1887

Abstract

The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2012-09-01
2024-04-23
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References

  1. Ambrose H. E., Clewley J. P. 2006; Virus discovery by sequence-independent genome amplification. Rev Med Virol 16:365–383 [View Article][PubMed]
    [Google Scholar]
  2. Anders S., Huber W. 2010; Differential expression analysis for sequence count data. Genome Biol 11:R106 [View Article][PubMed]
    [Google Scholar]
  3. Anonymous. 2003; Acute respiratory syndrome. China, Hong Kong Special Administrative Region of China, and Viet Nam. Wkly Epidemiol Rec 78:73–74[PubMed]
    [Google Scholar]
  4. Anonymous 2012; ENHanCEd Infectious Diseases (eid2) database. http://www.zoonosis.ac.uk/EID2/ 20 April 2012
  5. Baillie G. J., Galiano M., Agapow P. M., Myers R., Chiam R., Gall A., Palser A. L., Watson S. J., Hedge J. other authors 2012; Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis. J Virol 86:11–18 [View Article][PubMed]
    [Google Scholar]
  6. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Sayers E. W. 2011; GenBank. Nucleic Acids Res 39:Database issueD32–D37 [View Article][PubMed]
    [Google Scholar]
  7. Bexfield N., Kellam P. 2011; Metagenomics and the molecular identification of novel viruses. Vet J 190:191–198 [View Article][PubMed]
    [Google Scholar]
  8. Bimber B. N., Burwitz B. J., O’Connor S., Detmer A., Gostick E., Lank S. M., Price D. A., Hughes A., O’Connor D. 2009; Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol 83:8247–8253 [View Article][PubMed]
    [Google Scholar]
  9. Bimber B. N., Dudley D. M., Lauck M., Becker E. A., Chin E. N., Lank S. M., Grunenwald H. L., Caruccio N. C., Maffitt M. other authors 2010; Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol 84:12087–12092 [View Article][PubMed]
    [Google Scholar]
  10. Boyer M., Yutin N., Pagnier I., Barrassi L., Fournous G., Espinosa L., Robert C., Azza S., Sun S. other authors 2009; Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A 106:21848–21853 [View Article][PubMed]
    [Google Scholar]
  11. Breitbart M., Hewson I., Felts B., Mahaffy J. M., Nulton J., Salamon P., Rohwer F. 2003; Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185:6220–6223 [View Article][PubMed]
    [Google Scholar]
  12. Briese T., Paweska J. T., McMullan L. K., Hutchison S. K., Street C., Palacios G., Khristova M. L., Weyer J., Swanepoel R. other authors 2009; Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 5:e1000455 [View Article][PubMed]
    [Google Scholar]
  13. Burnside J., Bernberg E., Anderson A., Lu C., Meyers B. C., Green P. J., Jain N., Isaacs G., Morgan R. W. 2006; Marek’s disease virus encodes microRNAs that map to meq and the latency-associated transcript. J Virol 80:8778–8786 [View Article][PubMed]
    [Google Scholar]
  14. Byrne D., Grzela R., Lartigue A., Audic S., Chenivesse S., Encinas S., Claverie J. M., Abergel C. 2009; The polyadenylation site of mimivirus transcripts obeys a stringent ‘hairpin rule’. Genome Res 19:1233–1242 [View Article][PubMed]
    [Google Scholar]
  15. Cantalupo P. G., Calgua B., Zhao G., Hundesa A., Wier A. D., Katz J. P., Grabe M., Hendrix R. W., Girones R., Wang D., Pipas J. M. 2011; Raw sewage harbors diverse viral populations. mBio 2:,e00180–e001811 [CrossRef]
    [Google Scholar]
  16. Chapman D. A., Darby A. C., Da Silva M., Upton C., Radford A. D., Dixon L. K. 2011; Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus. Emerg Infect Dis 17:599–605[PubMed] [CrossRef]
    [Google Scholar]
  17. Chevreux B., Wetter T., Suhai S. 1999; Genome sequence assembly using trace signals and additional sequence information. In Proceedings of the GCB ’99: German Conference on Bioinformatics, 4–6 October 1999, Hannover, Germany http://www.bioinfo.de/isb/gcb99/talks/chevreux/
    [Google Scholar]
