Correlation of polymerase replication fidelity with genetic evolution of influenza A/Fujian/411/02(H3N2) viruses

Journal of Medical Virology

Volumn 83, Issue 3, 2011, Pages 510-516

  Wong, Karen Ka Yin ^a,b   Bull, Rowena A ^a   Rockman, Steve ^c   Scott, Gillian ^a,b   Stelzer Braid, Sacha ^a,b   Rawlinson, William ^a,b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b PRINCE OF WALES HOSPITAL   (Australia)

^c CSL LIMITED   (Australia)

Author keywords

Mutation frequencies; Polymerase; Sequencing based plaque assay

Indexed keywords

HEMAGGLUTININ; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA BASE; GENE FREQUENCY; GENETIC REASSORTMENT; GENETIC VARIABILITY; INFLUENZA VIRUS A H3N2; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA EXTRACTION; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS CULTURE; VIRUS ISOLATION; VIRUS REPLICATION; VIRUS STRAIN;

AMINO ACID SUBSTITUTION; CELL LINE; EVOLUTION, MOLECULAR; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H3N2 SUBTYPE; MUTATION; POLYMORPHISM, GENETIC; REASSORTANT VIRUSES; VIRAL NONSTRUCTURAL PROTEINS; VIRAL PROTEINS; VIRUS REPLICATION;

ORTHOMYXOVIRIDAE;

EID: 78851471998     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.21991     Document Type: Article

References (54)

