High-throughput sequencing in veterinary infection biology and diagnostics

OIE Revue Scientifique et Technique

Volumn 32, Issue 3, 2013, Pages 893-915

  Belak S ^a,b,c   Karlsson, O E ^b,c   Leijon, M ^a,c   Granberg, F ^b,c  

^a NATIONAL VETERINARY INSTITUTE   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c Centre collaborateur de l'Organisation mondiale de la santé animale   (Sweden)

Author keywords

Aetiology; Detection of viruses and bacteria; Diagnosis; Emerging viruses and bacteria; High throughput sequencing; Metagenomics; Next generation sequencing

Indexed keywords

ANIMAL; ANIMAL DISEASE; ARTICLE; COMMUNICABLE DISEASE; ECONOMICS; EUROPEAN UNION; GENE LIBRARY; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MICROBIOLOGY; MOLECULAR DIAGNOSIS; VETERINARY MEDICINE;

ANIMAL DISEASES; ANIMALS; COMMUNICABLE DISEASES; EUROPEAN UNION; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR DIAGNOSTIC TECHNIQUES; VETERINARY MEDICINE;

EID: 84898431119     PISSN: 02531933     EISSN: 16080645     Source Type: Journal    
DOI: 10.20506/rst.32.2.2206     Document Type: Article

References (114)

1. Belák S. (2007). - Molecular diagnosis of viral diseases, present trends and future aspects. A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine. Vaccine, 25 (30), 5444-5452.
2. Belák S. (2007). - Experiences of an OIE Collaborating Centre in molecular diagnosis of transboundary animal diseases: a review. Dev. Biol. (Basel), 128, 103-112.
3. Belák S. & Liu L. (2013). - Recent advances in veterinary diagnostic virology: report from a Collaborating Centre of the World Organisation for Animal Health (OIE). In Advanced techniques in diagnostic microbiology (Y.-W. Tang & C.W. Stratton, eds). Springer, New York, 661-678.
4. Belák S., Thorén R, LeBlanc N. & Viljoen G. (2009).-Advances in viral disease diagnostic and molecular epidemiological technologies. Expert Rev. mol. Diagn., 9 (4), 367-381.
5. Sanger E, Nicklen S. & Coulson A.R. (1977). - DNA sequencing with chain-terminating inhibitors. Proc. natl Acad. Sci. USA, 74 (12), 5463-5467.
6. Sanger F., Air G.M., Barrell B.G., Brown N.L., Coulson A.R., Fiddes CA., Hutchison CA., Slocombe RM. & Smith M. (1977). - Nucleotide sequence of bacteriophage phi X174 DNA. Nature, 265 (5596), 687-695.
7. Mullis K., Faloona E, Scharf S., Saiki R., Horn G. & Erlich H. (1986). - Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Barb. Symp. quant Biol., 51 (Pt 1), 263-273.
8. Bartlett J.M. & Stirling D. (2003). - A short history of the polymerase chain reaction. Meth. molec. Biol., 226, 3-6.
9. Smith L.M., Sanders J.Z., Kaiser R.J., Hughes R., Dodd C, Connell CR, Heiner C., Kent S.B. & Hood LE. (1986). - Fluorescence detection in automated DNA sequence analysis. Nature, 321 (6071), 674-679.