  18. Clyde K., Glaunsinger B. A. 2011; Deep sequencing reveals direct targets of gammaherpesvirus-induced mRNA decay and suggests that multiple mechanisms govern cellular transcript escape. PLoS ONE 6:e19655 [View Article][PubMed]
    [Google Scholar]
  19. Coetzee B., Freeborough M. J., Maree H. J., Celton J. M., Rees D. J., Burger J. T. 2010; Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157–163 [View Article][PubMed]
    [Google Scholar]
  20. Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S. V., Eiglmeier K., Gas S. other authors 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544 [View Article][PubMed]
    [Google Scholar]
  21. Daly G. M., Bexfield N., Heaney J., Stubbs S., Mayer A. P., Palser A., Kellam P., Drou N., Caccamo M. other authors 2011; A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS ONE 6:e28879 [View Article][PubMed]
    [Google Scholar]
  22. 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 [View Article][PubMed]
    [Google Scholar]
  23. Delwart E. L. 2007; Viral metagenomics. Rev Med Virol 17:115–131 [View Article][PubMed]
    [Google Scholar]
  24. Depledge D. P., Palser A. L., Watson S. J., Lai I. Y., Gray E. R., Grant P., Kanda R. K., Leproust E., Kellam P., Breuer J. 2011; Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS ONE 6:e27805 [View Article][PubMed]
    [Google Scholar]
  25. Dolgin E. 2011; Sequencing reveals suite of commensal and pathogenic viruses. Nat Med 17:399 [View Article][PubMed]
    [Google Scholar]
  26. Donaldson E. F., Haskew A. N., Gates J. E., Huynh J., Moore C. J., Frieman M. B. 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 [View Article][PubMed]
    [Google Scholar]
  27. Drosten C., Günther S., Preiser W., van der Werf S., Brodt H. R., Becker S., Rabenau H., Panning M., Kolesnikova L. other authors 2003; Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967–1976 [View Article][PubMed]
    [Google Scholar]
  28. Eisenstein M. 2012; Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295–296 [View Article][PubMed]
    [Google Scholar]
  29. Eriksson N., Pachter L., Mitsuya Y., Rhee S. Y., Wang C., Gharizadeh B., Ronaghi M., Shafer R. W., Beerenwinkel N. 2008; Viral population estimation using pyrosequencing. PLOS Comput Biol 4:e1000074 [View Article][PubMed]
    [Google Scholar]
  30. Ertl R., Birzele F., Hildebrandt T., Klein D. 2011; Viral transcriptome analysis of feline immunodeficiency virus infected cells using second generation sequencing technology. Vet Immunol Immunopathol 143:314–324 [View Article][PubMed]
    [Google Scholar]
  31. Gardner M. J., Hall N., Fung E., White O., Berriman M., Hyman R. W., Carlton J. M., Pain A., Nelson K. E. other authors 2002; Genome sequence of the human malaria parasite Plasmodium falciparum . Nature 419:498–511 [View Article][PubMed]
    [Google Scholar]
  32. Gatherer D., Seirafian S., Cunningham C., Holton M., Dargan D. J., Baluchova K., Hector R. D., Galbraith J., Herzyk P. other authors 2011; High-resolution human cytomegalovirus transcriptome. Proc Natl Acad Sci U S A 108:19755–19760 [View Article][PubMed]
    [Google Scholar]
  33. Geret C. P., Cattori V., Meli M. L., Riond B., Martínez F., López G., Vargas A., Simón M. A., López-Bao J. V. other authors 2011; Feline leukemia virus outbreak in the critically endangered Iberian lynx (Lynx pardinus): high-throughput sequencing of envelope variable region A and experimental transmission. Arch Virol 156:839–854 [View Article][PubMed]
    [Google Scholar]
  34. Gilles A., Meglécz E., Pech N., Ferreira S., Malausa T., Martin J. F. 2011; Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12:245 [View Article][PubMed]
    [Google Scholar]
  35. Görzer I., Guelly C., Trajanoski S., Puchhammer-Stöckl E. 2010; Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time. J Virol 84:7195–7203 [View Article][PubMed]
    [Google Scholar]
  36. Greninger A. L., Chen E. C., Sittler T., Scheinerman A., Roubinian N., Yu G., Kim E., Pillai D. R., Guyard C. other authors 2010; A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS ONE 5:e13381 [View Article][PubMed]
