Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples

Journal of Virological Methods

Volumn 222, Issue , 2015, Pages 72-80

  Rosseel, Toon ^a   Ozhelvaci, Orkun ^a   Freimanis, Graham ^b   Van Borm, Steven ^a  

^a VETERINARY AND AGROCHEMICAL RESEARCH CENTRE   (Belgium)

^b INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

Author keywords

Clinical samples; Next generation sequencing; Pretreatment; RNA virus discovery; RRNA depletion; Viral metagenomics

Indexed keywords

COMPLEMENTARY DNA; DEOXYRIBONUCLEASE; RIBOSOME RNA;

ARTICLE; BLOOD; CONTROLLED STUDY; DNA SYNTHESIS; GENE AMPLIFICATION; GENE SEQUENCE; LUNG PARENCHYMA; METAGENOMICS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA EXTRACTION; RNA VIRUS; SENSITIVITY ANALYSIS; VIRION; ANIMAL; CHICKEN; GENETICS; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; LUNG; PROCEDURES; SERUM; VIROLOGY;

RNA VIRUSES;

ANIMALS; CHICKENS; LUNG; METAGENOMICS; RNA VIRUSES; SERUM; SPECIMEN HANDLING; VIROLOGY;

EID: 84931271178     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2015.05.010     Document Type: Article

References (49)