10. Venter J.C., Adams M.D., Myers E.W., Li R.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans CA, Holt R.A., Gocayne J.D., Amanatides R., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira CD., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick VA., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V, Dunn R., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong E., Gu Z., Guan R., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Un X., Lu F., Merkulov G.V, Milshina N., Moore H.M., Naik A.K., Narayan VA., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., Yao A., Ye J., Zhan M., Zhang W., Zhang H., Zhao Q., Zheng L., Zhong E., Zhong W., Zhu S., Zhao S., Gilbert D., Baumhueter S., Spier G., Carter C., Cravchik A., Woodage T., Ali F., An H., Awe A., Baldwin D., Baden H., Barnstead M., Barrow I., Beeson K., Busam D., Carver A., Center A., Cheng M.L., Curry L., Danaher S., Davenport L., Desilets R., Dietz S., Dodson K., Doup L., Ferriera S., Garg N., Gluecksmann A., Hart B., Haynes J., Haynes C., Heiner C., Hladun S., Hostin D., Houck J., Howland T., Ibegwam C., Johnson J., Kalush F., Kline L., Koduru S., Love A., Mann E., May D., McCawley S., Mcintosh T., McMullen I., Moy M., Moy L., Murphy B., Nelson K., Pfannkoch C., Pratts E., Puri V., Qureshi H., Reardon M., Rodriguez R., Rogers Y.H., Romblad D., Ruhfel B., Scott R., Sitter C., Smallwood M., Stewan E., Strong R., Suh E., Thomas R., Tint N.N., Tse S., Vech C., Wang G., Wetter J., Williams S., Williams M., Windsor S., Winn-Deen E., Wolfe K., Zaveri J., Zaveri K., Abril J.F., Guigo R., Campbell M.J., Sjolander K.V, Karlak B., Kejariwal A., Mi H., Lazareva B., Hatton T., Narechania A., Diemer K., Muruganujan A., Guo N., Sato S., Baína V, Istrail S., Lippert R., Schwartz R., Walenz B., Yooseph S., Allen D., Basu A., Baxendale J., Blick L., Caminha M., Carnes-Stine J., Caulk R., Chiang Y.H., Coyne M., Dahlke C., Mays A., Dombroski M., Donnelly M., Ely D., Esparham S., Fosler C., Gire H., Glanowski S., Glasser K., Glodek A., Gorokhov M., Graham K., Gropman B., Harris M., Heil J., Henderson S., Hoover J., Jennings D., Jordan C., Jordan J., Kasha J., Kagan L., Kraft C., Levitsky A., Lewis M., Liu X., Lopez J., Ma D., Majoras W., McDaniel J., Murphy S., Newman M., Nguyen X., Nguyen N., Nodell M., Pan S., Peck J., Peterson M., Rowe W., Sanders R., Scott J., Simpson M., Smith T., Sprague A., Stockwell T., Turner R., Venter E., Wang M., Wen M., Wu D., Wu M., Xia A., Zandieh A. & Zhu X. (2001). - The sequence of the human genome. Science, 291 (5507), 1304-1351.
11. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan R., McKernan K., Meldrim J., Mesirov J.P, Miranda C., Morris W., Naylor J., Raymond G., Rosetti M., Santos R., Sheridan A., Sougnez G., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee G., Carter N., Coulson A., Deadman R., Deloukas R., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd G., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.G, Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish WR., Chissoe S.L, Wendl M.G, Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L, Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W, Hawkins T., Branscomb E., Predki R., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.E, Olsen A., Lucas S., Elkin G., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.G, Rives GM., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe G., Watanabe H., Totoki Y., Taylor X., Weissenbach J., Heilig R., Saurin W., Artiguenave E., Brottier P., Bruls X., Pelletier E., Robert G., Wincker R., Smith D.R., Doucette-Stamm L, Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W, Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmuu J., Dickson M., Grimwood J., Cox D.R., Olson M.V, Kaul R., Raymond G., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen E., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie WR., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork R., Brown D.G., Bürge C.B., Cerutti L., Chen H.G, Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey TS., Galagan J., Gilbert J.G., Harmon G., Hayashizaki Y., Haussier D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., KasifS., Kaspryzk A., Kennedy S., Kent WJ., Kitts P., Koonin E.V, Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen X., Moran J.V, Mulder N., Pollara VJ., Ponting CR, Schüler G., Schultz J., Slater G., Smit A.E, Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.R, Yeh R.E, Collins E., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., Chen Y.J. & International Human Genome Sequencing Consortium (2001). - Initial sequencing and analysis of the human genome. Nature, 409 (6822), 860-921.
12. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P, Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D. & Church G.M. (2005). - Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309 (5741), 1728-1732.
