575
Views
6
CrossRef citations to date
0
Altmetric
Research Paper

Possibility of cross-species/subtype reassortments in influenza A viruses

An analysis of nonstructural protein variations

&
Pages 716-725 | Received 18 Jun 2013, Accepted 25 Sep 2013, Published online: 08 Oct 2013

References

  • Yang JR, Lin YC, Huang YP, Su CH, Lo J, Ho YL, Yao CY, Hsu LC, Wu HS, Liu MT. Reassortment and mutations associated with emergence and spread of oseltamivir-resistant seasonal influenza A/H1N1 viruses in 2005-2009. PLoS One 2011; 6:e18177; http://dx.doi.org/10.1371/journal.pone.0018177; PMID: 21483816
  • Christman MC, Kedwaii A, Xu J, Donis RO, Lu G. Pandemic (H1N1) 2009 virus revisited: an evolutionary retrospective. Infect Genet Evol 2011; 11:803 - 11; http://dx.doi.org/10.1016/j.meegid.2011.02.021; PMID: 21382522
  • Ducatez MF, Hause B, Stigger-Rosser E, Darnell D, Corzo C, Juleen K, Simonson R, Brockwell-Staats C, Rubrum A, Wang D, et al. Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis 2011; 17:1624 - 9; PMID: 21892996
  • Bokhari SH, Pomeroy LW, Janies DA. Reassortment Networks and the evolution of pandemic H1N1 swine-origin influenza. IEEE/ACM Trans Comput Biol Bioinform 2012; 9:214 - 27; http://dx.doi.org/10.1109/TCBB.2011.95; PMID: 22076498
  • Michaelis M, Doerr HW, Cinatl J Jr.. Of chickens and men: avian influenza in humans. Curr Mol Med 2009; 9:131 - 51; http://dx.doi.org/10.2174/156652409787581565; PMID: 19275623
  • Amendola A, Ranghiero A, Zanetti A, Pariani E. Is avian influenza virus A(H5N1) a real threat to human health?. J Prev Med Hyg 2011; 52:107 - 10; PMID: 22010536
  • Li C, Hatta M, Watanabe S, Neumann G, Kawaoka Y. Compatibility among polymerase subunit proteins is a restricting factor in reassortment between equine H7N7 and human H3N2 influenza viruses. J Virol 2008; 82:11880 - 8; http://dx.doi.org/10.1128/JVI.01445-08; PMID: 18815312
  • Mehle A, Dugan VG, Taubenberger JK, Doudna JA. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol 2012; 86:1750 - 7; http://dx.doi.org/10.1128/JVI.06203-11; PMID: 22090127
  • Noda T, Sugita Y, Aoyama K, Hirase A, Kawakami E, Miyazawa A, Sagara H, Kawaoka Y. Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus. Nat Commun 2012; 3:639; http://dx.doi.org/10.1038/ncomms1647; PMID: 22273677
  • Sarkar M, Chanda S, Chakrabarti S, Mazumdar J, Ganguly A, Chadha MS, Mishra AC, Chawla-Sarkar M. Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. Virol J 2012; 9:3; http://dx.doi.org/10.1186/1743-422X-9-3; PMID: 22217077
  • Yurovsky A, Moret BM. FluReF, an automated flu virus reassortment finder based on phylogenetic trees. BMC Genomics 2011; 12:Suppl 2 S3; http://dx.doi.org/10.1186/1471-2164-12-S2-S3; PMID: 21989112
  • Greenbaum BD, Li OT, Poon LL, Levine AJ, Rabadan R. Viral reassortment as an information exchange between viral segments. Proc Natl Acad Sci U S A 2012; 109:3341 - 6; http://dx.doi.org/10.1073/pnas.1113300109; PMID: 22331898
  • Wu G, Yan S. Randomness in the primary structure of protein: methods and implications. Mol Biol Today 2002; 3:55 - 69
  • Wu G, Yan SM. Mutation trend of hemagglutinin of influenza A virus: a review from a computational mutation viewpoint. Acta Pharmacol Sin 2006; 27:513 - 26; http://dx.doi.org/10.1111/j.1745-7254.2006.00329.x; PMID: 16626505
  • Wu G, Yan S. Lecture Notes on Computational Mutation. New York: Nova Science Publishers, 2008:1-130.
