Quantitative characterization of defective virus emergence by deep sequencing

Journal of Virology

Volumn 88, Issue 5, 2014, Pages 2623-2632

  Timm, Collin ^a   Akpinar, Fulya ^a   Yin, John ^a  

^a University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DEFECTIVE VIRUS; GENETIC VARIABILITY; GENOME; HAMSTER; HOST CELL; LIMIT OF DETECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY; VESICULAR STOMATITIS VIRUS; VIRUS CHARACTERIZATION; VIRUS PARTICLE;

ANIMALS; BASE SEQUENCE; CELL LINE; CRICETINAE; DEFECTIVE VIRUSES; GENETIC VARIATION; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; RNA VIRUSES; SEQUENCE DELETION; VESICULAR STOMATITIS INDIANA VIRUS; VIRAL INTERFERENCE; VIRUS REPLICATION;

EID: 84896727346     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02675-13     Document Type: Article

References (50)

1. Von Magnus P. 1954. Incomplete forms of influenza virus. Adv. Virus Res. 2:59-79.
2. Huang AS, Baltimore D. 1970. Defective viral particles and viral disease processes. Nature 226:325-327. http://dx.doi.org/10.1038/226325a0.
3. Lazzarini RA, Keene JD, Schubert M. 1981. The origins of defective interfering particles of the negative-strand RNA viruses. Cell 26:145-154. http://dx.doi.org/10.1016/0092-8674(81)90298-1.
4. Roux L, Simon AE, Holland JJ. 1991. Effects of defective interfering viruses on virus replication and pathogenesis in vitro and in vivo. Adv. Virus Res. 40:181-211.
5. Bean WJ, Kawaoka Y, Wood JM, Pearson JE, Webster RG. 1985. Characterization of virulent and avirulent A/chicken/Pennsylvania/83 influenza A viruses: potential role of defective interfering RNAs in nature. J. Virol. 54:151-160.
6. Pesko KN, Fitzpatrick KA, Ryan EM, Shi P-Y, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD. 2012. Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice. Virology 427:10-17. http://dx.doi.org/10.1016/j.virol .2012.01.028.
7. Li D, Lott WB, Lowry K, Jones A, Thu HM, Aaskov J. 2011. Defective interfering viral particles in acute dengue infections. PLoS One 6:e19447. http://dx.doi.org/10.1371/journal.pone.0019447.
8. Saira K, Lin X, DePasse JV, Halpin R, Twaddle A, Stockwell T, Angus B, Cozzi-Lepri A, Delfino M, Dugan V, Dwyer DE, Freiberg M, Horban A, Losso M, Lynfield R, Wentworth DN, Holmes EC, Davey R, Wentworth DE, Ghedin E. 2013. Sequence analysis of in vivo defectiveinterfering (DI)-like RNA of influenza A H1N1 pandemic virus. J. Virol. 87:8064-8074. http://dx.doi.org/10.1128/JVI.00240-13.
9. Epstein DA, Herman RC, Chien I, Lazzarini RA. 1980. Defective interfering particle generated by internal deletion of the vesicular stomatitis virus genome. J. Virol. 33:818-829.
10. Re GG, Gupta KC, Kingsbury DW. 1983. Genomic and copy-back 3= termini in Sendai virus defective interferingRNAspecies. J. Virol. 45:659-664.
11. Davis AR, Hiti AL, Nayak DP. 1980. Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA. Biochemistry 77: 215-219.
12. Meier E, Harmison GG, Keene JD, Schubert M. 1984. Sites of copy choice replication involved in generation of vesicular stomatitis virus defective-interfering particle RNAs. J. Virol. 51:515-521.
13. O'Hara PJ, Horodyski FM, Nichol ST, Holland JJ. 1984. Vesicular stomatitis virus mutants resistant to defective-interfering particles accumulate stable 5=-terminal and fewer 3=-terminal mutations in a stepwise manner. J. Virol. 49:793-798.
14. Huang AS, Greenawalt JW, Wagner RR. 1966. Defective T particles of vesicular stomatitis virus I. Preparation, morphology, and some biologic properties. Virology 30:161-172.
15. Reichmann ME, Pringle CR, Follett EAC. 1971. Defective particles in BHKcells infected with temperature-sensitive mutants of vesicular stomatitis virus. J. Virol. 8:154-160.
16. Hartford SL. 1975. Physical properties of New Jersey serotype of vesicular stomatitis virus and its defective particles. Proc. Natl. Acad. Sci. U. S. A. 72:1202-1205. http://dx.doi.org/10.1073/pnas.72.3.1202.
17. Nonoyama M, Watanabe Y, Graham AF. 1970. Defective virions of reovirus. J. Virol. 6:226-236.
18. Petric M. 1970. Vesicular stomatitis virus-a new interfering particle, intracellular structures and virus-specific RNA. Virology 41:615-630. http://dx.doi.org/10.1016/0042-6822(70)90427-7.
19. Bellett AJD, Cooper PD. 1959. Some properties of the transmissible interfering component of vesicular stomatitis virus preparations. Microbiology 21:498-509.
20. Stauffer Thompson KA, Rempala GA, Yin J. 2009. Multiple-hit inhibition of infection by defective interfering particles. J. Gen. Virol. 90:888-899. http://dx.doi.org/10.1099/vir.0.005249-0.
21. Janda JM, Davis AR, Nayak DP, De BK. 1979. Diversity and generation of defective interfering influenza virus particles. Virology 95:48-58. http: //dx.doi.org/10.1016/0042-6822(79)90400-8.
22. Marcus PI, Sekellick MJ. 1974. Cell killing by viruses. I. Comparison of cell-killing, plaque-forming, and defective-interfering particles of vesicular stomatitis virus. Virology 57:321-338.
23. Thompson K, Yin J. 2010. Population dynamics of an RNA virus and its defective interfering particles in passage cultures. Virol. J. 7:257. http://dx.doi.org/10.1186/1743-422X-7-257.