13. Margulies M., Egholm M., Altman WE, Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho GH., Irzyk G.R, Jando S.G, Alenquer M.L, Jarvie TP, Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W, Nickerson E., Nobile J.R., Plant R., Puc B.P, Ronan M.T., Roth G.T., Sarkis G.J., Simons J.E, Simpson J.W, Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.E & Rothberg J.M. (2005). - Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437 (7057), 376-380.
14. Palacios G., Druce J., Du L., Tran T., Birch C., Briese T., Conlan S., Quan P.L., Hui J., Marshall J., Simons J.E, Egholm M., Paddock CD., Shieh WJ., Goldsmith C.S., Zaki S.R., Catton M. & Lipkin W.I. (2008). - A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med., 358 (10), 991-998.
15. Briese X, Paweska J.T., McMullan L.K., Hutchison S.K., Street C., Palacios G., Khristova M.L., Weyer J., Swanepoel R., Egholm M., Nichol S.T. & Lipkin WI. (2009). - Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog., 5 (5), e1000455.
16. Cox-Foster D.L., Conlan S., Holmes E.C., Palacios G., Evans J.D., Moran N.A., Quan P.L., Briese T., Hornig M., Geiser D.M., Martinson V., van Engelsdorp D., Kalkstein A.L., Drysdale A., Hui J., Zhai J., Cui L., Hutchison S.K., Simons J.E, Egholm M., Pettis J.S. & Lipkin WI. (2007). - A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318 (5848), 283-287.
17. Bennett S. (2004). - Solexa Ltd. Pharmacogenomics, 5 (4), 433-438.
18. Moore G.E. (1998). - Cramming more components onto integrated circuits [Reprinted from Electronics, 19 April 1965, 38 (8), 114-117].
19. In Proc. IEEE, 86 (1), 82-85. doi:10.1109/JPROC.1998.658762.
20. Sboner A., Mu X.J., Greenbaum D., Auerbach R.K. & Gerstein M.B. (2011). - The real cost of sequencing: higher than you thinkl. Genome Biol., 12 (8), 125.
21. Schadt E.E., Turner S. & Kasarskis A. (2010). - A window into third-generation sequencing. Hum. molec. Genet., 19, R227-R240.
22. Cheval J., Sauvage V, Frangeul L., Dacheux L., Guigon G., Dumey N., Pariente K., Rousseaux C., Dorange E, Berthet N., Brisse S., Moszer I., Bourhy H., Manuguerra C.J., Lecuit M., Burguiere A., Caro V & Eloit M. (2011). - Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J. din. Microbiol, 49 (9), 3268-3275.
23. Daly G.M., Bexfield N., Heaney J., Stubbs S., Mayer A.R, Palser A., Kellam P., Drou N., Caccamo M., Tiley L., Alexander G.J., Bernai W & Heeney J.L (2011). - A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS ONE, 6(12), e28879.
24. World Organisation for Animal Health (OIE) (2012). - Manual of Diagnostic Tests and Vaccines for Terrestrial Animals, 7th Ed. OIE, Paris. Available at: www.oie.int/international-standard-setting/terrestrial-manual/access-online/ (accessed on 20 October 2013).
25. World Organisation for Animal Health (OIE) (2009). - Manual of Diagnostic Tests for Aquatic Animals, 6th Ed. OIE, Paris. Available at: www.oie.int/intemational-standard-setting/aquatic-manual/access-online/ (accessed on 20 October 2013).
26. Field D., Amaral-Zettler L, Cochrane G., Cole J.R., Dawyndt P., Garrity G.M., Gilbert J., Glöckner EO., Hirschman L., Karsch-Mizrachi I., Klenk H.-R. Knight R., Kottmann R., Kyrpides N., Meyer F., San Gil I., Sansone S.-A., Schriml L.M., Sterk P., Tatusova T., Ussery D.W., White O. & Wooley J. (2011). - The Genomic Standards Consortium. PLoS Biol., 9 (6), e1001088.
27. Thurber R.V, Haynes M., Breitbart M., Wegley L. & Rohwer E (2009). - Laboratory procedures to generate viral metagenomes. Nat. Protoc, 4 (4), 470-483.