  • Yan S, Wu G. Creation and application of computational mutation. J Guangxi Acad Sci 2010; 17:145 - 50
  • Yan SM, Wu G. Rationale for cross-species infection and cross-subtype mutation in hemagglutinins from influenza A virus. Interdiscip Sci 2009; 1:303 - 7; http://dx.doi.org/10.1007/s12539-009-0068-1; PMID: 20640809
  • Yan S, Wu G. Determination of inter- and intra-subtype variations in polymerase acidic protein from influenza A virus using amino-acid pair predictability. J Biomed Sci Eng 2009; 2:273 - 9; http://dx.doi.org/10.4236/jbise.2009.24041
  • Yan S, Wu G. Evidence obtained from ANOVA to reason cross-species infection and cross-subtype mutation in neuraminidases of influenza A viruses. Transbound Emerg Dis 2010; 57:254 - 61; PMID: 20545912
  • Yan S, Wu G. Evidence for cross-species infections and cross-subtype mutations in influenza a matrix proteins. Viral Immunol 2010; 23:105 - 11; http://dx.doi.org/10.1089/vim.2009.0080; PMID: 20121408
  • Yan SM, Zuo WP, Zhu QX, Huang YY, Pan LX, Wu G. Statistical evidence for cross-species infection and cross-subtype mutation in matrix protein 2 family of influenza A virus. J Guangxi Acad Sci 2010; 26:45 - 51
  • Yan SM, Wu G. Reasons for cross-species infection and cross-subtype reassortment in nucleoproteins from influenza A virus. Proceedings of the 5th International Conference on Bioinformatics and Biomedical Engineering 2011; IEEE Xplore 978-1-4244-5089-3/11.
  • Yan S, Wu G. Possible reason for cross-species and cross-subtype reassortment in polymerase basic protein 2 from influenza A virus. Protein Pept Lett 2011; 18:434 - 9; http://dx.doi.org/10.2174/092986611794927956; PMID: 21171947
  • Yan S, Wu G. Small variations between species/subtypes attributed to reassortment evidenced from polymerase basic protein 1 with other seven proteins from influenza a virus. Transbound Emerg Dis 2013; 60:110 - 9; http://dx.doi.org/10.1111/j.1865-1682.2012.01323.x; PMID: 22462488
  • Hale BG, Randall RE, Ortín J, Jackson D. The multifunctional NS1 protein of influenza A viruses. J Gen Virol 2008; 89:2359 - 76; http://dx.doi.org/10.1099/vir.0.2008/004606-0; PMID: 18796704
  • Salahuddin P, Khan AU. Structural and functional analysis of NS1 and NS2 proteins of H1N1 subtype. Genomics Proteomics Bioinformatics 2010; 8:190 - 9; http://dx.doi.org/10.1016/S1672-0229(10)60021-6; PMID: 20970747
  • Bavagnoli L, Dundon WG, Garbelli A, Zecchin B, Milani A, Parakkal G, Baldanti F, Paolucci S, Volmer R, Tu Y, et al. The PDZ-ligand and Src-homology type 3 domains of epidemic avian influenza virus NS1 protein modulate human Src kinase activity during viral infection. PLoS One 2011; 6:e27789; http://dx.doi.org/10.1371/journal.pone.0027789; PMID: 22110760
  • Munir M, Zohari S, Belák S, Berg M. Double-stranded RNA-induced activation of activating protein-1 promoter is differentially regulated by the non-structural protein 1 of avian influenza A viruses. Viral Immunol 2012; 25:79 - 85; PMID: 22239235
  • Pavesi A. Pattern of nucleotide substitution in the overlapping nonstructural genes of influenza A virus and implication for the genetic diversity of the H5N1 subtype. Gene 2007; 402:28 - 34; http://dx.doi.org/10.1016/j.gene.2007.07.013; PMID: 17825505
  • Hrincius ER, Hennecke AK, Gensler L, Nordhoff C, Anhlan D, Vogel P, McCullers JA, Ludwig S, Ehrhardt C. A single point mutation (Y89F) within the non-structural protein 1 of influenza A viruses limits epithelial cell tropism and virulence in mice. Am J Pathol 2012; 180:2361 - 74; http://dx.doi.org/10.1016/j.ajpath.2012.02.029; PMID: 22525464