    [Google Scholar]
  37. Handelsman J., Rondon M. R., Brady S. F., Clardy J., Goodman R. M. 1998; Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249 [View Article][PubMed]
    [Google Scholar]
  38. Hiraga N., Imamura M., Abe H., Hayes C. N., Kono T., Onishi M., Tsuge M., Takahashi S., Ochi H. other authors 2011; Rapid emergence of telaprevir resistant hepatitis C virus strain from wild type clone in vivo. Hepatology 54:781–788 [View Article]
    [Google Scholar]
  39. Hoffmann C., Minkah N., Leipzig J., Wang G., Arens M. Q., Tebas P., Bushman F. D. 2007; DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 35:e91 [View Article][PubMed]
    [Google Scholar]
  40. Hoffmann B., Scheuch M., Höper D., Jungblut R., Holsteg M., Schirrmeier H., Eschbaumer M., Goller K. V., Wernike K. other authors 2012; Novel orthobunyavirus in cattle, Europe, 2011. Emerg Infect Dis 18:469–472 [View Article][PubMed]
    [Google Scholar]
  41. Homs M., Buti M., Quer J., Jardí R., Schaper M., Tabernero D., Ortega I., Sanchez A., Esteban R., Rodriguez-Frias F. 2011; Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome. Nucleic Acids Res 39:8457–8471 [View Article][PubMed]
    [Google Scholar]
  42. Höper D., Hoffmann B., Beer M. 2009; Simple, sensitive, and swift sequencing of complete H5N1 avian influenza virus genomes. J Clin Microbiol 47:674–679 [View Article][PubMed]
    [Google Scholar]
  43. Höper D., Hoffmann B., Beer M. 2011; A comprehensive deep sequencing strategy for full-length genomes of influenza A. PLoS ONE 6:e19075 [View Article][PubMed]
    [Google Scholar]
  44. Hughes A. L., O’Connor S., Dudley D. M., Burwitz B. J., Bimber B. N., O’Connor D. 2010; Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus. Infect Genet Evol 10:555–560 [View Article][PubMed]
    [Google Scholar]
  45. Ji H., Massé N., Tyler S., Liang B., Li Y., Merks H., Graham M., Sandstrom P., Brooks J. 2010; HIV drug resistance surveillance using pooled pyrosequencing. PLoS ONE 5:e9263 [View Article][PubMed]
    [Google Scholar]
  46. Khalid S. S., Hamid S., Siddiqui A. A., Qureshi A., Qureshi N. 2011; Gene profiling of early and advanced liver disease in chronic hepatitis C patients. Hepatol Int 5:782–788 [CrossRef]
    [Google Scholar]
  47. Kristensen D. M., Mushegian A. R., Dolja V. V., Koonin E. V. 2010; New dimensions of the virus world discovered through metagenomics. Trends Microbiol 18:11–19 [View Article][PubMed]
    [Google Scholar]
  48. Ksiazek T. G., Erdman D., Goldsmith C. S., Zaki S. R., Peret T., Emery S., Tong S., Urbani C., Comer J. A. other authors 2003; A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348:1953–1966 [View Article][PubMed]
    [Google Scholar]
  49. Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M. other authors 2001; Initial sequencing and analysis of the human genome. Nature 409:860–921 [View Article][PubMed]
    [Google Scholar]
  50. Lauring A. S., Andino R. 2010; Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 6:e1001005 [View Article][PubMed]
    [Google Scholar]
  51. Legendre M., Audic S., Poirot O., Hingamp P., Seltzer V., Byrne D., Lartigue A., Lescot M., Bernadac A. other authors 2010; mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in mimivirus. Genome Res 20:664–674 [View Article][PubMed]
    [Google Scholar]
  52. Legendre M., Santini S., Rico A., Abergel C., Claverie J. M. 2011; Breaking the 1000-gene barrier for mimivirus using ultra-deep genome and transcriptome sequencing. Virol J 8:99 [View Article][PubMed]
    [Google Scholar]
  53. Levin J. Z., Yassour M., Adiconis X., Nusbaum C., Thompson D. A., Friedman N., Gnirke A., Regev A. 2010; Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7:709–715 [View Article][PubMed]
    [Google Scholar]
  54. Li H., Durbin R. 2009; Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760 [View Article][PubMed]