28. Tanle V., Van Doom H.R., Van der Hoek L, Minh Hien V, Jebbink M.E, Quang Ha D., Farrar J., Van Vinh Chau N. & de Jong M.D. (2011). - Random PCR and ultracentrifugation increases sensitivity and throughput of VIDISCA for screening of pathogens in clinical specimens. J. Inject, dev. Ctries, 5 (2), 142-148.
29. Lawrence J.E. & Steward G.E (2010). - Purification of viruses by centrifugation. In Manual of aquatic viral ecology (S. W Wilhelm, M.G. Weinbauer & CA. Suttle, eds). Association for the Sciences of Limnology and Oceanography (ASLO), Waco, Texas, 166-181. doi:10.4319/mave.2010.978-0-9845591- 0-7.
30. Djikeng A. & Spiro D. (2009). - Advancing full length genome sequencing for human RNA viral pathogens. Future Virology, 4 (1), 47-53.
31. Allander T., Emerson S.U., Engle R.E., Purcell R.H. & Bukh J. (2001). - A vims discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc. natl Acad. Sci. USA, 98 (20), 11609-11614.
32. Berthet N., Reinhardt A.K., Leclercq I., van Ooyen S., Batejat C., Dickinson P, Stamboliyska R., Old LG, Kong K.A., Dacheux L., Bourhy H., Kennedy G.C., Korfhage C., Cole S.T. Manuguerra J.C (2008). - Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC molec. Biol, 9, 77. doi:10.1186/1471-2199-9-77.
33. Reyes G.R. & Kim J.P. (1991). - Sequence-independent, single-primer amplification (SISPA) of complex DNA populations. Molec. cell. Probes, 5 (6), 473-481.
34. Kim K.H. & Bae J.W (2011). - Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl. environ. Microbiol., 77 (21), 7663-7668.
35. Hongoh Y. & Toyoda A. (2011). - Whole-genome sequencing of unculturable bacterium using whole-genome amplification. Meth. mokc. Biol, 733, 25-33.
36. Sergeant M.J., Constantinidou C, Cogan T., Penn C.W & Pallen MJ. (2012). - High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature. PLoS ONE, 7 (5), e38094.
37. Bybee S.M., Bracken-Grissom H., Haynes B.D., Hermansen R.A., Byers R.L, Clement M.J., Udall J.A., Wilcox E.R. & Crandall K.A. (2011). - Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol, 3, 1312-1323. doi:10.1093/gbe/evr106.
38. Linnarsson S. (2010). - Recent advances in DNA sequencing methods: general principles of sample preparation. Experim. Cell Res., 316(8), 1339-1343.
39. Aird D., Ross M.G., Chen WS, Danielsson M., Fennell T., Russ C., Jaffe D.B., Nusbaum C. & Gnirke A. (2011). - Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol, 12 (2), R18. doi:10.1186/gb-2011-12-2-r18.
40. Fedurco M., Romieu A., Williams S., Lawrence I. & Turcatti G. (2006). - BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res., 34 (3), e22.
41. Quail M.A., Smith M., Coupland R, Otto TD, Harris S.R., Connor T.R., Bertoni A., Swerdlow H.P & Gu Y. (2012). - A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
42. Rothberg J.M., Hinz W, Rearick TM, Schultz J., Mileski W., Davey M., Leamon J.H., Johnson K., Milgrew M.J., Edwards M., Hoon J., Simons J.E, Marran D., Myers J.W, Davidson J.E, Branting A., Nobile J.R., Puc B.P., Light D., Clark TA., Huber M., Branciforte J.T., Stoner LB., Cawley S.E., Lyons M., Fu Y., Homer N., Sedova M., Miao X., Reed B., Sabina J., Feierstein E., Schorn M., Alanjary M., Dimalanta E., Dressman D., Kasinskas R., Sokolsky T., Fidanza J.A., Namsaraev E., McKernan K.J., Williams A., Roth G.T. & Bustillo J. (2011). - An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475 (7356), 348-352.
43. Levene M.J., Korlach J., Turner S.W, Foquet M., Craighead H.G. & Webb WW (2003). - Zero-mode waveguides for single-molecule analysis at high concentrations. Science, 299 (5607), 682-686.
44. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P, Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians E., Cicero R., Clark S., Dalai R., Dewinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma G., Marks R., Maxham M., Murphy D., Park L., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong E., Korlach J. & Turner S. (2009). - Real-time DNA sequencing from single polymerase molecules. Science, 323 (5910), 133-138.
45. Dekker C. (2007). - Solid-state nanopores. Nat. Nanotechnol, 2(4), 209-215.
46. Howorka S., Cheley S. & Bayley H. (2001). - Sequence-specific detection of individual DNA strands using engineered nanopores. Nat. Biotechnol, 19 (7), 636-639.
47. Benner S., Chen R.J., Wilson N.A., Abu-Shumays R., Hurt N., Lieberman K.R., Deamer D.W, Dunbar WB. & Akeson M. (2007). - Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nat. Nanotechnol, 2 (11), 718-724.
48. Kasianowicz J.J., Brandin E., Branton D. & Deamer D.W (1996). - Characterization of individual polynucleotide molecules using a membrane channel. Proc. natl Acad. Sci. USA, 93 (24), 13770-13773.
49. Branton D., Deamer D.W, Marziali A., Bayley H., Benner S.A., Butler T., Di Ventra M., Garaj S., Hibbs A., Huang X., Jovanovich S.B., Krstic P.S., Lindsay S., Ling X.S., Mastrangelo C.H., Meiler A., Oliver J.S., Pershin Y.V., Ramsey J.M., Riehn R., Soni G.V, Tabard-Cossa V, Wanunu M., Wiggin M. & Schloss J.A. (2008). - The potential and challenges of nanopore sequencing. Nat. Biotechnol, 26(10), 1146-1153.
50. Metzker M.L. (2010). - Sequencing technologies: the next generation. Nat. Rev. Genet., 11 (1), 31-46.
51. Shendure J. & Ji H. (2008). - Next-generation DNA sequencing. Nat. Biotechnol, 26 (10), 1135-1345.
52. Cock P.J., Fields C.J., Goto N., Heuer M.L. & Rice EM. (2010). - The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38 (6), 1767-1771.
53. Schmieder R. & Edwards R. (2011). - Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27 (6), 863-864.
54. Schmieder R., Lim Y.W, Rohwer E & Edwards R. (2010). - TagCleaner: identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics, 11, 341.
55. Li H. & Homer N. (2010). - A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinjorm., 11 (5)473-483.
56. Pop M. (2009). - Genome assembly reborn: recent computational challenges. Brief. Bioinjorm., 10 (4), 354-366.
57. Scholz M.B., Lo C.C. & Chain P.S. (2012). - Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol, 23(1), 9-15.
58. Simon C. & Daniel R. (2011). - Metagenomic analyses: past and future trends. Appl. environ. Microbiol., 77 (4), 1153-1161.
59. Chen K. & Pachter L. (2005). - Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoScomput. Biol, 1 (2), 106-112.
60. Edwards R.A. & Rohwer E (2005). - Viralmetagenomics. Nat. Rev. Microbiol, 3 (6), 504-510.
61. Morozova O., Hirst M. & Marra M.A. (2009). - Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics hum. Genet., 10, 135-151.
62. Pepke S., Wold B. & Mortazavi A. (2009). - Computation for ChlP-seq and RNA-seq studies. Nat. Methods, 6 (11 Suppl.), S22-S32.
63. Editorial (2012). - The data deluge. Nat. Cell Biol, 14(11), 1231.
64. Editorial (2009). - Access denied? Nature, 462 (7271), 252. doi:10.1038/462252a.
65. Brooksbank G, Cameron G. & Thornton J. (2010). - The European Bioinformatics Institute's data resources. Nucleic Acids Res., 38 (Database issue), D17-D25.
66. Leinonen R., Sugawara H., Shumwy M. & International Nucleotide Sequence Database Collaboration (2011). - The Sequence Read Archive. Nucleic Acids Res., 39 (Database issue), D19-D21.
67. Kodama Y., Shumway M., Leinonen R. & International Nucleotide Sequence Database Collaboration (2012). - The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res., 40 (Database issue), D54-D56.