  • Fernandez-Sesma A. The influenza virus NS1 protein: inhibitor of innate and adaptive immunity. Infect Disord Drug Targets 2007; 7:336 - 43; http://dx.doi.org/10.2174/187152607783018754; PMID: 18220965
  • Robb NC, Smith M, Vreede FT, Fodor E. NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome. J Gen Virol 2009; 90:1398 - 407; http://dx.doi.org/10.1099/vir.0.009639-0; PMID: 19264657
  • Shimizu T, Takizawa N, Watanabe K, Nagata K, Kobayashi N. Crucial role of the influenza virus NS2 (NEP) C-terminal domain in M1 binding and nuclear export of vRNP. FEBS Lett 2011; 585:41 - 6; http://dx.doi.org/10.1016/j.febslet.2010.11.017; PMID: 21081124
  • Schickli JH, Flandorfer A, Nakaya T, Martinez-Sobrido L, García-Sastre A, Palese P. Plasmid-only rescue of influenza A virus vaccine candidates. Philos Trans R Soc Lond B Biol Sci 2001; 356:1965 - 73; http://dx.doi.org/10.1098/rstb.2001.0979; PMID: 11779399
  • De Clercq E, Neyts J. Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention. Trends Pharmacol Sci 2007; 28:280 - 5; http://dx.doi.org/10.1016/j.tips.2007.04.005; PMID: 17481739
  • Lee JH, Oh JY, Pascua PN, Kim EG, Choi YK, Kim HK. Impairment of the Staufen1-NS1 interaction reduces influenza viral replication. Biochem Biophys Res Commun 2011; 414:153 - 8; http://dx.doi.org/10.1016/j.bbrc.2011.09.042; PMID: 21945618
  • Akarsu H, Iwatsuki-Horimoto K, Noda T, Kawakami E, Katsura H, Baudin F, Horimoto T, Kawaoka Y. Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. Virus Res 2011; 155:240 - 8; http://dx.doi.org/10.1016/j.virusres.2010.10.014; PMID: 20970464
  • Van Kerkhove MD, Mumford E, Mounts AW, Bresee J, Ly S, Bridges CB, Otte J. Highly pathogenic avian influenza (H5N1): pathways of exposure at the animal-human interface, a systematic review. PLoS One 2011; 6:e14582; http://dx.doi.org/10.1371/journal.pone.0014582; PMID: 21283678
  • Dundon WG. Variability among the neuraminidase, non-structural 1 and PB1-F2 proteins in the influenza A virus genome. Virus Genes 2012; 44:363 - 73; http://dx.doi.org/10.1007/s11262-012-0714-0; PMID: 22261818
  • Pepin KM, Lass S, Pulliam JR, Read AF, Lloyd-Smith JO. Identifying genetic markers of adaptation for surveillance of viral host jumps. Nat Rev Microbiol 2010; 8:802 - 13; http://dx.doi.org/10.1038/nrmicro2440; PMID: 20938453
  • Bogoyavlenskiy A, Berezin V, Prilipov A, Korotetskiy I, Zaitseva I, Kydyrmanov A, Karamedin K, Ishmukhametova N, Asanova S, Sayatov M, et al. Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated in Kazakhstan in 2002-2009. Virol Sin 2011; 26:376 - 85; http://dx.doi.org/10.1007/s12250-011-3208-7; PMID: 22160937
  • Ma W, Lager KM, Lekcharoensuk P, Ulery ES, Janke BH, Solórzano A, Webby RJ, García-Sastre A, Richt JA. Viral reassortment and transmission after co-infection of pigs with classical H1N1 and triple-reassortant H3N2 swine influenza viruses. J Gen Virol 2010; 91:2314 - 21; http://dx.doi.org/10.1099/vir.0.021402-0; PMID: 20484565
  • Hoelzer K, Murcia PR, Baillie GJ, Wood JL, Metzger SM, Osterrieder N, Dubovi EJ, Holmes EC, Parrish CR. Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs. J Virol 2010; 84:5329 - 35; http://dx.doi.org/10.1128/JVI.02469-09; PMID: 20219907
  • Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, Mumford JA, Newton R, Parrish CR, Hoelzer K, Dougan G, et al. Intra- and interhost evolutionary dynamics of equine influenza virus. J Virol 2010; 84:6943 - 54; http://dx.doi.org/10.1128/JVI.00112-10; PMID: 20444896
  • Darapaneni V, Prabhaker VK, Kukol A. Large-scale analysis of influenza A virus sequences reveals potential drug target sites of non-structural proteins. J Gen Virol 2009; 90:2124 - 33; http://dx.doi.org/10.1099/vir.0.011270-0; PMID: 19420157
  • Kreijtz JH, Fouchier RA, Rimmelzwaan GF. Immune responses to influenza virus infection. Virus Res 2011; 162:19 - 30; http://dx.doi.org/10.1016/j.virusres.2011.09.022; PMID: 21963677
  • Qiu C, Huang Y, Wang Q, Tian D, Zhang W, Hu Y, Yuan Z, Zhang X, Xu J. Boosting heterosubtypic neutralization antibodies in recipients of 2009 pandemic H1N1 influenza vaccine. Clin Infect Dis 2012; 54:17 - 24; http://dx.doi.org/10.1093/cid/cir753; PMID: 22052887
  • Zhou GP, Assa-Munt N. Some insights into protein structural class prediction. Proteins: Struct, Func. Genet 2001; 44:57 - 9
  • Chou KC, Zhang CT. Prediction of protein structural classes. Crit Rev Biochem Mol Biol 1995; 30:275 - 349; http://dx.doi.org/10.3109/10409239509083488; PMID: 7587280
  • Zhou GP, Troy FA 2nd. NMR studies on how the binding complex of polyisoprenol recognition sequence peptides and polyisoprenols can modulate membrane structure. Curr Protein Pept Sci 2005; 6:399 - 411; http://dx.doi.org/10.2174/138920305774329377; PMID: 16248792
  • Chou KC. Structural bioinformatics and its impact to biomedical science. Curr Med Chem 2004; 11:2105 - 34; http://dx.doi.org/10.2174/0929867043364667; PMID: 15279552
  • Sharma AK, Zhou GP, Kupferman J, Surks HK, Christensen EN, Chou JJ, Mendelsohn ME, Rigby AC. Probing the interaction between the coiled coil leucine zipper of cGMP-dependent protein kinase Ialpha and the C terminus of the myosin binding subunit of the myosin light chain phosphatase. J Biol Chem 2008; 283:32860 - 9; http://dx.doi.org/10.1074/jbc.M804916200; PMID: 18782776
  • Zhou GP, Surks HK, Schnell JR, Chou JJ, Michael E, Mendelsohn ME, Rigby AC. The three-dimensional structure of the cGMP-dependent protein kinase I-α leucine zipper domain and its interaction with the myosin binding subunit. Blood 2004; 104:963a
  • Chou KC, Zhou GP. Role of the protein outside active site on the diffusion-controlled reaction of enzyme. J Am Chem Soc 1982; 104:1409 - 13; http://dx.doi.org/10.1021/ja00369a043
  • Zhou GP, Li TT, Chou KC. The flexibility during the juxtaposition of reacting groups and the upper limits of enzyme reactions. Biophys Chem 1981; 14:277 - 81; http://dx.doi.org/10.1016/0301-4622(81)85028-4; PMID: 7326350
  • Qi JP, Shao SH, Li DD, Zhou GP. A dynamic model for the p53 stress response networks under ion radiation. Amino Acids 2007; 33:75 - 83; http://dx.doi.org/10.1007/s00726-006-0454-3; PMID: 17072789
  • Zhou GP. Biological functions of soliton and extra electron motion in DNA structure. Phys Scr 1989; 40:698 - 701; http://dx.doi.org/10.1088/0031-8949/40/5/021
  • Chou KC. Low-frequency collective motion in biomacromolecules and its biological functions. Biophys Chem 1988; 30:3 - 48; http://dx.doi.org/10.1016/0301-4622(88)85002-6; PMID: 3046672
  • Chou KC. The biological functions of low-frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers 1987; 26:285 - 95; http://dx.doi.org/10.1002/bip.360260209; PMID: 3828475
