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Review Articles

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Pages 107-114 | Received 06 Jun 2011, Accepted 29 Jun 2011, Published online: 02 Aug 2011

References

  • Allander , T , Andreasson , K , Gupta , S , Bjerkner , A , Bogdanovic , G , Persson , MA , Dalianis , T , Ramqvist , T and Andersson , B . 2007 . Identification of a third human polyomavirus . J Virol , 81 ( 8 ) : 4130 – 4136 .
  • Allander , T , Emerson , SU , Engle , RE , Purcell , RH and Bukh , J . 2001 . A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species . Proc Nat Acad Sci USA , 98 ( 20 ) : 11609 – 11614 .
  • Allander , T , Tammi , MT , Eriksson , M , Bjerkner , A , Tiveljung-Lindell , A and Andersson , B . 2005 . Cloning of a human parvovirus by molecular screening of respiratory tract samples . Proc Nat Acad Sci USA , 102 ( 36 ) : 12891 – 12896 .
  • Ambrose , HE and Clewley , JP . 2006 . Virus discovery by sequence-independent genome amplification . Rev Med Virol , 16 ( 6 ) : 365 – 383 .
  • Armour , CD , Castle , JC , Chen , R , Babak , T , Loerch , P , Jackson , S , Shah , JK , Dey , J , Rohl , CA Johnson , JM . 2009 . Digital transcriptome profiling using selective hexamer priming for cDNA synthesis . Nat Methods , 6 ( 9 ) : 647 – 649 .
  • Bao , S , Jiang , R , Kwan , W , Wang , B , Ma , X and Song , YQ . 2011 . Evaluation of next-generation sequencing software in mapping and assembly . J Hum Genet , 56 ( 6 ) : 406 – 414 .
  • Berthet , N , Reinhardt , AK , Leclercq , I , van Ooyen , S , Batejat , C , Dickinson , P , Stamboliyska , R , Old , IG , Kong , KA Dacheux , L . 2008 . Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR . BMC Mol Biol , 9 : 77
  • Bexfield , N and Kellam , P . 2010 . Metagenomics and the molecular identification of novel viruses Vet J. in press doi: doi:10.1016/j.tvjl.2010.10.014
  • Blanco , L , Bernad , A , Lazaro , JM , Martin , G , Garmendia , C and Salas , M . 1989 . Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication . J Biol Chem , 264 ( 15 ) : 8935 – 8940 .
  • Blankenberg , D , Von Kuster , G , Coraor , N , Ananda , G , Lazarus , R , Mangan , M , Nekrutenko , A and Taylor , J . 2010 . Galaxy: a web-based genome analysis tool for experimentalists . Curr Protoc Mol Biol , Chapter 19 ( Unit 19.10 ) : 1 – 21 .
  • Blinkova , O , Victoria , J , Li , Y , Keele , BF , Sanz , C , Ndjango , JB , Peeters , M , Travis , D , Lonsdorf , EV Wilson , ML . 2010 . Novel circular DNA viruses in stool samples of wild-living chimpanzees . J Gen Virol , 91 ( Pt 1 ) : 74 – 86 .
  • Blomström , AL , Belak , S , Fossum , C , McKillen , J , Allan , G , Wallgren , P and Berg , M . 2009 . Detection of a novel porcine boca-like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome . Virus Res , 146 ( 1–2 ) : 125 – 129 .
  • Blomström , AL , Widen , F , Hammer , AS , Belak , S and Berg , M . 2010 . Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics . J Clin Microbiol , 48 ( 12 ) : 4392 – 4396 .
  • Breitbart , M and Rohwer , F . 2005 . Methods for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing . Biotechniques , 39 : 729 – 736 .
  • Breitbart , M , Salamon , P , Andresen , B , Mahaffy , JM , Segall , AM , Mead , D , Azam , F and Rohwer , F . 2002 . Genomic analysis of uncultured marine viral communities . Proc Nat Acad Sci USA , 99 ( 22 ) : 14250 – 14255 .
  • Chen , Z and Duan , X . 2011 . Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications . Methods Mol Biol , 733 : 93 – 103 .