68. European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) (2012). - How fast is life science data growing? European Life Sciences Infrastructure for Biological Information (ELIXIR). ELIXIR, Hinxton, Cambridge, United Kingdom. Available at: www.elixir-europe.org/news/how-fast- life-science-data-growing (accessed on 25 November 2012).
69. Rosegrant M.W., Paisner M.S., Meijer S. & Witcover J. (2001). - 2020 Global food outlook: trends, alternatives, and choices. International Food Policy Research Institute, Washington, DC.
70. Blomström A.L., Belák S., Fossum G., McKillen J., Allan G., Wallgren P. & 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.
71. Blomström A.L., Belák S., Fossum G., Fuxler L., Wallgren R & Berg M. (2010). - Studies of porcine circovirus type 2, porcine boca-like virus and Torque teno virus indicate the presence of multiple viral infections in postweaning multisystemic wasting syndrome pigs. Virus Res., 152 (1-2), 59-64.
72. Shan T., Li L, Simmonds P., Wang G, Moeser A. & Delwart E.(2011).-Thefecalvirome of pigsonahigh-densityfarm. J. Virol., 85 (22), 11697-11708.
73. Sachsenröder J., Twardziok S., Hammerl J.A., Janczyk P., Wrede R, Hertwig S. & Johne R. (2012). - Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing. PLoS ONE, 7 (4), e34631.
74. Reuter G., Nemes G, Boras A., Kapusinszky B., Delwart E. & Pankovics P. (2013). - Porcine kobuvirus in wild boars (Sus scrofa). Arch. Virol., 158 (1), 281-282. doi:10.1007/s00705-012-1456-y.
75. Reuter G., Nemes G, Boros A., Kapusinszky B., Delwart E. & Pankovics P. (2012). - Astrovirus in wild boars (Sus scrofa) in Hungary. Arch. Virol., 157 (6), 1143-1147.
76. Blomström A.L., Ståhl K., Masembe G., Okoth E., Okurut A.R., Atmnedi R., Kemp S., Bishop R., Belák S. & Berg M. (2012). - Viral metagenomic analysis of bushpigs (Potamochoerus larvatus) in Uganda identifies novel variants of porcine parvovirus 4 and Torque teno sus virus 1 and 2. Virol. J., 9, 192.
77. Masembe G, Michuki G., Onyango M., Rumberia G., Norling M., Bishop R.P., Djikeng A., Kemp S.J., Orth A., Skilton R.A., Stáhl K. & Fischer A. (2012). - Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus. Virol. J., 9 (1), 218.
78. Xiao S., Jia J., Mo D., Wang Q., Qin L., He Z., Zhao X., Huang Y., Li A., Yu J., Niu Y., Liu X. & Chen Y. (2010). - Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing. PLoS ONE, 5 (6), e11377.
79. Boyle D.B., Bulach D.M., Amos-Ritchie R., Adams M.M., Walker P.J. & Weir R. (2012). - Genomic sequences of Australian bluetongue virus prototype serotypes reveal global relationships and possible routes of entry into Australia. J. Virol., 86 (12), 6724-6731.
80. Wright CE, Morelli M.J., Thebaud G., Knowles N.J., Herzyk R., Paton D.J., Haydon D.T. & King D.P. (2011). - Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J. Virol., 85 (5), 2266-2275.
81. Beer M., Conraths FJ & van der Poel WH. (2012). - 'Schmallenberg virus': a novel orthobunyavirus emerging in Europe. Epidemiol. Inject., 141 (1), 1-8. doi:10.1017/S0950268812002245.
82. Hoffmann B., Scheuch M., Hoper D., Jungblut R., Holsteg M., Schirrmeier H., Eschbaumer M., Goller K.V, Wernike K., Fischer M., Breithaupt A., Mettenleiter TG. & Beer M. (2012). - Novel orthobunyavirus in cattle, Europe, 2011. Emerg. infect Dis., 18 (3), 469-472.
83. Rosseel T., Scheuch M., Hoper D., De Regge N., Caij A.B., Vandenbussche E & Van Borm S. (2012). - DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS ONE, 7 (7), e41967.