1. Allander T., Tammi M.T., Eriksson M., Bjerkner A., Tiveljung-Lindell A., Andersson B. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:12891-12896.
2. Ambrose H.E., Clewley J.P. Virus discovery by sequence-independent genome amplification. Rev. Med. Virol. 2006, 16:365-383.
3. Barzon L., Lavezzo E., Militello V., Toppo S., Palu G. Applications of next-generation sequencing technologies to diagnostic virology. Int. J. Mol. Sci. 2011, 12:7861-7884.
4. Belak S., Karlsson O.E., Blomstrom A.L., Berg M., Granberg F. New viruses in veterinary medicine, detected by metagenomic approaches. Vet. Microbiol. 2013, 165:95-101.
5. Bibby K. Metagenomic identification of viral pathogens. Trends Biotechnol. 2013, 31:275-279.
6. Bishop-Lilly K.A., Turell M.J., Willner K.M., Butani A., Nolan N.M., Lentz S.M., Akmal A., Mateczun A., Brahmbhatt T.N., Sozhamannan S., Whitehouse C.A., Read T.D. Arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing. PLoS Negl. Trop. Dis. 2010, 4:e878.
7. Blomstrom A.L. Viral metagenomics as an emerging and powerful tool in veterinary medicine. Vet. Q. 2011, 31:107-114.
8. Cattoli G., Susta L., Terregino C., Brown C. Newcastle disease: a review of field recognition and current methods of laboratory detection. J. Vet. Diagn. Invest. 2011, 23:637-656.
9. Cheval J., Sauvage V., Frangeul L., Dacheux L., Guigon G., Dumey N., Pariente K., Rousseaux C., Dorange F., Berthet N., Brisse S., Moszer I., Bourhy H., Manuguerra C.J., Lecuit M., Burguiere A., Caro V., Eloit M. Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J. Clin. Microbiol. 2011, 49:3268-3275.
10. Chiu C.Y. Viral pathogen discovery. Curr. Opin. Microbiol. 2013, 16:468-478.
11. Daly G.M., Bexfield N., Heaney J., Stubbs S., Mayer A.P., Palser A., Kellam P., Drou N., Caccamo M., Tiley L., Alexander G.J., Bernal W., Heeney J.L. A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS ONE 2011, 6:e28879.
12. de Vries M., Deijs M., Canuti M., van Schaik B.D., Faria N.R., van de Garde M.D., Jachimowski L.C., Jebbink M.F., Jakobs M., Luyf A.C., Coenjaerts F.E., Claas E.C., Molenkamp R., Koekkoek S.M., Lammens C., Leus F., Goossens H., Ieven M., Baas F., van der Hoek L. A sensitive assay for virus discovery in respiratory clinical samples. PLoS ONE 2011, 6:e16118.
13. Delwart E.L. Viral metagenomics. Rev. Med. Virol. 2007, 17:115-131.
14. Djikeng A., Halpin R., Kuzmickas R., Depasse J., Feldblyum J., Sengamalay N., Afonso C., Zhang X., Anderson N.G., Ghedin E., Spiro D.J. Viral genome sequencing by random priming methods. BMC Genomics 2008, 9:5.
15. Edwards R.A., Rohwer F. Viral metagenomics. Nat. Rev. Microbiol. 2005, 3:504-510.
16. Endoh D., Mizutani T., Kirisawa R., Maki Y., Saito H., Kon Y., Morikawa S., Hayashi M. Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res. 2005, 33:e65.
17. Frey K.G., Herrera-Galeano J.E., Redden C.L., Luu T.V., Servetas S.L., Mateczun A.J., Mokashi V.P., Bishop-Lilly K.A. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics 2014, 15:96.
18. Glenn T.C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 2011, 11:759-769.
19. Hall R.J., Wang J., Todd A.K., Bissielo A.B., Yen S., Strydom H., Moore N.E., Ren X., Huang Q.S., Carter P.E., Peacey M. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J. Virol. Methods 2014, 195:194-204.
20. He S., Wurtzel O., Singh K., Froula J.L., Yilmaz S., Tringe S.G., Wang Z., Chen F., Lindquist E.A., Sorek R., Hugenholtz P. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat. Methods 2010, 7:807-812.
21. Huang R., Jaritz M., Guenzl P., Vlatkovic I., Sommer A., Tamir I.M., Marks H., Klampfl T., Kralovics R., Stunnenberg H.G., Barlow D.P., Pauler F.M. An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS ONE 2011, 6:e27288.
22. Huson D.H., Mitra S., Ruscheweyh H.J., Weber N., Schuster S.C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011, 21:1552-1560.
23. Jones K.E., Patel N.G., Levy M.A., Storeygard A., Balk D., Gittleman J.L., Daszak P. Global trends in emerging infectious diseases. Nature 2008, 451:990-993.
24. Joshi N.A., Fass J. Sickle: A Sliding-Window, Adaptive, Quality-based Trimming Tool for FastQ Files (Version 1.33) [Software] 2011, Available at 〈https://github.com/najoshi/sickle〉;.
25. Karlsson O.E., Belak S., Granberg F. The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses. Biosecur. Bioterror. 2013, 11(Suppl. 1):S227-S234.
26. Kohl C., Brinkmann A., Dabrowski P.W., Radonic A., Nitsche A., Kurth A. Protocol for metagenomic virus detection in clinical specimens. Emerg. Infect. Dis. 2015, 21:48-57.
27. Kopylova E., Noe L., Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 2012, 28:3211-3217.
28. Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 2014, 30:2843-2851.
29. Li L., Deng X., Mee E.T., Collot-Teixeira S., Anderson R., Schepelmann S., Minor P.D., Delwart E. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J. Virol. Methods 2015, 213:139-146.
30. Lim Y.W., Schmieder R., Haynes M., Willner D., Furlan M., Youle M., Abbott K., Edwards R., Evangelista J., Conrad D., Rohwer F. Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J. Cyst. Fibros 2013, 12:154-164.
31. Lipkin W.I. Microbe hunting in the 21st century. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:6-7.
32. Marine R., Polson S.W., Ravel J., Hatfull G., Russell D., Sullivan M., Syed F., Dumas M., Wommack K.E. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl. Environ. Microbiol. 2011, 77:8071-8079.
33. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011, 17(1):10-12. ISSN 2226-6089.
34. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The genome analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
35. Moore R.A., Warren R.L., Freeman J.D., Gustavsen J.A., Chenard C., Friedman J.M., Suttle C.A., Zhao Y., Holt R.A. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS ONE 2011, 6:e19838.
36. Motley S.T., Picuri J.M., Crowder C.D., Minich J.J., Hofstadler S.A., Eshoo M.W. Improved multiple displacement amplification (iMDA) and ultraclean reagents. BMC Genomics 2014, 15:443.
37. Parkinson N.J., Maslau S., Ferneyhough B., Zhang G., Gregory L., Buck D., Ragoussis J., Ponting C.P., Fischer M.D. Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res. 2012, 22:125-133.
38. Perkins T.T., Tay C.Y., Thirriot F., Marshall B. Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes. PLoS ONE 2013, 8:e67539.
39. Pinard R., de Winter A., Sarkis G.J., Gerstein M.B., Tartaro K.R., Plant R.N., Egholm M., Rothberg J.M., Leamon J.H. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 2006, 7:216.
40. Radford A.D., Chapman D., Dixon L., Chantrey J., Darby A.C., Hall N. Application of next-generation sequencing technologies in virology. J. Gen. Virol. 2012, 93:1853-1868.
41. Rosseel T., Pardon B., De Clercq K., Ozhelvaci O., Van Borm S. False-positive results in metagenomic virus discovery: a strong case for follow-up diagnosis. Transbound. Emerg. Dis. 2014, 61:293-299.
42. Rosseel T., Scheuch M., Hoper D., De Regge N., Caij A.B., Vandenbussche F., Van Borm S. DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS ONE 2012, 7:e41967.
43. Rosseel T., Van Borm S., Vandenbussche F., Hoffmann B., van den Berg T., Beer M., Hoper D. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS ONE 2013, 8:e76144.
44. Sachsenroder J., Twardziok S., Hammerl J.A., Janczyk P., Wrede P., Hertwig S., Johne R. Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing. PLoS ONE 2012, 7:e34631.
45. Tang P., Chiu C. Metagenomics for the discovery of novel human viruses. Future Microbiol. 2010, 5:177-189.
46. Tao T. Standalone BLAST setup for Windows PC. BLAST® Help [Internet] 2010, National Center for Biotechnology Information (US), Bethesda, MD, [Updated 2012].
47. Thurber R.V., Haynes M., Breitbart M., Wegley L., Rohwer F. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 2009, 4:470-483.
48. Tosar J.P., Rovira C., Naya H., Cayota A. Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS. RNA 2014, 20:754-757.
49. Wise M.G., Suarez D.L., Seal B.S., Pedersen J.C., Senne D.A., King D.J., Kapczynski D.R., Spackman E. Development of a real-time reverse-transcription PCR for detection of Newcastle Disease virus RNA in clinical samples. J. Clin. Microbiol. 2004, 42:329-338.