  • Cox-Foster , DL , Conlan , S , Holmes , EC , Palacios , G , Evans , JD , Moran , NA , Quan , PL , Briese , T , Hornig , M Geiser , DM . 2007 . A metagenomic survey of microbes in honey bee colony collapse disorder . Science , 318 ( 5848 ) : 283 – 287 .
  • Daszak , P , Cunningham , AA and Hyatt , AD . 2000 . Emerging infectious diseases of wildlife-threats to biodiversity and human health . Science , 287 ( 5452 ) : 443 – 449 .
  • de Vries , M , Deijs , M , Canuti , M , van Schaik , BD , Faria , NR , van de Garde , MD , Jachimowski , LC , Jebbink , MF , Jakobs , M Luyf , AC . 2011 . A sensitive assay for virus discovery in respiratory clinical samples . PLoS One , 6 ( 1 ) : e16118
  • Dean , FB , Nelson , JR , Giesler , TL and Lasken , RS . 2001 . Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification . Genome Res , 11 ( 6 ) : 1095 – 1099 .
  • Delwart , EL . 2007 . Viral metagenomics . Rev Med Virol , 17 ( 2 ) : 115 – 131 .
  • Donaldson , EF , Haskew , AN , Gates , JE , Huynh , J , Moore , CJ and Frieman , MB . 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 ( 24 ) : 13004 – 13018 .
  • Endoh , D , Mizutani , T , Kirisawa , R , Maki , Y , Saito , H , Kon , Y , Morikawa , S and Hayashi , M . 2005 . Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription . Nucleic Acids Res , 33 ( 6 ) : e65
  • Esteban , JA , Salas , M and Blanco , L . 1993 . Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization . J Biol Chem , 268 ( 4 ) : 2719 – 2726 .
  • Feldmann , H , Czub , M , Jones , S , Dick , D , Garbutt , M , Grolla , A and Artsob , H . 2002 . Emerging and re-emerging infectious diseases . Med Microbiol Immunol , 191 ( 2 ) : 63 – 74 .
  • Fredericks , DN and Relman , DA . 1996 . Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates . Clin Microbiol Rev , 9 ( 1 ) : 18 – 33 .
  • Froussard , P . 1992 . A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA . Nucleic Acids Res , 20 ( 11 ) : 2900
  • Goecks , J , Nekrutenko , A and Taylor , J . 2010 . Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences . Genome Biol , 11 ( 8 ) : R86
  • Handelsman , J . 2004 . Metagenomics: application of genomics to uncultured microorganisms . Microbiol Mol Biol Rev , 68 ( 4 ) : 669 – 685 .
  • Harris , TD , Buzby , PR , Babcock , H , Beer , E , Bowers , J , Braslavsky , I , Causey , M , Colonell , J , DiMeo , J Efcavitch , JW . 2008 . Single-molecule DNA sequencing of a viral genome . Science , 320 : 106 – 109 .
  • He , S , Wurtzel , O , Singh , K , Froula , JL , Yilmaz , S , Tringe , SG , Wang , Z , Chen , F , Lindquist , EA Sorek , R . 2010 . Validation of two ribosomal RNA removal methods for microbial metatranscriptomics . Nat Methods , 7 ( 10 ) : 807 – 812 .
  • Honkavuori , KS , Shivaprasad , HL , Williams , BL , Quan , PL , Hornig , M , Street , C , Palacios , G , Hutchison , SK , Franca , M Egholm , M . 2008 . Novel borna virus in psittacine birds with proventricular dilatation disease . Emerg Infect Dis , 14 ( 12 ) : 1883 – 1886 .
  • Huson , DH , Auch , AF , Qi , J and Schuster , SC . 2007 . MEGAN analysis of metagenomic data . Genome Res , 17 ( 3 ) : 377 – 386 .
  • Huson , DH , Richter , DC , Mitra , S , Auch , AF and Schuster , SC . 2009 . Methods for comparative metagenomics . BMC Bioinformatics , 10 ( Suppl. 1 ) : S12
  • Johne , R , Muller , H , Rector , A , van Ranst , M and Stevens , H . 2009 . Rolling-circle amplification of viral DNA genomes using phi29 polymerase . Trends Microbiol , 17 ( 5 ) : 205 – 211 .
