This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Rabadan, R.
Right arrow Articles by Robins, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rabadan, R.
Right arrow Articles by Robins, H.

 Previous Article  |  Next Article 

Journal of Virology, December 2006, p. 11887-11891, Vol. 80, No. 23
0022-538X/06/$08.00+0     doi:10.1128/JVI.01414-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Comparison of Avian and Human Influenza A Viruses Reveals a Mutational Bias on the Viral Genomes{triangledown}

Raul Rabadan,1 Arnold J. Levine,1 and Harlan Robins1,2*

Institute for Advanced Study, Einstein Dr., Princeton, New Jersey 08540,1 Computational Biology Group, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, Washington 981092

Received 5 July 2006/ Accepted 11 September 2006

In the last few years, the genomic sequence data for thousands of influenza A virus strains, including the 1918 pandemic strain, and hundreds of isolates of the avian influenza virus H5N1, which is causing an increasing number of human fatalities, have become publicly available. This large quantity of sequence data allows us to do comparative genomics with the human and avian versions of the virus. We find that the nucleotide compositions of influenza A viruses infecting the two hosts are sufficiently different that we can determine the host at almost 100% accuracy. This assignment works at the segment level, which allows us to construct the reassortment history of individual segments within each strain. We suggest that the different nucleotide compositions can be explained by a host-dependent mutation bias. To support this idea, we estimate the fixation rates for the different polymerase segments and the ratios of synonymous to nonsynonymous changes. Additionally, we provide evidence supporting the hypothesis that the H1N1 influenza virus entered the human population just prior to the 1918 outbreak, with an earliest bound of 1910.

* Corresponding author. Mailing address: Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M2-B876, Seattle, WA 98105. Phone: (206) 667-2571. Fax: (206) 667-1319. E-mail: hrobins{at}fhcrc.org.

{triangledown} Published ahead of print on 20 September 2006.

Journal of Virology, December 2006, p. 11887-11891, Vol. 80, No. 23
0022-538X/06/$08.00+0     doi:10.1128/JVI.01414-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Dunham, E. J., Dugan, V. G., Kaser, E. K., Perkins, S. E., Brown, I. H., Holmes, E. C., Taubenberger, J. K. (2009). Different Evolutionary Trajectories of European Avian-Like and Classical Swine H1N1 Influenza A Viruses. J. Virol. 83: 5485-5494 [Abstract] [Full Text]  
  • Qi, L., Kash, J. C., Dugan, V. G., Wang, R., Jin, G., Cunningham, R. E., Taubenberger, J. K. (2009). Role of Sialic Acid Binding Specificity of the 1918 Influenza Virus Hemagglutinin Protein in Virulence and Pathogenesis for Mice. J. Virol. 83: 3754-3761 [Abstract] [Full Text]  
  • Kryazhimskiy, S., Bazykin, G. A., Dushoff, J. (2008). Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes. J. Virol. 82: 4938-4945 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»