84. Hubalek Z. (2004). - An annotated checklist of pathogenic microorganisms associated with migratory birds. J. Wildl. Dis., 40 (4), 639-659.
85. Alexander D.J. (2000). - A review of avian influenza in different bird species. Vet. Microbiol, 74 (1-2), 3-13.
86. Gilchrist P. (2005). - Involvement of free-flying wild birds in the spread of the viruses of avian influenza, Newcastle disease and infectious bursal disease from poultry products to commercial poultry. World Poult. Sci. J., 61 (2), 198-214.
87. Cardona C.J., Xing Z., Sandrock CE & Davis CE. (2009). - Avian influenza in birds and mammals. Comp. Immunol. Microbiol, infect. Dis., 32 (4), 255-273.
88. Hoper D., Hoffmann B. & Beer M. (2009). - Simple, sensitive, and swift sequencing of complete H5N1 avian influenza virus genomes. J. clin. Microbiol., 47 (3), 674-679.
89. Kampmann M.L., Fordyce S.L, Avila-Arcos M.C, Rasmussen M., Willerslev E., Nielsen LP. & Gilbert M.T. (2011). - A simple method for the parallel deep sequencing of full influenza A genomes. J. virol. Meth., 178 (1-2), 243-248.
90. Van Borm S., Rosseel X, Vangeluwe D., Vandenbussche E., van den Berg T. & Lambrecht B. (2012). - Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls. Arch. Virol., 157 (8), 1509-1522.
91. Hoper D., Kalthoff D., Hoffmann B. & Beer M. (2012). - Highly pathogenic avian influenza virus subtype H5N1 escaping neutralization: more than HA variation. J. Virol., 86 (3), 1394-1404.
92. Ramakrishnan M.A., Tu Z.J., Singh S., Chockalingam A.K., Gramer M.R., Wang E., Goyal S.M., Yang M., Halvorson D.A. & Sreevatsan S. (2009). - The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies. PloS ONE, 4 (9), e7105. doi:10.1371/journal.pone.0007105.
93. Dugan VG., Dunham E.J., Jin G., Sheng Z.M., Kaser E., Nolting J.M., Alexander H.L. Jr, Slemons R.D. & Taubenberger J.K. (2011). - Phylogenetic analysis of low pathogenicity H5N1 and H7N3 influenza A virus isolates recovered from sentinel, free flying, wild mallards at one study site during 2006. Virology, 417 (1), 98-105. doi:10.1016/j.virol.2011.05.004.
94. Croville G., Soubies S.M., Barbiert J., Klopp C., Mariette J., Bouchez O., Camus-Bouclainville C. & Guerin J.L. (2012). - Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing. J. din. Microbiol., 50 (9), 2881-2887.
95. Trojnar E., Sachsenroder J., Twardziok S., Reetz J., Otto PH & Johne R. (2013). - Identification of an avian group A rotavirus containing a novel VP4 gene of close relationship to those of mammalian rotaviruses. J. gen. Virol, 94 (Pt 1), 136-142. doi:10.1099/vir.0.047381-0.
96. Abolnik C, de Castro M. & Rees J. (2012). - Full genomic sequence of an African avian paramyxovirus type 4 strain isolated from a wild duck. Virus Genes, 45 (3), 537-541.
97. Spatz S.J., Volkening J.D., Keeler C.L., Kutish G.F., Riblet S.M., Boettger CM, Clark K.E, Zsak L., Afonso C.L., Mundt E.S., Rock D.L. & Garcia M. (2012). - Comparative full genome analysis of four infectious laryngotracheitis virus (Gallid herpesvirus-1) virulent isolates from the United States. Virus Genes, 44 (2), 273-285. doi:10.1007/s11262-011-0696-3.
98. Spatz S.J. & Rue C.A. (2008). - Sequence determination of a mildly virulent strain (CU-2) of Gallid herpesvirus type 2 using 454 pyrosequencing. Virus Genes, 36 (3), 479-489.
