(90)90016-5 2385956
32. Detection of Genogroup I and II human picobirnaviruses showing small genomic RNA profile causing acute watery diarrhoea among children in Kolkata, India. R Bhattacharya GC Sahoo MK Nayak K Rajendran P Dutta U Mitra MK Bhattacharya TN Naik SK Bhattacharya T Krishnan, Infection, Genetics and Evolution 2007 7 229 238 10.1016/j.meegid.2006.09.005 (Pubitemid 46201481)
33. Enteric Viruses and Diarrhea in HIV-Infected Patients. GS Grohmann RI Glass HG Pereira SS Monroe AW Hightower R Weber RT Bryan, New England Journal of Medicine 1993 329 14 20 10.1056/NEJM199307013290103 8099429
34. Molecular epidemiology of human astrovirus infections in Kolkata, India. R Bhattacharya GC Sahoo MK Nayak S Ghosh P Dutta MK Bhattacharya U Mitra D Gangopadhyay S Dutta SK Niyogi,,et al Infection, Genetics and Evolution 2006 6 425 435 10.1016/j.meegid.2006.02.001 (Pubitemid 44574167)
35. Characterization of novel porcine sapoviruses. Y L'Homme J Brassard M Ouardani MJ Gagne, Archives of Virology 2010 20352267
36. Incidence, diversity, and molecular epidemiology of sapoviruses in swine across Europe. G Reuter J Zimsek-Mijovski M Poljsak-Prijatelj I Di Bartolo FM Ruggeri T Kantala L Maunula I Kiss S Kecskemeti N Halaihel,,et al Journal of Clinical Microbiology 2010 48 363 368 10.1128/JCM.01279-09 19940055
37. Turkey origin reovirus induced immune dysfunction in specific pathogen free and commercial turkey poults. JM Day E Spackman M Pantin-Jackwood, Avian Dis 2008 52 387 391 10.1637/8190-120607-Reg 18939624
38. Pathology and virus tissue distribution of Turkey origin reoviruses in experimentally infected Turkey poults. MJ Pantin-Jackwood E Spackman JM Day, Vet Pathol 2007 44 185 195 10.1354/vp.44-2-185 17317795
39. Astrovirus, reovirus, and rotavirus concomitant infection causes decreased weight gain in broad-breasted white poults. E Spackman JM Day MJ Pantin-Jackwood, Avian Dis 2010 54 16 21 10.1637/8986-070909-Reg.1 20408393
40. Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins. L Noad J Shou KM Coombs R Duncan, Virus Res 2006 116 45 57 10.1016/j.virusres.2005.08.014 16297481
41. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein. W Xu KM Coombs, Virol J 2008 5 153 10.1186/1743-422X-5-153 19091125
42. Removal of real-time reverse transcription polymerase chain reaction (RT-PCR) inhibitors associated with cloacal swab samples and tissues for improved diagnosis of Avian influenza virus by RT-PCR. A Das E Spackman MJ Pantin-Jackwood DL Suarez, J Vet Diagn Invest 2009 21 771 778 19901277
43. MEGAN analysis of metagenomic data. DH Huson AF Auch J Qi SC Schuster, Genome Research 2007 17 377 386 10.1101/gr.5969107 17255551
44. MEGA4: Molecular Evolutionary Genetics Analyisis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Molecular Biology and Evolution 2007 24 1596 1599 10.1093/molbev/msm092 17488738