A phylogenetic approach to detecting reassortments in viruses with segmented genomes

Gene

Volumn 464, Issue 1-2, 2010, Pages 11-16

  Suzuki, Yoshiyuki ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Phylogenetic tree; Quartet; Reassortment; Segmented genome; Virus

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE MUTATION; GENE SEGREGATION; GENETIC REASSORTMENT; GENOMICS; HUMAN; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN LOCALIZATION; STATISTICAL SIGNIFICANCE; VIRUS; VIRUS STRAIN;

INFLUENZA A VIRUS;

EID: 77955275127     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2010.05.002     Document Type: Article

References (29)

1. Bao Y., et al. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 2008, 82:596-601.
2. Barr I.G., et al. An influenza A(H3) reassortant was epidemic in Australia and New Zealand in 2003. J. Med. Virol. 2005, 76:391-397.
3. Boni M.F., Zhou Y., Taubenberger J.K., Holmes E.C. Homologous recombination is very rare or absent in human influenza A virus. J. Virol. 2008, 82:4807-4811.
4. Downie J.C. Reassortment of influenza A virus genes linked to PB1 polymerase gene. Int. Congr. Ser. 2004, 1263:714-718.
5. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
6. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
7. Furuse Y., et al. Reassortment between amantadine-resistant and -sensitive H1N1 influenza A viruses generated an amantadine-sensitive virus during the 2007-2008 season. J. Infect. Dis. 2009, 200:1766-1773.
8. Ghedin E., et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 2005, 437:1162-1166.
9. Holmes E.C., et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005, 3:e300.
10. Hutchinson E.C., Curran M.D., Read E.K., Gog J.R., Digard P. Mutational analysis of cis-acting RNA signals in segment 7 of influenza A virus. J. Virol. 2008, 82:11869-11879.
11. Hutchinson E.C., Wise H.M., Kudryavtseva K., Curran M.D., Digard P. Characterisation of influenza A viruses with mutations in segment 5 packaging signals. Vaccine 2009, 27:6270-6275.
12. Hutchinson E.C., von Kirchbach J.C., Gog J.R., Digard P. Genome packaging in influenza A virus. J. Gen. Virol. 2010, 91:313-328.
13. Khiabanian, H., Trifonov, V., Rabadan, R., 2009a. Reassortment patterns in swine influenza viruses. PLoS Curr. Influenza RRN1008.
14. Khiabanian H., Trifonov V., Rabadan R. Reassortment patterns in swine influenza viruses. PLoS ONE 2009, 4:e7366.
15. Krasnitz M., Levine A.J., Rabadan R. Anomalies in the influenza virus genome database: new biology or laboratory errors?. J. Virol. 2008, 82:8947-8950.
16. 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, 82:11880-11888.
17. Li C., et al. Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence. Proc. Natl Acad. Sci. USA 2010, 107:4687-4692.
18. Lindstrom S.E., Cox N.J., Klimov A. Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957-1972: evidence for genetic divergence and multiple reassortment events. Virology 2004, 328:101-119.
19. Lubeck M.D., Palese P., Schulman J.L. Nonrandom association of parental genes in influenza A virus recombinants. Virology 1979, 95:269-274.
20. Marsh G.A., Hatami R., Palese P. Specific residues of the influenza A virus hemagglutinin viral RNA are important for efficient packaging into budding virions. J. Virol. 2007, 81:9727-9736.
21. Marsh G.A., Rabadan R., Levine A.J., Palese P. Highly conserved regions of influenza A virus polymerase gene segments are critical for efficient viral RNA packaging. J. Virol. 2008, 82:2295-2304.
22. Nei M., Kumar S. Molecular Evolution and Phylogenetics 2000, Oxford University Press, Oxford, New York.
23. Nelson M.I., et al. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 2008, 4:e1000012.
24. Noda T., et al. Architecture of ribonucleoprotein complexes in influenza A virus particles. Nature 2006, 439:490-492.
25. Rabadan R., Robins H. Evolution of the influenza A virus: some new advances. Evol. Bioinform. 2007, 3:299-307.
26. Rabadan R., Levine A.J., Krasnitz M. Non-random reassortment in human influenza A viruses. Influenza Other Respi. Viruses 2008, 2:9-22.
27. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
28. Varich N.L., Gitelman A.K., Shilov A.A., Smirnov Y.A., Kaverin N.V. Deviation from the random distribution pattern of influenza A virus gene segments in reassortants produced under non-selective conditions. Arch. Virol. 2008, 153:1149-1154.
29. Zaraket H., et al. Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. J. Clin. Microbiol. 2010, 48:1085-1092.