Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Jensen, Randi Holm ^a   Mollerup, Sarah ^a   Mourier, Tobias ^a   Hansen, Thomas Arn ^a   Fridholm, Helena ^a   Nielsen, Lars Peter ^b   Willerslev, Eske ^a   Hansen, Anders Johannes ^a   Vinner, Lasse ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b STATENS SERUM INSTITUT   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; RNA; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; MOLECULAR LIBRARY; RNA SEQUENCE; VIRION; VIRION ENRICHMENT; VIRUS DETECTION; VIRUS IDENTIFICATION; VIRUS PARTICLE; GENE LIBRARY; GENETICS; HUMAN PAPILLOMAVIRUS TYPE 18; ISOLATION AND PURIFICATION; NUCLEOTIDE SEQUENCE; PATHOGENICITY; VIROLOGY; VIRUS INFECTION;

DNA VIRUSES;

BASE SEQUENCE; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMAN PAPILLOMAVIRUS 18; HUMANS; RNA, VIRAL; VIRION; VIRUS DISEASES;

EID: 84928975094     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0122636     Document Type: Article

References (51)

1. Virgin HW. The Virome in Mammalian Physiology and Disease. Cell. 2014; 157(1):142-50. doi: 10. 1016/j.cell.2014.02.032 PMID: 24679532
2. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, et al. Origins of Highly Mosaic Mycobacteriophage Genomes. Cell. 2003; 113(2):171-82. PMID: 12705866
3. Chan JF, Lau SK, Woo PC. The emerging novel Middle East respiratory syndrome coronavirus: the "knowns" and "unknowns". Journal of the Formosan Medical Association = Taiwan yi zhi. 2013; 112(7): 372-81. doi: 10.1016/j.jfma.2013.05.010 PMID: 23883791
4. Geng H, Tan W. A novel human coronavirus: Middle East respiratory syndrome human coronavirus. Science China Life sciences. 2013; 56(8):683-7. doi: 10.1007/s11427-013-4519-8 PMID: 23917839
5. Chen Y, Liang W, Yang S, Wu N, Gao H, Sheng J, et al. Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. The Lancet. 2013; 381(9881):1916-25. doi: 10.1016/S0140-6736(13)60903-4 PMID: 23623390
6. Gao R, Cao B, Hu Y, Feng Z, Wang D, Hu W, et al. Human infection with a novel avian-origin influenza A (H7N9) virus. The New England journal of medicine. 2013; 368(20):1888-97. doi: 10.1056/ NEJMoa1304459 PMID: 23577628
7. zur Hausen H. The search for infectious causes of human cancers: Where and why. Virology. 2009; 392:1-10. doi: 10.1016/j.virol.2009.06.001 PMID: 19720205
8. zur Hausen H. Childhood leukemias and other hematopoietic malignancies: interdependence between an infectious event and chromosomal modifications. International journal of cancer Journal international du cancer. 2009; 125(8):1764-70. doi: 10.1002/ijc.24365 PMID: 19330827
9. Mesri EA, Feitelson MA, Munger K. Human Viral Oncogenesis: A Cancer Hallmarks Analysis. Cell host & microbe. 2014; 15(3):266-82.
10. Woese CR. Bacterial Evolution. Microbiological Reviews. 1987; 51(2):221-71. PMID: 2439888
11. Edwards RA, Rohwer F. Viral Metagenomics. Nature Reviews Microbiology. 2005; 3(6):504-10. PMID: 15886693
12. Bexfield N, Kellam P. Metagenomics and the molecular identification of novel viruses. The Veterinay Journal. 2011; 190(2):191-8. doi: 10.1016/j.tvjl.2010.10.014 PMID: 21111643
13. Culley AI, Lang AS, Suttle CA. High diversity of inknown picorna-like viruses in the sea. Nature. 2003; 424(6952):1054-7. PMID: 12944967
14. Kapoor A, Mehta N, Esper F, Poljsak-Prijatelj M, Quan PL, Qaisar N, et al. Identification and characterization of a new bocavirus species in gorillas. PloS one. 2010; 5(7):e11948. doi: 10.1371/journal.pone. 0011948 PMID: 20668709
15. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, et al. Viral discovery and sequence recovery using DNA microarrays. PLoS biology. 2003; 1(2):E2. PMID: 14624234