    [Google Scholar]
  55. Li L., Victoria J. G., Wang C., Jones M., Fellers G. M., Kunz T. H., Delwart E. 2010; Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84:6955–6965 [View Article][PubMed]
    [Google Scholar]
  56. Lin Z., Xu G., Deng N., Taylor C., Zhu D., Flemington E. K. 2010; Quantitative and qualitative RNA-Seq-based evaluation of Epstein–Barr virus transcription in type I latency Burkitt’s lymphoma cells. J Virol 84:13053–13058 [View Article][PubMed]
    [Google Scholar]
  57. Lipkin W. I. 2009; Microbe hunting in the 21st century. Proc Natl Acad Sci U S A 106:6–7 [View Article][PubMed]
    [Google Scholar]
  58. Lok A. S., Zoulim F., Locarnini S., Bartholomeusz A., Ghany M. G., Pawlotsky J. M., Liaw Y. F., Mizokami M., Kuiken C. Hepatitis B Virus Drug Resistance Working Group 2007; Antiviral drug-resistant HBV: standardization of nomenclature and assays and recommendations for management. Hepatology 46:254–265 [View Article][PubMed]
    [Google Scholar]
  59. Loman N. J., Misra R. V., Dallman T. J., Constantinidou C., Gharbia S. E., Wain J., Pallen M. J. 2012; Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439 [View Article][PubMed]
    [Google Scholar]
  60. López-Bueno A., Tamames J., Velázquez D., Moya A., Quesada A., Alcamí A. 2009; High diversity of the viral community from an Antarctic lake. Science 326:858–861 [View Article][PubMed]
    [Google Scholar]
  61. Lorusso A., Vincent A. L., Harland M. L., Alt D., Bayles D. O., Swenson S. L., Gramer M. R., Russell C. A., Smith D. J. other authors 2011; Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008. J Gen Virol 92:919–930 [View Article][PubMed]
    [Google Scholar]
  62. Mamanova L., Coffey A. J., Scott C. E., Kozarewa I., Turner E. H., Kumar A., Howard E., Shendure J., Turner D. J. 2010; Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111–118 [View Article][PubMed]
    [Google Scholar]
  63. Margeridon-Thermet S., Shulman N. S., Ahmed A., Shahriar R., Liu T., Wang C., Holmes S. P., Babrzadeh F., Gharizadeh B. other authors 2009; Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 199:1275–1285 [View Article][PubMed]
    [Google Scholar]
  64. Marioni J. C., Mason C. E., Mane S. M., Stephens M., Gilad Y. 2008; RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517 [View Article][PubMed]
    [Google Scholar]
  65. Mitsuya Y., Varghese V., Wang C., Liu T. F., Holmes S. P., Jayakumar P., Gharizadeh B., Ronaghi M., Klein D. other authors 2008; Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J Virol 82:10747–10755 [View Article][PubMed]
    [Google Scholar]
  66. Moore R. A., Warren R. L., Freeman J. D., Gustavsen J. A., Chénard C., Friedman J. M., Suttle C. A., Zhao Y., Holt R. A. 2011; The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS ONE 6:e19838 [View Article][PubMed]
    [Google Scholar]
  67. Mullis K., Faloona F., Scharf S., Saiki R., Horn G., Erlich H. 1986; Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273 [View Article][PubMed]
    [Google Scholar]
  68. Ng T. F., Willner D. L., Lim Y. W., Schmieder R., Chau B., Nilsson C., Anthony S., Ruan Y., Rohwer F., Breitbart M. 2011; Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS ONE 6:e20579 [View Article][PubMed]
    [Google Scholar]
  69. Ozsolak F., Platt A. R., Jones D. R., Reifenberger J. G., Sass L. E., McInerney P., Thompson J. F., Bowers J., Jarosz M., Milos P. M. 2009; Direct RNA sequencing. Nature 461:814–818 [View Article][PubMed]
    [Google Scholar]
  70. Palmer S., Kearney M., Maldarelli F., Halvas E. K., Bixby C. J., Bazmi H., Rock D., Falloon J., Davey R. T. Jr other authors 2005; Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 43:406–413 [View Article][PubMed]
    [Google Scholar]
  71. Pantaleo V., Saldarelli P., Miozzi L., Giampetruzzi A., Gisel A., Moxon S., Dalmay T., Bisztray G., Burgyan J. 2010; Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 408:49–56 [View Article][PubMed]
