False-positive results in metagenomic virus discovery: A strong case for follow-up diagnosis

Transboundary and Emerging Diseases

Volumn 61, Issue 4, 2014, Pages 293-299

  Rosseel, T ^a   Pardon, B ^b   De Clercq, K ^a   Ozhelvaci, O ^a   Van Borm, S ^a  

^a VETERINARY AND AGROCHEMICAL RESEARCH CENTRE   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Contamination; Next generation sequencing; Parvovirus; Viral metagenomics

Indexed keywords

VIRUS DNA; VIRUS RNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; CATTLE; CATTLE DISEASE; CLASSIFICATION; CONTAMINATION; FEMALE; GENETICS; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; METAGENOMICS; METHODOLOGY; NEXT-GENERATION SEQUENCING; PARVOVIRUS; PARVOVIRUS INFECTION; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRAL METAGENOMICS; VIROLOGY; VIRUS;

CONTAMINATION; NEXT-GENERATION SEQUENCING; PARVOVIRUS; VIRAL METAGENOMICS;

ANIMALS; CATTLE; CATTLE DISEASES; DNA, VIRAL; FALSE POSITIVE REACTIONS; FEMALE; METAGENOMICS; PARVOVIRIDAE INFECTIONS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SPECIMEN HANDLING; VIRUSES;

EID: 84903816710     PISSN: 18651674     EISSN: 18651682     Source Type: Journal    
DOI: 10.1111/tbed.12251     Document Type: Article

References (28)

1. Allander, T., M. T. Tammi, M. Eriksson, A. Bjerkner, A. Tiveljung-Lindell, and B. Andersson, 2005: Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl. Acad. Sci. U.S.A. 102, 12891-12896.
2. Barzon, L., E. Lavezzo, V. Militello, S. Toppo, and G. Palu, 2011: Applications of next-generation sequencing technologies to diagnostic virology. Int. J. Mol. Sci. 12, 7861-7884.
3. Belak, S., O. E. Karlsson, A. L. Blomstrom, M. Berg, and F. Granberg, 2013: New viruses in veterinary medicine, detected by metagenomic approaches. Vet. Microbiol. 165, 95-101.
4. Bishop-Lilly, K. A., M. J. Turell, K. M. Willner, A. Butani, N. M. Nolan, S. M. Lentz, A. Akmal, A. Mateczun, T. N. Brahmbhatt, S. Sozhamannan, C. A. Whitehouse, and T. D. Read, 2010: Arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing. Plos Negl. Trop. Dis. 4, e878.
5. Blomström, A. L., 2011: Viral metagenomics as an emerging and powerful tool in veterinary medicine. Vet. Q. 31, 107-114.
6. Blomström, A. L., S. Belak, C. Fossum, J. Mckillen, G. Allan, P. Wallgren, and M. Berg, 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, 125-129.
7. Blomström, A. L., F. Widen, A. S. Hammer, S. Belak, and M. Berg, 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, 4392-4396.
8. Blomström, A. L., K. Stahl, C. Masembe, E. Okoth, A. R. Okurut, P. Atmnedi, S. Kemp, R. Bishop, S. Belak, and M. Berg, 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.
9. Bodewes, R., J. Van Der Giessen, B. L. Haagmans, A. D. Osterhaus, and S. L. Smits, 2013: Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes. J. Virol. 87, 7758-7764.
10. Cox-Foster, D. L., S. Conlan, E. C. Holmes, G. Palacios, J. D. Evans, N. A. Moran, P. L. Quan, T. Briese, M. Hornig, D. M. Geiser, V. Martinson, D. Vanengelsdorp, A. L. Kalkstein, A. Drysdale, J. Hui, J. Zhai, L. Cui, S. K. Hutchison, J. F. Simons, M. Egholm, J. S. Pettis, and W. I. Lipkin, 2007: A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283-287.
11. Djikeng, A., R. Halpin, R. Kuzmickas, J. Depasse, J. Feldblyum, N. Sengamalay, C. Afonso, X. Zhang, N. G. Anderson, E. Ghedin, and D. J. Spiro, 2008: Viral genome sequencing by random priming methods. BMC Genomics 9, 5.
12. Editorial, 2014: Correction For Xu et al., Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc. Natl. Acad. Sci. U.S.A. 110, 10264-10269.
13. Fredericks, D. N., and D. A. Relman, 1996: Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin. Microbiol. Rev. 9, 18-33.
14. Ge, X., Y. Li, X. Yang, H. Zhang, P. Zhou, Y. Zhang, and Z. Shi, 2012: Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J. Virol. 86, 4620-4630.
15. Granberg, F., M. Vicente-Rubiano, C. Rubio-Guerri, O. E. Karlsson, D. Kukielka, S. Belak, and J. M. Sanchez-Vizcaino, 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, e57459.
16. Honkavuori, K. S., H. L. Shivaprasad, T. Briese, C. Street, D. L. Hirschberg, S. K. Hutchison, and W. I. Lipkin, 2011: Novel picornavirus in Turkey poults with hepatitis, California, USA. Emerg. Infect. Dis. 17, 480-487.
17. Huson, D. H., S. Mitra, H. J. Ruscheweyh, N. Weber, and S. C. Schuster, 2011: Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21, 1552-1560.
18. Li, L., J. G. Victoria, C. Wang, M. Jones, G. M. Fellers, T. H. Kunz, and E. Delwart, 2010: Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J. Virol. 84, 6955-6965.
19. Lysholm, F., A. Wetterbom, C. Lindau, H. Darban, A. Bjerkner, K. Fahlander, A. M. Lindberg, B. Persson, T. Allander, and B. Andersson, 2012: Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One 7, e30875.
20. Mokili, J. L., F. Rohwer, and B. E. Dutilh, 2012: Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2, 63-77.
21. Naccache, S. N., A. L. Greninger, D. Lee, L. L. Coffey, T. Phan, A. Rein-Weston, A. Aronsohn, J. Jr Hackett, E. L. Delwart, and C. Y. Chiu, 2013: The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J. Virol. 87, 11966-11977.
22. Naccache, S. N., J.Jr Hackett, E. L. Delwart, and C. Y. Chiu, 2014: Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Proc. Natl. Acad. Sci. U.S.A. 111, e976.
23. Rosseel, T., B. Lambrecht, F. Vandenbussche, T. Van Den Berg, and S. Van Borm, 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.
24. Rosseel, T., M. Scheuch, D. Hoper, N. De Regge, A. B. Caij, F. Vandenbussche, and S. Van Borm, 2012: Dnase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS One 7, e41967.
25. Smuts, H., M. Kew, A. Khan, and S. Korsman, 2014: Novel hybrid parvovirus-like virus, NIH-CQV/PHV, contaminants in silica column-based nucleic acid extraction kits. J. Virol. 88, 1398.
26. Tao, T., 2010 [Updated 2012]: Standalone BLAST setup for Windows PC. In: BLAST® Help [Internet]. National Center For Biotechnology Information, Bethesda, MD, USA; 2008. Available at http://Www.Ncbi.Nlm.Nih.Gov/Books/NBK52637/ (accessed August 22, 2013).
27. Xu, B., N. Zhi, G. Hu, Z. Wan, X. Zheng, X. Liu, S. Wong, S. Kajigaya, K. Zhao, Q. Mao, and N. S. Young, 2013: Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc. Natl. Acad. Sci. U.S.A. 110, 10264-10269.
28. Ye, J., G. Coulouris, I. Zaretskaya, I. Cutcutache, S. Rozen, and T. L. Madden, 2012: Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134.