24. Kirkwood TB, Bangham CR. 1994. Cycles, chaos, and evolution in virus cultures: a model of defective interfering particles. Proc. Natl. Acad. Sci. U. S. A. 91:8685-8689. http://dx.doi.org/10.1073/pnas.91.18.8685.
25. Zwart M, Pijlman G, Sardanyés J, Duarte J, Januário C, Elena S. 2013. Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. J. Biol. Phys. 39:327-342. http://dx.doi.org/10.1007 /s10867-013-9317-9.
26. Ke R, Aaskov J, Holmes EC, Lloyd-Smith JO. 2013. Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses. PLoS Pathog. 9:e1003193. http://dx.doi.org/10.1371/journal.ppat.1003193.
27. Tsibris AMN, Korber B, Arnaout R, Russ C, Lo C-C, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR. 2009. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 4:e5683. http: //dx.doi.org/10.1371/journal.pone.0005683.
28. Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, Hughes AL, O'Connor DH. 2010. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J. Virol. 84:12087-12092. http://dx.doi.org/10.1128/JVI.01378-10.
29. Nasu A, Marusawa H, Ueda Y, Nishijima N, Takahashi K, Osaki Y, Yamashita Y, Inokuma T, Tamada T, Fujiwara T, Sato F, Shimizu K, Chiba T. 2011. Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS One 6:e24907. http://dx.doi.org/10.1371/journal.pone.0024907.
30. 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. http://dx.doi.org/10.1128/JVI.01217-10.
31. Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, Hata S, Watanabe M, Sata T. 2010. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 5:e10256. http://dx.doi.org/10.1371/journal.pone.0010256.
32. Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Yu G, Kim E, Pillai DR, Guyard C, Mazzulli T, Isa P, Arias CF, Hackett J, Schochetman G, Miller S, Tang P, Chiu CY. 2010. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 5:e13381. http://dx.doi.org/10.1371/journal.pone.0013381.
33. 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. http: //dx.doi.org/10.1128/JVI.00475-10.
34. Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo C-C, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT. 2010. Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One 5:e12303. http://dx.doi.org/10.1371/journal.pone.0012303.
35. Wright CF, Morelli MJ, Thébaud G, Knowles NJ, Herzyk P, Paton DJ, Haydon DT, King DP. 2011. Beyond the consensus: dissecting withinhost viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J. Virol. 85:2266-2275. http://dx.doi.org/10.1128/JVI.01396-10.
36. Komarova AV, Combredet C, Sismeiro O, Dillies M-A, Jagla B, Sanchez David RY, Vabret N, Coppee J-Y, Vidalain P-O, Tangy F. 2013. Identification of RNA partners of viral proteins in infected cells. RNA Biol. 10:944-957. http://dx.doi.org/10.4161/rna.24453.
37. Killip MJ, Young DF, Gatherer D, Ross CS, Short JAL, Davison AJ, Goodbourn S, Randall RE. 2013. Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction. J. Virol. 87:4798-4807. http://dx.doi.org/10.1128/JVI.03383-12.
38. Baum A, Sachidanandam R, García-Sastre A. 2010. Preference of RIG-I for short viralRNAmolecules in infected cells revealed by next-generation sequencing. Proc. Natl. Acad. Sci. U. S. A. 107:16303-16308. http://dx.doi.org/10.1073/pnas.1005077107.
39. Holland JJ. 1987. Defective interfering rhabdoviruses, p 297-360. In Wagner RR (ed), The rhabdoviruses. Springer, New York, NY.
40. Wertz GW, Perepelitsa VP, Ball L. 1998. Gene rearrangement attenuates expression and lethality of a nonsegmented negative strand RNA virus. Proc. Natl. Acad. Sci. U. S. A. 95:3501-3506. http://dx.doi.org/10.1073 /pnas.95.7.3501.
41. Stampfer M, Baltimore D, Huang AS. 1971. Absence of interference during high-multiplicity infection by clonally purified vesicular stomatitis virus. J. Virol. 7:409-411.
42. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:1-8. http://dx.doi.org/10.1038/nmeth1153.
43. Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. 2009. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 10: 221. http://dx.doi.org/10.1186/1471-2164-10-221.
44. Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T. 2009. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 15:2028-2034. http://dx.doi.org/10.1261/rna.1699809.
45. Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M. 2010. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 6:e1000834. http://dx.doi.org/10.1371 /journal.ppat.1000834.
46. Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ. 2009. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641. http://dx.doi.org/10.1186/1471-2164-10-641.
47. Cole CN, Smoler D, Wimmer E, Baltimore D. 1971. Defective interfering particles of poliovirus. I. Isolation and physical properties. J. Virol. 7:478-485.
48. Kuge S, Saito I, Nomoto A. 1986. Primary structure of poliovirus defective-interfering particle genomes and possible generation mechanisms of the particles. J. Mol. Biol. 192:473-487. http://dx.doi.org/10.1016/0022-2836(86)90270-6.
49. Turner PE, Chao L. 1999. Prisoner's dilemma in an RNA virus. Nature 398:441-443. http://dx.doi.org/10.1038/18913.
50. Lim K, Lang T, Lam V, Yin J. 2006. Model-based design of growthattenuated viruses. PLoS Comput. Biol. 2(9):e116. http://dx.doi.org/10.1371/journal.pcbi.0020116.