Predicting the evolution of human influenza A

Science

Volumn 286, Issue 5446, 1999, Pages 1921-1925

  Bush, Robin M ^a   Bender, Catherine A ^b   Subbarao, Kanta ^b   Cox, Nancy J ^b   Fitch, Walter M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGENICITY; ARTICLE; CODON; GENE MUTATION; INFLUENZA VIRUS; INFLUENZA VIRUS A; NONHUMAN; PRIORITY JOURNAL; STRAIN DIFFERENCE;

AMINO ACID SUBSTITUTION; ANTIGENIC VARIATION; BINDING SITES; CODON; EPITOPES; EVOLUTION, MOLECULAR; FORECASTING; GENES, VIRAL; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS; INFLUENZA, HUMAN; MUTATION; PHYLOGENY; PROBABILITY; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CELL SURFACE; RETROSPECTIVE STUDIES; SELECTION (GENETICS);

EID: 0033521173     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.286.5446.1921     Document Type: Article

References (14)

1. W. M. Fitch, R. M. Bush, C. A. Bender, N. J. Cox, Proc. Natl. Acad. Sci. U.S.A. 94, 7712 (1997).
2. R. M. Bush, W. M. Fitch, C. A. Bender, N. J. Cox, Mol. Biol. Evol. 16, 1457 (1999).
3. The technique for identifying those codons under positive selection excludes amino acid replacements that may have occurred during culture in eggs in the laboratory by ignoring replacements that occur on the branches joining isolate sequences to the tree.
4. Sequences were generated at the Centers for Disease Control and Prevention by the protocols described in (1). They have been deposited in GenBank (accession nos. AF008656 to AF008909 and AF180564 to AF180666).
5. D. L. Swofford, PAUP* (Phylogenetic Analysis Using Parsimony and other methods) version 4.0.0d60.
6. We used trees constructed from the 1983-1997 data both to derive the set of positively selected codons (2) and to score the prediction tests. This does not bias our scoring because the location of the trunk is not a factor in determining which codons are under positive selection.
7. Trunk nodes present in at least 50% of the bootstrap replicates were consistently present in nucleotide parsimony and neighbor-joining trees and also in trees constructed from amino acids using either parsimony, neighbor-joining (5), or the protML maximum likelihood routine of Molphy 2.2 (made available by J. Adachi and M. Hasegawa). The method we used for evaluating the success of a prediction test is thus robust with regard to the algorithm and type of data used. Computational restraints prevented applying maximum-likelihood algorithms to our entire data set at once, so we used multiple overlapping subsets of sequences to perform these analyses. The data set was also too large for standard bootstrap analysis, so we estimated bootstrap values by using 10,000 PAUP FastStep bootstrap replicates. This number was determined by increasing the number of replicates until we obtained a consistent set of bootstrap values.
8. I. A. Wilson and N. J. Cox, Annu. Rev. Immunol. 8, 737 (1990); D. C. Wiley, I. A. Wilson, J. J. Skehel, Nature 289, 373 (1981).
9. I. A. Wilson and N. J. Cox, Annu. Rev. Immunol. 8, 737 (1990); D. C. Wiley, I. A. Wilson, J. J. Skehel, Nature 289, 373 (1981).
10. Supplementary tables showing the codons used in alternative prediction tests are available at www. sciencemag.org/feature/data/1044188.shl
11. C. A. Bender and N. J. Cox, unpublished data.
12. N. J. Cox and C. A. Bender, Semin. Virol. 6, 359 (1995).
13. W. Weis et al., Nature 333, 426 (1988).
14. Supported in part by funds provided by the University of California for the conduct of discretionary research by Los Alamos National Laboratory, conducted under the auspices of the US Department of Energy. We gratefully acknowledge the technical expertise of H. Jing and the critical comments of S. Frank.