  • Zhou GP, Cai YD. Predicting protease types by hybridizing gene ontology and pseudo amino acid composition Proteins Struct, Func. Bioinformat 2006; 63:681 - 4
  • Cai YD, Zhou GP, Chou KC. Support vector machines for predicting membrane protein types by using functional domain composition. Biophys J 2003; 84:3257 - 63; http://dx.doi.org/10.1016/S0006-3495(03)70050-2; PMID: 12719255
  • Zhou GP, Huang RB. The pH-triggered conversion of the PrP(c) to PrP(sc.). Curr Top Med Chem 2013; 13:1152 - 63; http://dx.doi.org/10.2174/15680266113139990003; PMID: 23647538
  • Bjorndahl TC, Zhou GP, Liu XH, Perez-Pineiro R, Semenchenko V, Saleem F, Acharya S, Bujold A, Sobsey CA, Wishart DS. Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process. Biochemistry 2011; 50:1162 - 73; http://dx.doi.org/10.1021/bi101435c; PMID: 21189021
  • Zhou GP. The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism. J Theor Biol 2011; 284:142 - 8; http://dx.doi.org/10.1016/j.jtbi.2011.06.006; PMID: 21718705
  • Zhou GP. The structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase Iα and its interaction with the myosin binding subunit of the myosin light chains phosphase. Protein Pept Lett 2011; 18:966 - 78; http://dx.doi.org/10.2174/0929866511107010966; PMID: 21592084
  • National Center for Biotechnology Information. Influenza virus resources. 2013; http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/multiple.cgi.
  • Furuse Y, Suzuki A, Kamigaki T, Oshitani H. Evolution of the M gene of the influenza A virus in different host species: large-scale sequence analysis. Virol J 2009; 6:67 - 79; http://dx.doi.org/10.1186/1743-422X-6-67; PMID: 19476650
  • Wu G, Yan S. Fate of influenza A virus proteins. Protein Pept Lett 2006; 13:377 - 84; http://dx.doi.org/10.2174/092986606775974474; PMID: 16712514
  • Wu G, Yan S. Prediction of mutations engineered by randomness in H5N1 neuraminidases from influenza A virus. Amino Acids 2008; 34:81 - 90; http://dx.doi.org/10.1007/s00726-007-0579-z; PMID: 17721674
  • Wu G, Yan S. Prediction of mutations in H3N2 hemagglutinins of influenza A virus from North America based on different datasets. Protein Pept Lett 2008; 15:144 - 52; http://dx.doi.org/10.2174/092986608783489571; PMID: 18289106
  • Wu G, Yan S. Three sampling strategies to predict mutations in H5N1 hemagglutitins from influenza A virus. Protein Pept Lett 2008; 15:731 - 8; http://dx.doi.org/10.2174/092986608785133735; PMID: 18782070
  • Yan SM, Wu G. Prediction of mutation position, mutated amino acid and timing in hemagglutinins from North America H1 influenza A virus. J Biomed Sci Eng 2009; 2:117 - 22; http://dx.doi.org/10.4236/jbise.2009.22021
  • Yan S, Wu G. Prediction of mutation positions in H5N1 neuraminidases from influenza A virus by means of neural network. Ann Biomed Eng 2010; 38:984 - 92; http://dx.doi.org/10.1007/s10439-010-9907-7; PMID: 20336836
  • Spackman E. A brief introduction to the avian influenza virus. Methods Mol Biol 2008; 436:1 - 6; PMID: 18370034
  • Sokal RR, Rohlf FJ. Biometry: The Principles and Practices of Statistics in Biological Research. 3nd ed. New York: W. H. Freeman, 1995:203-17.
  • Wu G, Baraldo M, Furlanut M. Inter-patient and intra-patient variations in the baseline tapping test in patients with Parkinson’s disease. Acta Neurol Belg 1999; 99:182 - 4; PMID: 10544726

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.