1. Ansaldi F, Icardi G, Gasparini R, Campello C, Puzelli S, Bella A, Donatelli I, Salmaso S, Crovari P. 2005. New A/H3N2 influenza variant: A small genetic evolution but a heavy burden on the Italian population during the 2004-2005 season. J Clin Microbiol 43: 3027-3029.
2. Argos P. 1988. A sequence motif in many polymerases. Nucleic Acids Res 16: 9909-9916.
3. Barr I, Komadina N, Hurt A, Iannello P, Tomasov C, Shaw R, Durrant C, Sjogren H, Hampson A. 2005. An influenza A (H3) reassortant was epidemic in Australia and New Zealand in 2003. J Med Virol 76: 391-397.
4. Braam J, Ulmanen I, Krug R. 1983. Molecular model of a eukaryotic transcription complex: Functions and movements of influenza P proteins during capped RNA-primed transcription. Cell 34: 609-618.
5. Bull R, Eden J, Rawlinson W, White P. 2010. Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathog 6: e1000831.
6. Buonagurio D, Nakada S, Parvin J, Krystal M, Palese P, Fitch W. 1986. Evolution of human influenza A viruses over 50 years: Rapid, uniform rate of change in NS gene. Science 232: 980-982.
7. Chen W, Calvo P, Malide D, Gibbs J, Schubert U, Bacik I, Basta S, O'Neill R, Schickli J, Palese P, Henklein P, Bennink J, Yewdell J. 2001. A novel influenza A virus mitochondrial protein that induces cell death. Nat Med 7: 1306-1312.
8. Chen H, Subbarao K, Swayne D, Chen Q, Lu X, Katz J, Cox N, Matsuoka Y. 2003. Generation and evaluation of a high-growth reassortant H9N2 influenza A virus as a pandemic vaccine candidate. Vaccine 21: 1974-1979.
9. Chi X, Bolar T, Zhao P, Tam J, Rappaport R, Cheng S. 2005. Molecular evolution of human influenza A/H3N2 viruses in Asia and Europe from 2001 to 2003. J Clin Microbiol 43: 6130-6132.
10. Daum L, Shaw M, Klimov A, Canas L, Macias E, Niemeyer D, Chambers J, Renthal R, Shrestha S, Acharya R, Huzdar S, Rimal N, Myint K, Gould P. 2005. Influenza A (H3N2) outbreak, Nepal. Emerg Infect Dis 11: 1186-1191.
11. Detjen B, Angelo C, Katze M, Krug R. 1987. The three influenza virus polymerase (P) proteins not associated with viral nucleocapsids in the infected cell are in the form of a complex. J Virol 61: 16-22.
12. Domingo E, Escarmís C, Sevilla N, Moya A, Elena S, Quer J, Novella I, Holland J. 1996. Basic concepts in RNA virus evolution. FASEB J 10: 859-864.
13. Ferguson N, Galvani A, Bush R. 2003. Ecological and immunological determinants of influenza evolution. Nature 422: 428-433.
14. Hay A, Gregory V, Douglas A, Lin Y. 2001. The evolution of human influenza viruses. Philos Trans R Soc Lond B Biol Sci 356: 1861-1870.
15. Holmes E, Ghedin E, Miller N, Taylor J, Bao Y, St. George K, Grenfell B, Salzberg S, Fraser C, Lipman D, Taubenberger J. 2005. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3: 1579-1589.
16. Honda A, Mukaigawa J, Yokoiyama A, Kato A, Ueda S, Nagata K, Krystal M, Nayak D, Ishihama A. 1990. Purification and molecular structure of RNA polymerase from influenza virus A/PR8. J Biochem 107: 624-628.
17. Horimoto T, Kawaoka Y. 2005. Influenza: Lessons from past pandemics, warnings from current incidents. Nat Rev Microbiol 3: 591-600.
18. Johnson T, Barton N. 2002. The effect of deleterious alleles on adaptation in asexual populations. Genetics 162: 395-411.
19. Kang S, Yang I, Lee J, Park Y, Oh H, Kang C, Kim K. 2010. Epidemiologic study of human influenza infection in Korea from 1999 to 2007: Origin and evolution of A/Fujian/411/2002-like strains. J Clin Microbiol [Epub ahead of print].
20. Kawaoka Y, Krauss S, Webster R. 1989. Avian-to-human transmission of the PB1 gene of influenza A virus in the 1957 and 1968 pandemics. J Virol 63: 4603-4608.
21. Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
22. Klenk H, Rott R, Orlich M, Blodorn J. 1975. Activation of influenza A viruses by trypsin treatment. Virology 68: 426-439.
23. Koelle K, Cobey S, Grenfell B, Pascual M. 2006. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314: 1898-1903.
24. Krystal M, Buonagurio D, Young J, Palese P. 1983. Sequential mutations in the NS genes of influenza virus field strains. J Virol 45: 547-554.
25. Lindstrom S, Cox N, Klimov A. 2004. Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957-1972: Evidence for genetic divergence and multiple reassortment events. Virology 328: 101-119.
26. Ludwig S, Stitz L, Planz O, Van H, Fitch W, Scholtissek C. 1995. European swine virus as a possible source for the next influenza pandemic? Virology 212: 555-561.
27. Memoli M, Jagger B, Dugan V, Qi L, Jackson J, Taubenberger J. 2009. Recent human influenza A/H3N2 virus evolution driven by novel selection factors in addition to antigenic drift. J Infect Dis 200: 1232-1241.