16. Tang P, Chiu C. Metagenomics for the discovery of novel human viruses. Future Microbiology. 2010; 5(2):177-89. doi: 10.2217/fmb.09.120 PMID: 20143943
17. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, et al. The complete genome of klassevirus-a novel picornavirus in pediatric stool. Virology journal. 2009; 6:82. doi: 10.1186/1743-422X-6-82 PMID: 19538752
18. Delwart E. Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development. Current opinion in virology. 2012; 2(3):344-52. doi: 10.1016/j.coviro.2012.02. 012 PMID: 22463981
19. Kapoor A, Simmonds P, Scheel TK, Hjelle B, Cullen JM, Burbelo PD, et al. Identification of rodent homologs of hepatitis C virus and pegiviruses. mBio. 2013; 4(2):e00216-13. doi: 10.1128/mBio.00216-13 PMID: 23572554
20. Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. PNAS. 2001; 98(20): 11609-14. PMID: 11562506
21. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. New DNA viruses identified in patients with acute viral infection syndrome. Journal of virology. 2005; 79(13):8230-6. PMID: 15956568
22. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, et al. Microarray-based detection and genotyping of viral pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2002; 99(24):15687-92. PMID: 12429852
23. Hu Y, Hirshfield I. Rapid approach to identify an unrecognized viral agent. Journal of virological methods. 2005; 127(1):80-6. PMID: 15893569
24. Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. Next generation sequencing in clinicl medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform. 2012; 3(40). doi: 10.4103/2153-3539.103013 PMID: 23248761
25. Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, et al. A new arenavirus in a cluster of fatal trans-plant-associated diseases. The New England journal of medicine. 2008; 358(10):991-8. doi: 10.1056/ NEJMoa073785 PMID: 18256387
26. Li L, Pesavento PA, Shan T, Leutenegger CM, Wang C, Delwart E. Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses. The Journal of general virology. 2011; 92(Pt 11):2534-41. doi: 10. 1099/vir.0.034611-0 PMID: 21775584
27. Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, et al. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. Journal of virological methods. 2014; 195:194-204. doi: 10.1016/j.jviromet.2013.08.035 PMID: 24036074
28. Radecke F, Spielhofer P, Schneider H, Kailen K, Huber M, Dotsch C, et al. Rescue of measles viruses form cloned DNA. EMBO J. 1995; 14:5773-84. PMID: 8846771
29. Lizard G, Chignol M, Chardonnet Y, Souchier C, Bordes M, Schmitt D, et al. Detection of human papillomavirus DNA in CaSki and HeLa cells by flourescent in situ hybridization. Analysis by flow cytometri and confocal laser scanning microscopy. J Immunol Methods. 1993; 157(1-2):31-8. PMID: 8423376
30. Meissner JD. Nucleotide sequences and further characterization of human papillomavirus DNA present in the CaSki, SiHa and HeLa cervical carcinoma cell lines. Journal of General Virology. 1999; 80: 1725-33. PMID: 10423141
31. Folks TM, Powell D, Lightfoote M, Koenig S, Faugi AS, Benn S, et al. Biological and biochemical characterization of a cloned Leu-3- cell surviving infection with the Acquired Immune Deficiency Syndrome retrovirus. J Exp Med. 1986; 164:280-90. PMID: 3014036
32. Gendelman HE, Theodore T, Willey R, McCoy J, Adachi A, Mervis R, et al. Molecular characterization of a polymerase mutant human immunodeficiency virus. Virology. 1992; 160(2):323-9.
33. Drosten C, Panning M, Drexler JF, Hansel F, Pedroso C, Yeats J, et al. Ultrasensitive monitoring of HIV-1 viral load by a low-cost real-time reverse transcription-PCR assay with internal control for the 5' long terminal repeat domain. Clinical chemistry. 2006; 52(7):1258-66. PMID: 16627558