99. Honkavuori K.S., Shivaprasad H.L., Williams B.L., Quan P.L., Hornig M., Street C., Palacios G., Hutchison S.K., Franca M., Egholm M., Bliese T. & Lipkin WI. (2008). - Novel borna virus in psittacine birds with proventricular dilatation disease. Emerg. infect. Dis., 14 (12), 1883-1886.
100. Honkavuori K.S., Shivaprasad H.L., Briese T., Street C, Hirschberg D.L, Hutchison S.K. & Lipkin WI. (2011). - Novel picomavirus in Turkey poults with hepatitis, California, USA. Emerg. infect. Dis., 17 (3), 480-487.
101. Rosseel T., Lambrecht B., Vandenbussche E, van den Berg T. & Van Borm S. (2011). - Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies. Virol. J., 8, 463.
102. Day J.M., Ballard L.L., Duke M.V, Scheffler B.E. & Zsak L (2010). - Metagenomic analysis of the turkey gut RNA virus community. Virol. J., 7, 313.
103. Kim T. & Mundt E. (2011). - Metagenomic analysis of intestinal microbiomes in chickens. Meth. molec. Biol, 733, 185-194.
104. Nordentoft S., Molbak L, Bjerrum L., De Vylder J., Van Immerseel F. & Pedersen K. (2011). - The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing. BMC Microbiol., 11, 187.
105. Dumas M.D., Poison S.W, Ritter D., Ravel J., Gelb J. Jr, Morgan R. & Wommack K.E. (2011). - Impacts of poultry house environment on poultry litter bacterial community composition. PLoS ONE, 6 (9), e24785.
106. Nie Q., Sandford E.E., Zhang X., Nolan LK & Lamont S.J. (2012). - Deep sequencing-based transcriptome analysis of chicken spleen in response to avian pathogenic Escherichia coli (APEC) infection. PLoS ONE, 7 (7), e41645.
107. Wang Y., Brahmakshatriya V, Lupiani B., Reddy S.M., Soibam B., Benham A.L, Gunaratne P., Liu H.C., Trakooljul N., Ing N., Okimoto R. & Zhou H. (2012). - Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. BMC Genomics, 13, 278.
108. Spatz SJ. (2010). - Accumulation of attenuating mutations in varying proportions within a high passage very virulent plus strain of Gallid herpesvirus type 2. Virus Res., 149 (2), 135-142.
109. Chandra Y.G., Lee J. & Kong B.W. (2012).-Genome sequence comparison of two United States live attenuated vaccines of infectious laryngotracheitis virus (ILTV). Virus Genes, 44 (3), 470-474.
110. Lee S.W., Markham P.F., Coppo M.J., Legione A.R., Markham J.E, Noormohammadi A.H., Browning G.F., Ficorilli N., Hartley CA. & Devlin J.M. (2012). - Attenuated vaccines can recombine to form virulent field viruses. Science, 337 (6091), 188.
111. Marston D.A., Ellis R.J., Horton D.L., Kuzmin I.V, Wise E.L., McElhinney L.M., Banyard A.C., Ngeleja C., Keyyu J., Cleaveland S., Lembo T., Rupprecht CE. & Fooks A.R. (2012). - Complete genome sequence of Ikoma lyssavirus. J. Virol., 86 (18), 10242-10243.
112. Marston D.A., Horton D.L, Ngeleja C., Hampson K., McElhinney L.M., Banyard A.C., Haydon D., Cleaveland S., Rupprecht CE., Bigambo M., Fooks A.R. & Lembo T. (2012). - Ikoma lyssavirus, highly divergent novel lyssavirus in an African civet. Emerg. inject. Dis., 18 (4), 664-667.
113. Granberg E, Vicente-Rubiano M., Rubio-Guerri C, Karlsson O.E., Kukielka D., Belák S. & Sanchez-Vizcaino J.M. (2013). - Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by aphid lethal paralysis, Israel acute paralysis and Lake Sinai viruses. PLoS ONE, 8 (2), e57459.
114. Dunne WM. Jr, Westblade L.E & Ford B. (2012). - Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur. J. clin. Microbiol, inject. Dis., 31 (8), 1719-1726.