Phylogenetic patterns of the three polymerase (PB2, PB1 and PA) genes of a total of 20 influenza B viruses isolated during a 58 year period, 1940–1998, were analysed in detail in a parallel manner. All three polymerase genes consistently showed evolutionary divergence into two major distinct lineages and their amino acid profiles demonstrated conserved lineage-specific substitutions. Dendrogram topologies of the PB2 and PB1 genes were very similar and contrasted with that of the PA gene. It was of particular interest to reveal that even though the PA gene evolved into two major lineages, that of three recent Asian Victoria/1/87-like strains formed a branch cluster located in the same lineage as that of recent Yamagata/16/88-like isolates. Differences in the phylogenetic pathways of three polymerase genes were not only a reflection of genetic reassortment between co-circulating influenza B viruses, but also an indication that the polymerase genes were not co-evolving as a unit. As a result, comparison of the phylogenetic patterns of the three polymerase genes with previously determined patterns of the HA, NP, M and NS genes of 18 viruses defined the existence of eight distinct genome constellations. Also, similar phylogenetic profiles among the PA, NP and M genes, as well as between the PB2 and PB1 genes, were observed, suggesting possible functional interactions among these proteins. Completion of evolutionary analysis of the six internal genes and the HA gene of influenza B viruses revealed frequent genetic reassortment among co-circulating variable strains and suggested co-dependent evolution of genes.


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  1. Akoto-Amanfu, E., Sivasubramanian, N. & Nayak, D. P. (1987). Primary structure of the polymerase acidic (PA) gene of an influenza B virus (B/Sing/222/79).Virology 159, 147-153.[CrossRef] [Google Scholar]
  2. Biswas, S. K. & Nayak, D. P. (1994). Mutational analysis of the conserved motifs of influenza A virus polymerase basic protein 1.Journal of Virology 68, 1819-1826. [Google Scholar]
  3. Biswas, S. K. & Nayak, D. P. (1996). Influenza virus polymerase basic protein 1 interacts with influenza virus polymerase basic protein 2 at multiple sites.Journal of Virology 70, 6716-6722. [Google Scholar]
  4. Braam, J., Ulmanen, I. & Krug, R. M. (1983). Molecular model of a eucaryotic transcription complex: functions and movements of influenza P proteins during capped RNA-primed transcription.Cell 34, 609-618. [Google Scholar]
  5. Buonagurio, D. A., Nakada, S., Parvin, J. D., Krystal, M., Palese, P. & Fitch, W. M. (1986). Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in the NS gene.Science 232, 980-982.[CrossRef] [Google Scholar]
  6. Burmeister, W. P., Baudin, F., Cusack, S. & Ruigrok, R. W. (1993). Comparison of structure and sequence of influenza B/Yamagata and B/Beijing neuraminidases shows a conserved ‘head’ but much greater variability in the ‘stalk’ and NB protein.Virology 192, 683-686.[CrossRef] [Google Scholar]
  7. DeBorde, D. C., Naeve, C. W., Herlocher, M. L. & Maassab, H. F. (1987). Nucleotide sequences of the PA and PB1 genes of B/Ann Arbor/ 1/66 virus: comparison with genes of B/Lee/40 and type A influenza viruses.Virus Research 8, 33-41.[CrossRef] [Google Scholar]
  8. DeBorde, D. C., Donabedian, A. M., Herlocher, M. L., Naeve, C. W. & Maassab, H. F. (1988). Sequence comparison of wild-type and cold-adapted B/Ann Arbor/1/66 influenza virus genes.Virology 163, 429-443.[CrossRef] [Google Scholar]
  9. Detjen, B. M., St Angelo, C., Katze, M. G. & Krug, R. M. (1987). The three influenza virus polymerase (P) proteins not associated with viral nucleocapsids in the infected cell are in the form of a complex.Journal of Virology 61, 16-22. [Google Scholar]
  10. Digard, P., Blok, V. C. & Inglis, S. C. (1989). Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes.Virology 171, 162-169.[CrossRef] [Google Scholar]
  11. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap.Evolution 39, 783-791.[CrossRef] [Google Scholar]
  12. Felsenstein, J. (1995). PHYLIP (Phylogeny Inference Package) version 3.57c, Distributed by the author. Department of Genetics, University of Washington, Seattle, WA, USA.