28. Naffakh N, Massin P, Escriou N, Crescenzo-Chaigne B, Werf S. 2000. Genetic analysis of the compatibility between polymerase proteins from human and avian strains of influenza A viruses. J Gen Virol 81: 1283-1291.
29. Nobusawa E, Sato K. 2006. Comparison of the mutation rates of human influenza A and B viruses. J Virol 80: 3675-3678.
30. Orr H. 2000. The rate of adaptation in asexuals. Genetics 155: 961-968.
31. Palese P, Schulman J. 1974. Isolation and characterization of influenza virus recombinants with high and low neuraminidase activity. Use of 2-(3'-methoxyphenyl)-n-acetylneuraminic acid to identify cloned populations. Virology 57: 227-237.
32. Parvin J, Moscona A, Pan W, Leider J, Palese P. 1986. Measurement of the mutation rates of animal viruses: Influenza A virus and poliovirus type I. J Virol 59: 377-383.
33. Parvin J, Palese P, Honda A, Ishihama A, Krystal M. 1989. Promoter analysis of influenza virus RNA polymerase. J Virol 63: 5142-5152.
34. Pfeiffer J, Kirkegaard K. 2005. Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice. PLoS Pathog 1: e11.
35. Plotkin J, Dushoff J, Levin S. 2002. Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proc Natl Acad Sci USA 99: 6263-6268.
36. Russell C, Jones T, Barr I, Cox N, Garten R, Gregory V, Gust I, Hampson A, Hay A, Hurt A, de Jong J, Kelso A, Klimov A, Kageyama T, Komadina N, Lapedes A, Lin Y, Mosterin A, Obuchi M, Odagiri T, Osterhaus A, Rimmelzwaan G, Shaw M, Skepner E, Stohr K, Tashiro M, Fouchier R, Smith D. 2008. The global circulation of seasonal influenza A (H3N2) viruses. Science 320: 340-346.
37. Schweiger B, Bruns L, Meixenberger K. 2006. Reassortment between human A (H3N2) viruses is an important evolutionary mechanism. Vaccine 24: 6683-6690.
38. Shih A, Hsiao T, Ho M, Li W. 2007. Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci USA 104: 6283-6288.
39. Sierra M, Airaksinen A, González-López C, Agudo R, Arias A, Domingo E. 2007. Foot-and-mouth disease virus mutant with decreased sensitivity to ribavirin: Implications for error catastrophe. J Virol 81: 2012-2024.
40. Smith D, Lapedes A, de Jong J, Bestebroer T, Rimmelzwaan G, Osterhaus A, Fouchier R. 2004. Mapping the antigenic and genetic evolution of influenza virus. Science 305: 371-376.
41. Stech J, Xiong X, Scholtissek C, Webster R. 1999. Independence of evolutionary and mutational rates after transmission of avian influenza viruses to swine. J Virol 73: 1878-1884.
42. Steinhauer D, Domingo E, Holland J. 1992. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 122: 281-288.
43. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
44. Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, Fanning T. 2005. Characterization of the 1918 influenza virus polymerase genes. Nature 437: 889-893.
45. Ulmanen I, Broni B, Krug R. 1981. Role of two of the influenza virus core P proteins in recognising cap 1 structures (m7GpppNm) on RNAs and in initiating viral RNA transcription. Proc Natl Acad Sci USA 78: 7355-7359.
46. Vignuzzi M, Stone J, Andino R. 2005. Ribavirin and lethal mutagenesis of poliovirus: Molecular mechanisms, resistance and biological implications. Virus Res 107: 173-181.
47. Vignuzzi M, Stone J, Arnold J, Cameron C, Andino R. 2006. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439: 344-348.
48. Vignuzzi M, Wendt E, Andino R. 2008. Engineering attentuated virus vaccines by controlling replication fidelity. Nat Med 14: 154-160.
49. Webster R, Kendal A, Gerhard W. 1979. Analysis of antigenic drift in recently isolated influenza A(H1N1) viruses using monoclonal antibodies preparation. Virology 96: 258-264.
50. Wiley D, Wilson I, Skehel J. 1981. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature 289: 373-378.
51. Wise H, Foeglein A, Sun J, Dalton R, Patel S, Howard W, Anderson E, Barclay W, Digard P. 2009. A complicated message: Identification of a novel PB1-related protein translated from influenza A virus segment 2 mRNA. J Virol 83: 8021-8031.
52. Wolf Y, Viboud C, Holmes E, Koonin E, Lipman D. 2006. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 1: 34.
53. Zamarin D, García-Sastre A, Xiao X, Wang R, Palese P. 2005. Influenza virus PB1-F2 protein induces cell death through mitochondrial ANT3 and VDAC1. PLoS Pathog 1: e4.
54. Zhou N, Senne D, Landgraf J, Swenson S, Erickson G, Rossow K, Liu L, Yoon K, Krauss S, Webster R. 1999. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J Virol 73: 8851-8856.