    [Google Scholar]
  72. Raymond S., Saliou A., Nicot F., Delobel P., Dubois M., Cazabat M., Sandres-Sauné K., Marchou B., Massip P., Izopet J. 2011; Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing. AIDS 25:1668–1670 [View Article][PubMed]
    [Google Scholar]
  73. Reyes A., Haynes M., Hanson N., Angly F. E., Heath A. C., Rohwer F., Gordon J. I. 2010; Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334–338 [View Article][PubMed]
    [Google Scholar]
  74. Riley K. J., Rabinowitz G. S., Yario T. A., Luna J. M., Darnell R. B., Steitz J. A. 2012; EBV and human microRNAs co-target oncogenic and apoptotic viral and human genes during latency. EMBO J 31:2207–2221 [View Article][PubMed]
    [Google Scholar]
  75. Robinson M. D., McCarthy D. J., Smyth G. K. 2010; edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140 [View Article][PubMed]
    [Google Scholar]
  76. Rodriguez-Brito B., Li L., Wegley L., Furlan M., Angly F., Breitbart M., Buchanan J., Desnues C., Dinsdale E. other authors 2010; Viral and microbial community dynamics in four aquatic environments. ISME J 4:739–751 [View Article][PubMed]
    [Google Scholar]
  77. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467 [View Article][PubMed]
    [Google Scholar]
  78. Sayed D., Abdellatif M. 2011; MicroRNAs in development and disease. Physiol Rev 91:827–887 [View Article][PubMed]
    [Google Scholar]
  79. Schmieder R., Edwards R. 2011; Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6:e17288 [View Article][PubMed]
    [Google Scholar]
  80. Smith G. J., Vijaykrishna D., Bahl J., Lycett S. J., Worobey M., Pybus O. G., Ma S. K., Cheung C. L., Raghwani J. other authors 2009; Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122–1125 [View Article][PubMed]
    [Google Scholar]
  81. Solmone M., Vincenti D., Prosperi M. C., Bruselles A., Ippolito G., Capobianchi M. R. 2009; Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen. J Virol 83:1718–1726 [View Article][PubMed]
    [Google Scholar]
  82. Stark T. J., Arnold J. D., Spector D. H., Yeo G. W. 2012; High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J Virol 86:226–235 [View Article][PubMed]
    [Google Scholar]
  83. Sullivan P. F., Allander T., Lysholm F., Goh S., Persson B., Jacks A., Evengård B., Pedersen N. L., Andersson B. 2011; An unbiased metagenomic search for infectious agents using monozygotic twins discordant for chronic fatigue. BMC Microbiol 11:2 [View Article][PubMed]
    [Google Scholar]
  84. Szpara M. L., Parsons L., Enquist L. W. 2010; Sequence variability in clinical and laboratory isolates of herpes simplex virus 1 reveals new mutations. J Virol 84:5303–5313 [View Article][PubMed]
    [Google Scholar]
  85. Tang P., Chiu C. 2010; Metagenomics for the discovery of novel human viruses. Future Microbiol 5:177–189 [View Article][PubMed]
    [Google Scholar]
  86. Tapparel C., Cordey S., Junier T., Farinelli L., Van Belle S., Soccal P. M., Aubert J. D., Zdobnov E., Kaiser L. 2011; Rhinovirus genome variation during chronic upper and lower respiratory tract infections. PLoS ONE 6:e21163 [View Article][PubMed]
    [Google Scholar]
  87. Towner J. S., Sealy T. K., Khristova M. L., Albariño C. G., Conlan S., Reeder S. A., Quan P. L., Lipkin W. I., Downing R. other authors 2008; Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 4:e1000212 [View Article][PubMed]
    [Google Scholar]
  88. Trapnell C., Pachter L., Salzberg S. L. 2009; TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111 [View Article][PubMed]
    [Google Scholar]
  89. Umbach J. L., Kramer M. F., Jurak I., Karnowski H. W., Coen D. M., Cullen B. R. 2008; MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454:780–783[PubMed]
    [Google Scholar]
  90. Varghese V., Shahriar R., Rhee S. Y., Liu T., Simen B. B., Egholm M., Hanczaruk B., Blake L. A., Gharizadeh B. other authors 2009; Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr 52:309–315 [View Article][PubMed]