  • Jones , MS , Kapoor , A , Lukashov , VV , Simmonds , P , Hecht , F and Delwart , E . 2005 . New DNA viruses identified in patients with acute viral infection syndrome . J Virol , 79 ( 13 ) : 8230 – 8236 .
  • Jones , KE , Patel , NG , Levy , MA , Storeygard , A , Balk , D , Gittleman , JL and Daszak , P . 2008 . Global trends in emerging infectious diseases . Nature , 451 ( 7181 ) : 990 – 993 .
  • Kircher , M and Kelso , J . 2010 . High-throughput DNA sequencing – concepts and limitations . BioEssays , 32 ( 6 ) : 524 – 536 .
  • Kirkland , PD , Frost , MJ , Finlaison , DS , King , KR , Ridpath , JF and Gu , X . 2007 . Identification of a novel virus in pigs – Bungowannah virus: a possible new species of pestivirus . Virus Res , 129 ( 1 ) : 26 – 34 .
  • Kistler , AL , Gancz , A , Clubb , S , Skewes-Cox , P , Fischer , K , Sorber , K , Chiu , CY , Lublin , A , Mechani , S Farnoushi , Y . 2008 . Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent . Virol J , 5 : 88
  • Kostic , AD , Ojesina , AI , Pedamallu , CS , Jung , J , Verhaak , RG , Getz , G and Meyerson , M . 2011 . PathSeq: software to identify or discover microbes by deep sequencing of human tissue . Nat Biotechnol , 29 ( 5 ) : 393 – 396 .
  • Lauck , M , Hyeroba , D , Tumukunde , A , Weny , G , Lank , SM , Chapman , CA , O’Connor , DH , Friedrich , TC and Goldberg , TL . 2011 . Novel, divergent simian hemorrhagic fever viruses in a wild ugandan red colobus monkey discovered using direct pyrosequencing . PLoS One , 6 ( 4 ) : e19056
  • Leland , DS and Ginocchio , CC . 2007 . Role of cell culture for virus detection in the age of technology . Clin Microbiol Rev , 20 ( 1 ) : 49 – 78 .
  • Li , L , Victoria , JG , Wang , C , Jones , M , Fellers , GM , Kunz , TH and Delwart , E . 2010 . Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses . J Virol , 84 ( 14 ) : 6955 – 6965 .
  • MacLachlan , JN and Dubovi , EJ . 2001 . Fenner's veterinary virology, , 4th , London : Academic Press .
  • Margulies , M , Egholm , M , Altman , WE , Attiya , S , Bader , JS , Bemben , LA , Berka , J , Braverman , MS , Chen , YJ Chen , Z . 2005 . Genome sequencing in microfabricated high-density picolitre reactors . Nature , 437 ( 7057 ) : 376 – 380 .
  • Matsui , SM , Kim , JP , Greenberg , HB , Su , W , Sun , Q , Johnson , PC , DuPont , HL , Oshiro , LS and Reyes , GR . 1991 . The isolation and characterization of a Norwalk virus-specific cDNA . J Clin Invest , 87 ( 4 ) : 1456 – 1461 .
  • Metzker , ML . 2010 . Sequencing technologies - the next generation . Nat Rev Genet , 11 ( 1 ) : 31 – 46 .
  • Miller , JR , Koren , S and Sutton , G . 2010 . Assembly algorithms for next-generation sequencing data . Genomics , 95 ( 6 ) : 315 – 327 .
  • Ng , TF , Manire , C , Borrowman , K , Langer , T , Ehrhart , L and Breitbart , M . 2009 . Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics . J Virol , 83 ( 6 ) : 2500 – 2509 .
  • Ng , TF , Wheeler , E , Greig , D , Waltzek , TB , Gulland , F and Breitbart , M . 2011 . Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years . J Gen Virol , 92 ( Pt 6 ) : 1318 – 1323 .
  • Pareek , CS , Smoczynski , R and Tretyn , A . 2011. Sequencing technologies and genome sequencing. J. Appl. Genet. Jun 23 Epub
  • Pop , M . 2009 . Genome assembly reborn: recent computational challenges . Brief Bioinform , 10 ( 4 ) : 354 – 366 .
