Genomic and evolutionary characterization of a novel influenza-C-like virus from swine

Archives of Virology

Volumn 159, Issue 2, 2014, Pages 249-255

  Sheng, Zizhang ^a   Ran, Zhiguang ^a   Wang, Dan ^a   Hoppe, Adam D ^a   Simonson, Randy ^b   Chakravarty, Suvobrata ^a   Hause, Ben M ^a,b   Li, Feng ^a,c  

^a SOUTH DAKOTA STATE UNIVERSITY   (United States)

^b Newport Laboratories   (United States)

^c SHANDONG PEANUT RESEARCH INSTITUTE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; INFLUENZA VIRUS C; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ORTHOMYXOVIRUS INFECTION; PHYLOGENY; SWINE; SWINE DISEASE; UNITED STATES; VIROLOGY;

ANIMALS; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; INFLUENZAVIRUS C; MOLECULAR SEQUENCE DATA; OKLAHOMA; ORTHOMYXOVIRIDAE INFECTIONS; PHYLOGENY; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SWINE; SWINE DISEASES;

EID: 84895075229     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-013-1815-3     Document Type: Article

References (30)

1. Boivin S, Cusack S, Ruigrok RWH, Hart DJ (2010) Influenza A virus polymerase: structural insights into replication and host adaptation mechanisms. J Biol Chem 285: 28411-28417.
2. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
3. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
4. Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277: 396-404.
5. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. Chapter 2: Unit 2. 9.
6. Gambaryan AS, Marinina VP, Tuzikov AB, Bovin NV, Rudneva IA, Sinitsyn BV, Shilov AA, Matrosovich MN (1998) 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 247: 170-177.
7. Gatherer D (2010) Tempo and mode in the molecular evolution of influenza C. PLoS Curr 2: RRN1199.
8. Guilligay D, Tarendeau F, Resa-Infante P, Coloma R, Crepin T, Sehr P, Lewis J, Ruigrok RW, Ortin J, Hart DJ, Cusack S (2008) The structural basis for cap binding by influenza virus polymerase subunit PB2. Nat Struct Mol Biol 15: 500-506.
9. Guo YJ, Jin FG, Wang P, Wang M, Zhu JM (1983) Isolation of influenza C virus from pigs and experimental infection of pigs with influenza C virus. J Gen Virol 64(Pt 1): 177-182.
10. Hause BM, Ducatez M, Collin EA, Ran Z, Liu R, Sheng Z, Armien A, Kaplan B, Chakravarty S, Hoppe AD, Webby RJ, Simonson RR, Li F (2013) Isolation of a Novel Swine Influenza Virus from Oklahoma in 2011 Which Is Distantly Related to Human Influenza C Viruses. PLoS pathog 9: e1003176.
11. He XJ, Zhou J, Bartlam M, Zhang RG, Ma JY, Lou ZY, Li XM, Li JJ, Joachimiak A, Zeng ZH, Ge RW, Rao ZH, Liu YF (2008) Crystal structure of the polymerase PA(C)-PB1(N) complex from an avian influenza H5N1 virus. Nature 454: 1123-1126.
12. Ito T, Kawaoka Y, Vines A, Ishikawa H, Asai T, Kida H (1998) Continued circulation of reassortant H1N2 influenza viruses in pigs in Japan. Arch Virol 143: 1773-1782.
13. Kall L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027-1036.
14. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580.
15. Osterhaus ADME, Rimmelzwaan GF, Martina BEE, Bestebroer TM, Fouchier RAM (2000) Influenza B virus in seals. Science 288: 1051-1053.
16. Palese PSM (2007) Orthomyxoviridae: The viruses and their replication. In: Knipe DM, Howley PM (eds) Fields Virology, 5th edn. Lippincott Williams & Wilkins, Philadelphia, pp 1647-1690.
17. Pease CM (1987) An evolutionary epidemiological mechanism, with applications to type A influenza. Theor Popul Biol 31: 422-452.
18. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4. 0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
19. Poeppl W, Hell M, Herkner H, Stoiser B, Fritsche G, Schurz-Bamieh N, Poeppl G, Gattringer R, Jones N, Maass M, Egle A, Burgmann H (2011) Clinical aspects of 2009 pandemic influenza A (H1N1) virus infection in Austria. Infection 39: 341-352.
20. Pond SLK, Posada D, Gravenor MB, Woelk CH, Frost SDW (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 23: 1891-1901.
21. Schulze IT (1997) Effects of glycosylation on the properties and functions of influenza virus hemagglutinin. J Infect Dis 176(Suppl 1): S24-S28.
22. Sun SS, Wang QZ, Zhao F, Chen WT, Li Z (2011) Glycosylation Site Alteration in the Evolution of Influenza A (H1N1) Viruses. PLoS One 6(7): e22844.
23. Szepanski S, Veit M, Pleschka S, Klenk HD, Schmidt MF, Herrler G (1994) Post-translational folding of the influenza C virus glycoprotein HEF: defective processing in cells expressing the cloned gene. J Gen Virol 75(Pt 5): 1023-1030.
24. Takashita E, Muraki Y, Sugawara K, Asao H, Nishimura H, Suzuki K, Tsuji T, Hongo S, Ohara Y, Kawaoka Y, Ozawa M, Matsuzaki Y (2012) Intrinsic temperature sensitivity of influenza C virus hemagglutinin-esterase-fusion protein. J Virol 86: 13108-13111.
25. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
26. Tarendeau F, Boudet J, Guilligay D, Mas PJ, Bougault CM, Boulo S, Baudin F, Ruigrok RWH, Daigle N, Ellenberg J, Cusack S, Simorre JP, Hart DJ (2007) Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit. Nat Struct Mol Biol 14: 229-233.
27. Tong S, Li Y, Rivailler P, Conrardy C, Castillo DA, Chen LM, Recuenco S, Ellison JA, Davis CT, York IA, Turmelle AS, Moran D, Rogers S, Shi M, Tao Y, Weil MR, Tang K, Rowe LA, Sammons S, Xu X, Frace M, Lindblade KA, Cox NJ, Anderson LJ, Rupprecht CE, Donis RO (2012) A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci USA 109(11): 4269-4274.
28. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56: 152-179.
29. Yamashita M, Krystal M, Fitch WM, Palese P (1988) Influenza B virus evolution: co-circulating lineages and comparison of evolutionary pattern with those of influenza A and C viruses. Virology 163: 112-122.
30. Yuan PW, Bartlam M, Lou ZY, Chen SD, Zhou J, He XJ, Lv ZY, Ge RW, Li XM, Deng T, Fodor E, Rao ZH, Liu YF (2009) Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site. Nature 458: 909-913.