Deep sequencing approach for genetic stability evaluation of influenza A viruses

Journal of Virological Methods

Volumn 199, Issue , 2014, Pages 68-75

  Bidzhieva, Bella ^a   Zagorodnyaya, Tatiana ^a   Karagiannis, Konstantinos ^a   Simonyan, Vahan ^a   Laassri, Majid ^a   Chumakov, Konstantin ^a  

^a CENTER FOR BIOLOGICS EVALUATION AND RESEARCH   (United States)

Author keywords

Illumina Solexa sequencing; Profiles of mutations; Pyrosequencing; Sequence heterogeneity; Sequencing libraries preparation

Indexed keywords

ILLUMINA SOLEXA SEQUENCING; PROFILES OF MUTATIONS; PYROSEQUENCING; SEQUENCE HETEROGENEITY; SEQUENCING LIBRARIES PREPARATION;

ANIMALS; CELL LINE; CHICKENS; DOGS; GENOMIC INSTABILITY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INFLUENZA A VIRUS, H1N1 SUBTYPE; VIROLOGY; VIRUS CULTIVATION;

EID: 84893460220     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2013.12.018     Document Type: Article

References (35)

1. Adeyefa C.A., Quayle K., McCauley J.W. A rapid method for the analysis of influenza virus genes: application to the reassortment of equine influenza virus genes. Virus Res. 1994, 32:391-399.
2. Amexis G., Oeth P., Abel K., Ivshina A., Pelloquin F., Cantor C.R., Braun A., Chumakov K. Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. USA 2001, 98:12097-12102.
3. Bainbridge M.N., Warren R.L., Hirst M., Romanuik T., Zeng T., Go A., Delaney A., Griffith M., Hickenbotham M., Magrini V., Mardis E.R., Sadar M.D., Siddiqui A.S., Marra M.A., Jones S.J. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 2006, 7:246.
4. Cherkasova E., Laassri M., Chizhikov V., Korotkova E., Dragunsky E., Agol V.I., Chumakov K. Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses. Proc. Natl. Acad. Sci. USA 2003, 100:9398-9403.
5. 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.
6. Chumakov K.M. Molecular consistency monitoring of oral poliovirus vaccine and other live viral vaccines. Dev. Biol. Stand. 1999, 100:67-74.
7. Chumakov K.M., Powers L.B., Noonan K.E., Roninson I.B., Levenbook I.S. Correlation between amount of virus with altered nucleotide sequence and the monkey test for acceptability of oral poliovirus vaccine. Proc. Natl. Acad. Sci. USA 1991, 88:199-203.
8. Dimmock N.J., Rainsford E.W., Scott P.D., Marriott A.C. Influenza virus protecting RNA: an effective prophylactic and therapeutic antiviral. J. Virol. 2008, 82:8570-8578.
9. Domingo E., Martinez-Salas E., Sobrino F., de la Torre J.C., Portela A., Ortin J., Lopez-Galindez C., Perez-Brena P., Villanueva N., Najera R., et al. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance--a review. Gene 1985, 40:1-8.
10. Duhaut S.D., Dimmock N.J. Heterologous protection of mice from a lethal human H1N1 influenza A virus infection by H3N8 equine defective interfering virus: comparison of defective RNA sequences isolated from the DI inoculum and mouse lung. Virology 1998, 248:241-253.
11. Gambaryan A.S., Marinina V.P., Tuzikov A.B., Bovin N.V., Rudneva I.A., Sinitsyn B.V., Shilov A.A., Matrosovich M.N. Effects of host-dependent glycosylation of hemagglutinin on receptor-binding properties on H1N1 human influenza A virus grown in MDCK cells and in embryonated eggs. Virology 1998, 247:170-177.
12. Girard M.P., Steele D., Chaignat C.L., Kieny M.P. A review of vaccine research and development: human enteric infections. Vaccine 2006, 24:2732-2750.
13. Greninger A.L., Chen E.C., Sittler T., Scheinerman A., Roubinian N., Yu G., Kim E., Pillai D.R., Guyard C., Mazzulli T., Isa P., Arias C.F., Hackett J., Schochetman G., Miller S., Tang P., Chiu C.Y. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 2010, 5:e13381.
14. Hansen H., Okeke M.I., Nilssen O., Traavik T. Recombinant viruses obtained from co-infection in vitro with a live vaccinia-vectored influenza vaccine and a naturally occurring cowpox virus display different plaque phenotypes and loss of the transgene. Vaccine 2004, 23:499-506.
