Rapid Sequencing of Influenza A Virus VRNA, CRNA and MRNA Non-coding Regions

Overview

Journal J Virol Methods

Specialty Microbiology

Date 2013 Oct 8

PMID 24096269

Citations 4

Authors

Ruixue Wang

Yongli Xiao

Jeffery K Taubenberger

Affiliations

Soon will be listed here.

Abstract

Characterizing the genomic sequences of influenza A viruses is important for pathophysiological and evolutionary studies. Noncoding regions (NCR) of influenza A virus have been shown to play critical roles in replication and transcription but their sequences are infrequently determined. In this study, a method employing poly(A) addition and SMART (switching mechanism at 5' end of RNA transcript) technology is described for directly determining and discriminating both NCR ends of viral RNA (vRNA), complementary RNA (cRNA), or NCR and cap sequences from viral mRNA. This modified method may also be used to characterize the NCRs of influenza A virus samples in which the RNA has been degraded.

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References

Hutchinson E, von Kirchbach J, Gog J, Digard P . Genome packaging in influenza A virus. J Gen Virol. 2009; 91(Pt 2):313-28. DOI: 10.1099/vir.0.017608-0. View

Qi L, Kash J, Dugan V, Wang R, Jin G, Cunningham R . Role of sialic acid binding specificity of the 1918 influenza virus hemagglutinin protein in virulence and pathogenesis for mice. J Virol. 2009; 83(8):3754-61. PMC: 2663248. DOI: 10.1128/JVI.02596-08. View

KRAFFT , Duncan , Bijwaard , Taubenberger , Lichy . Optimization of the Isolation and Amplification of RNA From Formalin-fixed, Paraffin-embedded Tissue: The Armed Forces Institute of Pathology Experience and Literature Review. Mol Diagn. 1999; 2(3):217-230. DOI: 10.1054/MODI00200217. View

Yuan P, Bartlam M, Lou Z, Chen S, Zhou J, He X . Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site. Nature. 2009; 458(7240):909-13. DOI: 10.1038/nature07720. View

Scull M, Rice C . A big role for small RNAs in influenza virus replication. Proc Natl Acad Sci U S A. 2010; 107(25):11153-4. PMC: 2895133. DOI: 10.1073/pnas.1006673107. View

Jagger B, Wise H, Kash J, Walters K, Wills N, Xiao Y . An overlapping protein-coding region in influenza A virus segment 3 modulates the host response. Science. 2012; 337(6091):199-204. PMC: 3552242. DOI: 10.1126/science.1222213. View

Fodor E, Pritlove D, Brownlee G . Characterization of the RNA-fork model of virion RNA in the initiation of transcription in influenza A virus. J Virol. 1995; 69(7):4012-9. PMC: 189134. DOI: 10.1128/JVI.69.7.4012-4019.1995. View

Gill J, Sheng Z, Ely S, Guinee D, Beasley M, Suh J . Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections. Arch Pathol Lab Med. 2010; 134(2):235-43. PMC: 2819217. DOI: 10.5858/134.2.235. View

de Wit E, Bestebroer T, Spronken M, Rimmelzwaan G, Osterhaus A, Fouchier R . Rapid sequencing of the non-coding regions of influenza A virus. J Virol Methods. 2006; 139(1):85-9. DOI: 10.1016/j.jviromet.2006.09.015. View

10.

Wise H, Hutchinson E, Jagger B, Stuart A, Kang Z, Robb N . Identification of a novel splice variant form of the influenza A virus M2 ion channel with an antigenically distinct ectodomain. PLoS Pathog. 2012; 8(11):e1002998. PMC: 3486900. DOI: 10.1371/journal.ppat.1002998. View

11.

Zhou B, Donnelly M, Scholes D, St George K, Hatta M, Kawaoka Y . Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J Virol. 2009; 83(19):10309-13. PMC: 2748056. DOI: 10.1128/JVI.01109-09. View

12.

Dias A, Bouvier D, Crepin T, McCarthy A, Hart D, Baudin F . The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature. 2009; 458(7240):914-8. DOI: 10.1038/nature07745. View

13.

Szymkowiak C, Kwan W, Su Q, Toner T, Shaw A, Youil R . Rapid method for the characterization of 3' and 5' UTRs of influenza viruses. J Virol Methods. 2002; 107(1):15-20. DOI: 10.1016/s0166-0934(02)00184-2. View

14.

Liang Y, Huang T, Ly H, Parslow T, Liang Y . Mutational analyses of packaging signals in influenza virus PA, PB1, and PB2 genomic RNA segments. J Virol. 2007; 82(1):229-36. PMC: 2224372. DOI: 10.1128/JVI.01541-07. View

15.

Engelhardt O, Smith M, Fodor E . Association of the influenza A virus RNA-dependent RNA polymerase with cellular RNA polymerase II. J Virol. 2005; 79(9):5812-8. PMC: 1082766. DOI: 10.1128/JVI.79.9.5812-5818.2005. View

16.

ROBERTSON J . 5' and 3' terminal nucleotide sequences of the RNA genome segments of influenza virus. Nucleic Acids Res. 1979; 6(12):3745-57. PMC: 327975. DOI: 10.1093/nar/6.12.3745. View

17.

Plotch S, Bouloy M, Ulmanen I, KRUG R . A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell. 1981; 23(3):847-58. DOI: 10.1016/0092-8674(81)90449-9. View

18.

Memoli M, Jagger B, Dugan V, Qi L, Jackson J, Taubenberger J . Recent human influenza A/H3N2 virus evolution driven by novel selection factors in addition to antigenic drift. J Infect Dis. 2009; 200(8):1232-41. PMC: 2778484. DOI: 10.1086/605893. View

19.

Furuse Y, Oshitani H . Evolution of the influenza A virus untranslated regions. Infect Genet Evol. 2011; 11(5):1150-4. DOI: 10.1016/j.meegid.2011.04.006. View

20.

Jagger B, Memoli M, Sheng Z, Qi L, Hrabal R, Allen G . The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. mBio. 2010; 1(1). PMC: 2912665. DOI: 10.1128/mBio.00067-10. View