  13. Gojobori, T., Ishii, K. & Nei, M. (1982). Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide.Journal of Molecular Evolution 18, 414-423.[CrossRef] [Google Scholar]
  14. Gonzalez, S. & Ortin, J. (1999a). Characterization of influenza virus PB1 protein binding to viral RNA: two separate regions of the protein contribute to the interaction domain.Journal of Virology 73, 631-637. [Google Scholar]
  15. Gonzalez, S. & Ortin, J. (1999b). Distinct regions of influenza virus PB1 polymerase subunit recognize vRNA and cRNA templates.EMBO Journal 18, 3767-3775.[CrossRef] [Google Scholar]
  16. Gonzalez, S., Zurcher, T. & Ortin, J. (1996). Identification of two separate domains in the influenza virus PB1 protein involved in the interaction with the PB2 and PA subunits: a model for the viral RNA polymerase structure.Nucleic Acids Research 24, 4456-4463.[CrossRef] [Google Scholar]
  17. Gorman, O. T., Donis, R. O., Kawaoka, Y. & Webster, R. G. (1990). Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus.Journal of Virology 64, 4893-4902. [Google Scholar]
  18. Honda, A., Mukaigawa, J., Yokoiyama, A., Kato, A., Ueda, S., Nagata, K., Krystal, M., Nayak, D. P. & Ishihama, A. (1990). Purification and molecular structure of RNA polymerase from influenza virus A/PR8.Journal of Biochemistry (Tokyo) 107, 624-628. [Google Scholar]
  19. Ito, T., Gorman, O. T., Kawaoka, Y., Bean, W. J. & Webster, R. G. (1991). Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins.Journal of Virology 65, 5491-5498. [Google Scholar]
  20. Jambrina, E., Barcena, J., Uez, O. & Portela, A. (1997). The three subunits of the polymerase and the nucleoprotein of influenza B virus are the minimum set of viral proteins required for expression of a model RNA template.Virology 235, 209-217.[CrossRef] [Google Scholar]
  21. Kanegae, Y., Sugita, S., Endo, A., Ishida, M., Senya, S., Osaka, K., Nerome, K. & Oya, A. (1990). Evolutionary pattern of the haemagglutinin gene of influenza B viruses isolated in Japan: cocirculating lineages in the same epidemic season.Journal of Virology 64, 2860-2865. [Google Scholar]
  22. Kato, A., Mizumoto, K. & Ishihama, A. (1985). Purification and enzymatic properties of an RNA polymerase–RNA complex from influenza virus.Virus Research 3, 115-127.[CrossRef] [Google Scholar]
  23. Kawaoka, Y., Krauss, S. & Webster, R. G. (1989). Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics.Journal of Virology 63, 4603-4608. [Google Scholar]
  24. Kemdirim, S., Palefsky, J. & Briedis, D. J. (1986). Influenza B virus PB1 protein; nucleotide sequence of the genome RNA segment predicts a high degree of structural homology with the corresponding influenza A virus polymerase protein.Virology 152, 126-135.[CrossRef] [Google Scholar]
  25. Kobayashi, M., Toyoda, T. & Ishihama, A. (1996). Influenza virus PB1 protein is the minimal and essential subunit of RNA polymerase.Archives of Virology 141, 525-539.[CrossRef] [Google Scholar]
  26. Krug, R. M., Alonso-Caplen, F. V., Julkunen, I. & Katze, M. G. (1989). Expression and replication of the influenza virus genome. In The Influenza Viruses, pp. 89–152. New York: Plenum Press.
  27. Lamb, R. A. & Krug, R. M. (1996). Orthomyxoviruses: the viruses and their replication. In Fields Virology, pp. 1353-1392. Edited by B. N. Fields, D. M. Knipe & P. M. Howley. Philadelphia: Lippincott–Raven.
  28. Lee, Y. S. & Seong, B. L. (1996). Mutational analysis of influenza B virus RNA transcription in vitro.Journal of Virology 70, 1232-1236. [Google Scholar]
  29. Lee, Y. S. & Seong, B. L. (1998). Nucleotides in the panhandle structure of the influenza B virus virion RNA are involved in the specificity between influenza A and B viruses.Journal of General Virology 79, 673-681. [Google Scholar]
  30. Lindstrom, S., Endo, A., Sugita, S., Pecoraro, M., Hiromoto, Y., Kamada, M., Takahashi, T. & Nerome, K. (1998a). Phylogenetic analyses of the matrix and non-structural genes of equine influenza viruses.Archives of Virology 143, 1585-1598.[CrossRef] [Google Scholar]
  31. Lindstrom, S. E., Hiromoto, Y., Nerome, R., Omoe, K., Sugita, S., Yamazaki, Y., Takahashi, T. & Nerome, K. (1998b). Phylogenetic analysis of the entire genome of influenza A (H3N2) viruses from Japan: evidence for genetic reassortment of the six internal genes.Journal of Virology 72, 8021-8031. [Google Scholar]
  32. Lindstrom, S. E., Hiromoto, Y., Nishimura, H., Saito, T., Nerome, R. & Nerome, K. (1999). Comparative analysis of evolutionary mechanisms of the hemagglutinin and three internal protein genes of influenza B virus: multiple cocirculating lineages and frequent reassortment of the NP, M and NS genes.Journal of Virology 73, 4413-4426. [Google Scholar]
  33. Mahy, B. M. J. (1983). Mutants of influenza virus. In Genetics of Influenza Virus, pp. 192-254. Edited by P. Palese & D. W. Kingsbury. New York: Springer–Verlag.
  34. Murphy, B. R. & Webster, R. (1996). Orthomyxoviruses. In Fields Virology, pp. 1397-1446. Edited by B. N. Fields, D. M. Knipe & P. M. Howley. Philadelphia: Lippincott–Raven.
