Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

Biology Direct

Volumn 11, Issue 1, 2016, Pages

  Li, Dingchen ^a,b   Li, Zongwei ^a,b   Zhou, Zhe ^a,b   Li, Zhen ^a,b   Qu, Xinyan ^a,b   Xu, Peisong ^c   Zhou, Pingkun ^a   Bo, Xiaochen ^a,b   Ni, Ming ^a,b  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b BEIJING INSTITUTE OF MICROBIOLOGY AND EPIDEMIOLOGY   (China)

^c Beijing Key Laboratory for Radiobiology ^*  (China)

Author keywords

Background Depletion; Next generation sequencing; Nonculture; Pathogen genome recovery; Whole Transcriptome Amplification

Indexed keywords

GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLUENZA A VIRUS (H1N1); PROCEDURES; VIRUS GENOME;

GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE;

EID: 84953868470     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/s13062-016-0105-x     Document Type: Article

References (43)

1. Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, et al. De novo assembly of highly diverse viral populations. BMC Genomics. 2012;13:475. doi: 10.1186/1471-2164-13-475.
2. Kupferschmidt K. Epidemiology. Outbreak detectives embrace the genome era. Science. 2011;333(6051):1818-9. doi: 10.1126/science.333.6051.1818.
3. Jin DZ, Wen SY, Chen SH, Lin F, Wang SQ. Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol Cell Probes. 2006;20(6):337-47. doi: 10.1016/j.mcp.2006.03.005.
4. Kapgate SS, Barbuddhe SB, Kumanan K. Next generation sequencing technologies: tool to study avian virus diversity. Acta Virol. 2015;59(1):3-13.
5. Pallen MJ, Loman NJ, Penn CW. High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol. 2010;13(5):625-31. doi: 10.1016/j.mib.2010.08.003.
6. Gilchrist CA, Turner SD, Riley MF, Petri Jr WA, Hewlett EL. Whole-Genome Sequencing in Outbreak Analysis. Clin Microbiol Rev. 2015;28(3):541-63. doi: 10.1128/CMR.00075-13.
7. Bexfield N, Kellam P. Metagenomics and the molecular identification of novel viruses. Vet J. 2011;190(2):191-8. doi: 10.1016/j.tvjl.2010.10.014.
8. Su Z, Ning B, Fang H, Hong H, Perkins R, Tong W, et al. Next-generation sequencing and its applications in molecular diagnostics. Expert Rev Mol Diagn. 2011;11(3):333-43. doi: 10.1586/erm.11.3.
9. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. Application of next-generation sequencing technologies in virology. J Gen Virol. 2012;93(Pt 9):1853-68. doi: 10.1099/vir.0.043182-0.
10. 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(11):7861-84. doi: 10.3390/ijms12117861.
11. Capobianchi MR, Giombini E, Rozera G. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect. 2013;19(1):15-22. doi: 10.1111/1469-0691.12056.
12. Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palu G. Next-generation sequencing technologies in diagnostic virology. J Clin Virol. 2013;58(2):346-50. doi: 10.1016/j.jcv.2013.03.003.
13. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345(6202):1369-72. doi: 10.1126/science.1259657.
14. Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, et al. Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med. 2014;371(15):1418-25. doi: 10.1056/NEJMoa1404505.
15. Maganga GD, Kapetshi J, Berthet N, Kebela Ilunga B, Kabange F, Mbala Kingebeni P, et al. Ebola virus disease in the Democratic Republic of Congo. N Engl J Med. 2014;371(22):2083-91. doi: 10.1056/NEJMoa1411099.
16. Meyers L, Frawley T, Goss S, Kang C. Ebola virus outbreak 2014: clinical review for emergency physicians. Ann Emerg Med. 2015;65(1):101-8. doi: 10.1016/j.annemergmed.2014.10.009.
17. Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med. 2008;358(10):991-8. doi: 10.1056/NEJMoa073785.
18. Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, et al. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One. 2009;4(1):e4219. doi: 10.1371/journal.pone.0004219.
19. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis. 2012;6(2):e1485. doi: 10.1371/journal.pntd.0001485.
20. McMullan LK, Frace M, Sammons SA, Shoemaker T, Balinandi S, Wamala JF, et al. Using next generation sequencing to identify yellow fever virus in Uganda. Virology. 2012;422(1):1-5. doi: 10.1016/j.virol.2011.08.024.
21. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, et al. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA. 2013;309(14):1502-10. doi: 10.1001/jama.2013.3231.
22. Morlan JD, Qu K, Sinicropi DV. Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue. PLoS One. 2012;7(8):e42882. doi: 10.1371/journal.pone.0042882.
23. Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, et al. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol. 2014;15(11):519. doi: 10.1186/PREACCEPT-1698056557139770.
24. Ma Z, Lee RW, Li B, Kenney P, Wang Y, Erikson J, et al. Isothermal amplification method for next-generation sequencing. Proc Natl Acad Sci U S A. 2013;110(35):14320-3. doi: 10.1073/pnas.1311334110.
25. Hoeijmakers WA, Bartfai R, Francoijs KJ, Stunnenberg HG. Linear amplification for deep sequencing. Nat Protoc. 2011;6(7):1026-36. doi: 10.1038/nprot.2011.345.
26. Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods. 2013;10(7):623-9. doi: 10.1038/nmeth.2483.
27. Dabney J, Meyer M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques. 2012;52(2):87-94. doi: 10.2144/000113809.
28. 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 Res. 2013;41(1):e13. doi: 10.1093/nar/gks794.
29. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A. 2013;110(2):594-9. doi: 10.1073/pnas.1217322109.
30. Batty EM, Wong TH, Trebes A, Argoud K, Attar M, Buck D, et al. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One. 2013;8(6):e66129. doi: 10.1371/journal.pone.0066129.
31. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat Methods. 2009;6(4):291-5. doi: 10.1038/nmeth.1311.
32. Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, et al. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics. 2012;13:1. doi: 10.1186/1471-2164-13-1.
33. Kozarewa I, Turner DJ. Amplification-free library preparation for paired-end Illumina sequencing. Methods Mol Biol. 2011;733:257-66. doi: 10.1007/978-1-61779-089-8_18.
34. Yu Z, Cheng K, Sun W, Zhang X, Li Y, Wang T, et al. A PB1 T296R substitution enhance polymerase activity and confer a virulent phenotype to a 2009 pandemic H1N1 influenza virus in mice. Virology. 2015;486:180-6. doi: 10.1016/j.virol.2015.09.014.
35. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. doi: 10.1038/nmeth.1923.
36. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2.
37. Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, et al. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011;29(5):393-6. doi: 10.1038/nbt.1868.
38. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
39. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644-52. doi: 10.1038/nbt.1883.
40. Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28(11):1420-8. doi: 10.1093/bioinformatics/bts174.
41. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9. doi: 10.1101/gr.074492.107.
42. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335.
43. Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017-8. doi: 10.1093/bioinformatics/btr064.