34. Lindgreen S. AdaptorRemoval: easy cleaning of next-generation sequencing reads. BMC Research Notes. 2012; 5(337). doi: 10.1186/1756-0500-5-337 PMID: 22748135
35. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589-95. doi: 10.1093/bioinformatics/btp698 PMID: 20080505
36. Chandriani S, Skewes-Cow P, Zhong W, Ganem D, Divers T, Van Blaricum A, et al. Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110: E1407-E15. doi: 10.1073/pnas.1219217110 PMID: 23509292
37. Chen EC, Yagi S, Kelly KR, Mendoza SP, Tarara RP, Canfield DR, et al. Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony. PLoS pathogens. 2011; 7(7):e1002155. doi: 10.1371/journal.ppat.1002155 PMID: 21779173
38. Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, et al. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS pathogens. 2012; 8(9):e1002924. doi: 10.1371/journal. ppat.1002924 PMID: 23028323
39. McMullan LK, Folk SM, Kelly AJ, MacNeil A, Goldsmith CS, Metcalfe MG, et al. A new phlebovirus associated with severe febrile illness in Missouri. The New England journal of medicine. 2012; 367(9): 834-41. doi: 10.1056/NEJMoa1203378 PMID: 22931317
40. Phan TG, Vo NP, Bonkoungou IJ, Kapoor A, Barro N, O'Ryan M, et al. Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus. Journal of virology. 2012; 86(20): 11024-30. PMID: 22855485
41. Siebrasse EA, Reyes A, Lim ES, Zhao G, Mkakosya RS, Manary MJ, et al. Identification of MWpolyomavirus, a novel polyomavirus in human stool. Journal of virology. 2012; 86(19):10321-6. doi: 10. 1128/JVI.01210-12 PMID: 22740408
42. Xu B, Liu L, Huang X, Ma H, Zhang Y, Du Y, et al. Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan Province, China: discovery of a new bunyavirus. PLoS pathogens. 2011; 7(11):e1002369. doi: 10.1371/journal.ppat.1002369 PMID: 22114553
43. Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic acids research. 2011; 40(1):1-8. doi: 10.1093/nar/gkr648 PMID: 21908400
44. McClenahan SD, Uhlenhaut C, Krause PR. Optimization of virus detection in cells using massive parallel sequencing. Biologicals. 2013; 42:34-41. doi: 10.1016/j.biologicals.2013.11.002 PMID: 24309095
45. Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, et al. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic acids research. 2012; 41(1):e13. doi: 10.1093/nar/gks794 PMID: 22962364
46. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, et al. Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. Journal of clinical microbiology. 2011; 49(9):3268-75. doi: 10.1128/JCM.00850-11 PMID: 21715589
47. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chenard C, Friedman JM, et al. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PloS one. 2011; 6(5):e19838. doi: 10.1371/journal.pone.0019838 PMID: 21603639
48. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid Amplification of Plasmid and Phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome research. 2001; 11:1095-9. PMID: 11381035
49. Johne R, Müller H, Rector A, van Ranst M, Stevens H. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends in Microbiology. 2009; 17(5):205-11. doi: 10.1016/j.tim.2009.02.004 PMID: 19375325
50. Erlandsson L, Rosenstierne MW, McLoughlin K, Jaing C, Fomsgaard A. The microbial detection array combined with random Phi29-amplification used as a diagnostic tool for virus detection in clinical samples. PloS one. 2011; 6(8):e22631. doi: 10.1371/journal.pone.0022631 PMID: 21853040
51. Vinner L, Mourier T, Friis-Nielsen J. Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Submitted. 2014.