  35. Nakagawa, Y., Kimura, N., Toyoda, T., Mizumoto, K., Ishihama, A., Oda, K. & Nakada, S. (1995). The RNA polymerase PB2 subunit is not required for replication of the influenza virus genome but is involved in capped mRNA synthesis.Journal of Virology 69, 728-733. [Google Scholar]
  36. Nakagawa, Y., Oda, K. & Nakada, S. (1996). The PB1 subunit alone can catalyze cRNA synthesis, and the PA subunit in addition to the PB1 subunit is required for viral RNA synthesis in replication of the influenza virus genome.Journal of Virology 70, 6390-6394. [Google Scholar]
  37. Nei, M. & Gojobori, T. (1986). Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions.Molecular Biology and Evolution 34, 418-426. [Google Scholar]
  38. Nerome, R., Hiromoto, Y., Sugita, S., Tanabe, N., Ishida, M., Matsumoto, M., Lindstrom, S. E., Takahashi, T. & Nerome, K. (1998). Evolutionary characteristics of influenza B virus since its first isolation in 1940: dynamic circulation of deletion and insertion mechanism.Archives of Virology 143, 1569-1583.[CrossRef] [Google Scholar]
  39. Okazaki, K., Kawaoka, Y. & Webster, R. G. (1989). Evolutionary pathways of the PA genes of influenza A viruses.Virology 172, 601-608.[CrossRef] [Google Scholar]
  40. Perez, D. R. & Donis, R. O. (1995). A 48-amino-acid region of influenza A virus PB1 protein is sufficient for complex formation with PA.Journal of Virology 69, 6932-6939. [Google Scholar]
  41. Rota, P. A., Wallis, T. R., Harmon, M. W., Rota, J. S., Kendal, A. P. & Nerome, K. (1990). Cocirculation of two distinct evolutionary lineages of influenza type B virus since 1983.Virology 175, 59-68.[CrossRef] [Google Scholar]
  42. Rota, P. A., Hemphill, M. L., Whistler, T., Regnery, H. L. & Kendal, A. P. (1992). Antigenic and genetic characterization of the haemagglutinins of recent cocirculating strains of influenza B virus.Journal of General Virology 73, 2737-2742.[CrossRef] [Google Scholar]
  43. Saitou, M. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution 4, 406-425. [Google Scholar]
  44. Sanz-Ezquerro, J. J., de la Luna, S., Ortin, J. & Nieto, A. (1995). Individual expression of influenza virus PA protein induces degradation of coexpressed proteins.Journal of Virology 69, 2420-2426. [Google Scholar]
  45. Sanz-Ezquerro, J. J., Zurcher, T., de la Luna, S., Ortin, J. & Nieto, A. (1996). The amino-terminal one-third of the influenza virus PA protein is responsible for the induction of proteolysis.Journal of Virology 70, 1905-1911. [Google Scholar]
  46. Shu, L. L., Bean, W. J. & Webster, R. G. (1993). Analysis of the evolution and variation of the human influenza A virus nucleoprotein gene from 1933 to 1990.Journal of Virology 67, 2723-2729. [Google Scholar]
  47. Stevens, M. P. & Barclay, W. S. (1998). The N-terminal extension of the influenza B virus nucleoprotein is not required for nuclear accumulation or the expression and replication of a model RNA.Journal of Virology 72, 5307-5312. [Google Scholar]
  48. Stoeckle, M. Y., Shaw, M. W. & Choppin, P. W. (1987). Segment-specific and common nucleotide sequences in the noncoding regions of influenza B virus genome RNAs.Proceedings of the National Academy of Sciences, USA 84, 2703-2707.[CrossRef] [Google Scholar]
  49. Toyoda, T., Adyshev, D. M., Kobayashi, M., Iwata, A. & Ishihama, A. (1996a). Molecular assembly of the influenza virus RNA polymerase: determination of the subunit–subunit contact sites.Journal of General Virology 77, 2149-2157.[CrossRef] [Google Scholar]
  50. Toyoda, T., Kobayashi, M., Nakada, S. & Ishihama, A. (1996b). Molecular dissection of influenza virus RNA polymerase: PB1 subunit alone is able to catalyze RNA synthesis.Virus Genes 12, 155-163.[CrossRef] [Google Scholar]
  51. Ulmanen, I., Broni, B. & Krug, R. M. (1983). Influenza virus temperature-sensitive cap (m7GpppNm)-dependent endonuclease.Journal of Virology 45, 27-35. [Google Scholar]
  52. Xu, X., Cox, N. J., Bender, C. A., Regnery, H. L. & Shaw, M. W. (1996). Genetic variation in neuraminidase genes of influenza A (H3N2) viruses.Virology 224, 175-183.[CrossRef] [Google Scholar]
  53. Yamashita, M., Krystal, M., Fitch, W. M. & 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.[CrossRef] [Google Scholar]
  54. Zürcher, T., de la Luna, S., Sanz-Ezquerro, J. J., Nieto, A. & Ortı́n, J. (1996). Mutational analysis of the influenza virus A/Victoria/3/75 PA protein: studies of interaction with PB1 protein and identification of a dominant negative mutant.Journal of General Virology 77, 1745-1749.[CrossRef] [Google Scholar]

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