  • Quan , PL , Wagner , TA , Briese , T , Torgerson , TR , Hornig , M , Tashmukhamedova , A , Firth , C , Palacios , G , Baisre-De-Leon , A Paddock , CD . 2010 . Astrovirus encephalitis in boy with X-linked agammaglobulinemia . Emerg Infect Dis , 16 ( 6 ) : 918 – 925 .
  • Rector , A , Bossart , GD , Ghim , SJ , Sundberg , JP , Jenson , AB and Van Ranst , M . 2004 . Characterization of a novel close-to-root papillomavirus from a Florida manatee by using multiply primed rolling-circle amplification: trichechus manatus latirostris papillomavirus type 1 . J Virol , 78 ( 22 ) : 12698 – 12702 .
  • Reyes , GR and Kim , JP . 1991 . Sequence-independent, single-primer amplification (SISPA) of complex DNA populations . Mol Cell Probes , 5 ( 6 ) : 473 – 481 .
  • Runckel , C , Flenniken , ML , Engel , JC , Ruby , JG , Ganem , D , Andino , R and DeRisi , JL . 2011 . Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, Crithidia . PLoS ONE , 6 ( 6 ) : e20656
  • Sanger , F , Nicklen , S and Coulson , AR . 1977 . DNA sequencing with chain-terminating inhibitors . Proc Nat Acad Sci USA , 74 : 5463 – 5467 .
  • Schadt , EE , Turner , S and Kasarskis , A . 2010 . A window into third-generation sequencing . Hum Mol Genet , 19 ( R2 ) : R227 – 240 .
  • Seshadri , R , Kravitz , SA , Smarr , L , Gilna , P and Frazier , M . 2007 . CAMERA: a community resource for metagenomics . PLoS Biol , 5 ( 3 ) : e75
  • Stewart , FJ , Ottesen , EA and DeLong , EF . 2010 . Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics . ISME J , 4 ( 7 ) : 896 – 907 .
  • Sun , S , Chen , J , Li , W , Altintas , I , Lin , A , Peltier , S , Stocks , K , Allen , EE , Ellisman , M Grethe , J . 2011 . Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource . Nucleic Acids Res , 39 ( Database issue ) : D546 – 551 .
  • Tang , P and Chiu , C . 2010 . Metagenomics for the discovery of novel human viruses . Future Microbiol , 5 ( 2 ) : 177 – 189 .
  • Thurber , RV , Haynes , M , Breitbart , M , Wegley , L and Rohwer , F . 2009 . Laboratory procedures to generate viral metagenomes . Nat Protoc , 4 ( 4 ) : 470 – 483 .
  • Trifonov , V and Rabadan , R . 2010 . Frequency analysis techniques for identification of viral genetic data . MBio , 1 ( 3 ) : e00156 – 10 .
  • van der Hoek , L , Pyrc , K , Jebbink , MF , Vermeulen-Oost , W , Berkhout , RJ , Wolthers , KC , Wertheim-van Dillen , PM , Kaandorp , J , Spaargaren , J and Berkhout , B . 2004 . Identification of a new human coronavirus . Nat Med , 10 ( 4 ) : 368 – 373 .
  • Van Etten , JL , Lane , LC and Dunigan , DD . 2010 . DNA viruses: the really big ones (giruses) . Annu Rev Microbiol , 64 : 83 – 99 .
  • Victoria , JG , Kapoor , A , Li , L , Blinkova , O , Slikas , B , Wang , C , Naeem , A , Zaidi , S and Delwart , E . 2009 . Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis . J Virol , 83 ( 9 ) : 4642 – 4651 .
  • Weaver , SC and Reisen , WK . 2009 . Present and future arboviral threats . Antiviral Res , 85 ( 2 ) : 328 – 345 .
  • Wooley , JC , Godzik , A and Friedberg , I . 2010 . A primer on metagenomics . PLoS Comput Biol , 6 ( 2 ) : e1000667
  • Wu , Q , Luo , Y , Lu , R , Lau , N , Lai , EC , Li , WX and Ding , SW . 2010 . Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs . Proc Nat Acad Sci USA , 107 ( 4 ) : 1606 – 1611 .

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