    [Google Scholar]
  91. Verbinnen T., Van Marck H., Vandenbroucke I., Vijgen L., Claes M., Lin T. I., Simmen K., Neyts J., Fanning G., Lenz O. 2010; Tracking the evolution of multiple in vitro hepatitis C virus replicon variants under protease inhibitor selection pressure by 454 deep sequencing. J Virol 84:11124–11133 [View Article][PubMed]
    [Google Scholar]
  92. Victoria J. G., Kapoor A., Li L., Blinkova O., Slikas B., Wang C., Naeem A., Zaidi S., Delwart E. 2009; Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83:4642–4651 [View Article][PubMed]
    [Google Scholar]
  93. Victoria J. G., Wang C., Jones M. S., Jaing C., McLoughlin K., Gardner S., Delwart E. L. 2010; Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. J Virol 84:6033–6040 [View Article][PubMed]
    [Google Scholar]
  94. Vijaykrishna D., Smith G. J., Pybus O. G., Zhu H., Bhatt S., Poon L. L., Riley S., Bahl J., Ma S. K. other authors 2011; Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473:519–522 [View Article][PubMed]
    [Google Scholar]
  95. Wang C., Mitsuya Y., Gharizadeh B., Ronaghi M., Shafer R. W. 2007; Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17:1195–1201 [View Article][PubMed]
    [Google Scholar]
  96. Wellehan J. F. Jr, Yu F., Venn-Watson S. K., Jensen E. D., Smith C. R., Farmerie W. G., Nollens H. H. 2010; Characterization of San Miguel sea lion virus populations using pyrosequencing-based methods. Infect Genet Evol 10:254–260 [View Article][PubMed]
    [Google Scholar]
  97. Wilhelm B. T., Landry J. R. 2009; RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48:249–257 [View Article][PubMed]
    [Google Scholar]
  98. Willerth S. M., Pedro H. A., Pachter L., Humeau L. M., Arkin A. P., Schaffer D. V. 2010; Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS ONE 5:e13564 [View Article][PubMed]
    [Google Scholar]
  99. Willner D., Furlan M., Haynes M., Schmieder R., Angly F. E., Silva J., Tammadoni S., Nosrat B., Conrad D., Rohwer F. 2009; Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 4:e7370 [View Article][PubMed]
    [Google Scholar]
  100. Woodhouse S. D., Narayan R., Latham S., Lee S., Antrobus R., Gangadharan B., Luo S., Schroth G. P., Klenerman P., Zitzmann N. 2010; Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro. Hepatology 52:443–453 [View Article][PubMed]
    [Google Scholar]
  101. Woolhouse M., Gaunt E. 2007; Ecological origins of novel human pathogens. Crit Rev Microbiol 33:231–242 [View Article][PubMed]
    [Google Scholar]
  102. Woolhouse M. E., Howey R., Gaunt E., Reilly L., Chase-Topping M., Savill N. 2008; Temporal trends in the discovery of human viruses. Proc Biol Sci 275:2111–2115 [View Article][PubMed]
    [Google Scholar]
  103. Wu Y. H., Hu T. F., Chen Y. C., Tsai Y. N., Tsai Y. H., Cheng C. C., Wang H. W. 2011; The manipulation of miRNA-gene regulatory networks by KSHV induces endothelial cell motility. Blood 118:2896–2905 [View Article][PubMed]
    [Google Scholar]
  104. Yang Z., Bruno D. P., Martens C. A., Porcella S. F., Moss B. 2010; Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing. Proc Natl Acad Sci U S A 107:11513–11518 [View Article][PubMed]
    [Google Scholar]
  105. Yang Z., Bruno D. P., Martens C. A., Porcella S. F., Moss B. 2011a; Genome-wide analysis of the 5′ and 3′ ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts. J Virol 85:5897–5909 [View Article][PubMed]
    [Google Scholar]
  106. Yang Z., Reynolds S. E., Martens C. A., Bruno D. P., Porcella S. F., Moss B. 2011b; Expression profiling of the intermediate and late stages of poxvirus replication. J Virol 85:9899–9908 [View Article][PubMed]
    [Google Scholar]
  107. Zerbino D. R., Birney E. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829 [View Article][PubMed]
    [Google Scholar]
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