15. Hoffmann E., Stech J., Guan Y., Webster R.G., Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 2001, 146:2275-2289.
16. Hughes M.T., McGregor M., Suzuki T., Suzuki Y., Kawaoka Y. Adaptation of influenza A viruses to cells expressing low levels of sialic acid leads to loss of neuraminidase activity. J. Virol. 2001, 75:3766-3770.
17. Jennings P.A., Finch J.T., Winter G., Robertson J.S. Does the higher order structure of the influenza virus ribonucleoprotein guide sequence rearrangements in influenza viral RNA?. Cell 1983, 34:619-627.
18. Kreibich A., Stech J., Mettenleiter T.C., Stech O. Simultaneous one-tube full-length amplification of the NA, NP, M, and NS genes of influenza A viruses for reverse genetics. J. Virol. Methods 2009, 159:308-310.
19. 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. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 2010, 5. e10256.
20. Laassri M., Cherkasova E., Abu-Asab M.S., Chumakov K. Microarray techniques for evaluation of genetic stability of live viral vaccines. Viral Genomes - Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions 2012, 181-194. InTech. V. Romanowski, M.L. Garcia (Eds.).
21. Lamb R.A., Krug M.A. Orthomyxoviridae: The Viruses and Their Replication 2007, Vol. 2. Philadelphia, Lippincott Williams & Wilkins. 4th ed.
22. McCarthy M.W., Kockler D.R. Trivalent intranasal influenza vaccine, live. Ann. Pharmacother. 2004, 38:2086-2093.
23. Nakamura S., Yang C.S., Sakon N., Ueda M., Tougan T., Yamashita A., Goto N., Takahashi K., Yasunaga T., Ikuta K., Mizutani T., Okamoto Y., Tagami M., Morita R., Maeda N., Kawai J., Hayashizaki Y., Nagai Y., Horii T., Iida T., Nakaya T. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 2009, 4:e4219.
24. Neverov A., Chumakov K. Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proc. Natl. Acad. Sci. USA 2010, 107:20063-20068.
25. Orita M., Iwahana H., Kanazawa H., Hayashi K., Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 1989, 86:2766-2770.
26. Pettersson E., Zajac P., Stahl P.L., Jacobsson J.A., Fredriksson R., Marcus C., Schioth H.B., Lundeberg J., Ahmadian A. Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads. Hum. Mutat. 2008, 29:323-329.
27. Satkoski J.A., Malhi R., Kanthaswamy S., Tito R., Malladi V., Smith D. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 2008, 9:256.
28. Schild G.C., Oxford J.S., de Jong J.C., Webster R.G. Evidence for host-cell selection of influenza virus antigenic variants. Nature 1983, 303:706-709.
29. Scott P.D., Meng B., Marriott A.C., Easton A.J., Dimmock N.J. Defective interfering influenza virus confers only short-lived protection against influenza virus disease: evidence for a role for adaptive immunity in DI virus-mediated protection in vivo. Vaccine 2011, 29:6584-6591.
30. Scott P.D., Meng B., Marriott A.C., Easton A.J., Dimmock N.J. Defective interfering virus protects elderly mice from influenza. Virol. J. 2011, 8:212.
31. Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 1948, 27:379-423.
32. Steinhauer D.A., Domingo E., Holland J.J. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 1992, 122:281-288.
33. Torres T.T., Metta M., Ottenwalder B., Schlotterer C. Gene expression profiling by massively parallel sequencing. Genome Res. 2008, 18:172-177.
34. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., Makhijani V., Roth G.T., Gomes X., Tartaro K., Niazi F., Turcotte C.L., Irzyk G.P., Lupski J.R., Chinault C., Song X.Z., Liu Y., Yuan Y., Nazareth L., Qin X., Muzny D.M., Margulies M., Weinstock G.M., Gibbs R.A., Rothberg J.M. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876.
35. Zhou B., Donnelly M.E., Scholes D.T., St George K., Hatta M., Kawaoka Y., Wentworth D.E. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J. Virol. 2009, 83:10309-10313.