Positive selection on the H3 hemagglutinin gene of human influenza virus A

Molecular Biology and Evolution

Volumn 16, Issue 11, 1999, Pages 1457-1465

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

^a UNIVERSITY OF CALIFORNIA   (United States)

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

Author keywords

Evolution; Hemagglutinin; Influenza; Positive selection; Virus

Indexed keywords

HEMAGGLUTININ; MEMBRANE ANTIGEN;

AMINO ACID ANALYSIS; ANIMAL CELL; ARTICLE; BINDING SITE; CHICKEN; EPIDEMIC; EVOLUTION; GENE MUTATION; INFLUENZA VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; UNINDEXED SEQUENCE; VIRUS REPLICATION;

EID: 0032736987     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026057     Document Type: Article

References (28)

1. CATON, A. J., G. G. BROWNLEE, J. W. YEWDELL, and W. GERHARD. 1982. The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell 31:417-427.
2. COX, N. J., and C. A. BENDER. 1995. The molecular epidemiolgy of influenza viruses. Semin. Virol. 6:359-370.
3. FERRIN, T. E., C. C. JUANG, L. E. JARVIS, and J. LANGRIDGE. 1995. The MIDAS display system. J. Mol. Graph. 6:13-27.
4. FITCH, W. M., R. M. BUSH, C. A. BENDER, and N. J. COX. 1997. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl. Acad. Sci. USA 94:7712-7718.
5. FITCH, W. M., J. M. E. LEITER, X. LI, and P. PALESE. 1991. Positive Darwinian evolution in human influenza A viruses. Proc. Natl. Acad. Sci. USA 88:4270-4274.
6. GOLDING, B., and J. FELSENSTEIN. 1990. A maximum likelihood approach to the detection of selection from a phylogeny. J. Mol. Evol. 31:511-523.
7. GOLDING, G. B. 1987. The detection of deleterious selection using ancestors inferred from a phylogenetic history. Genet. Res. Camb. 49:71-82.
8. GOLDING, G. B., C. F. AQUADRO, and C. H. LANGLEY. 1986. Sequence evolution within populations under multiple types of mutation. Proc. Natl. Acad. Sci. USA 83:427-431.
9. GUBAREVA, L. V., J. M. WOOD, W. J. MEYER, J. M. KATZ, J. S. ROBERTSON, D. MAJOR, and R. G. WEBSTER. 1994. Codominant mixtures of viruses in reference strains of influenza virus due to host cell variation. Virology 199:89-97.
10. HARDY, C. T., S. A. YOUNG, R. G. WEBSTER, C. J. NAEVE, and R. J. OWENS. 1995. Egg fluids and cells of the chorioallantoic membrane of embryonated chicken eggs can select different variants of influenza A (H3N2) viruses. Virology 211:302-306.
11. HUGHES, A. L. 1992. Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. Mol. Biol. Evol. 9:381-393.
12. HUGHES, A. L., and M. NEI. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
13. _. 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86:958-962.
14. INA, Y., and T. GOJOBORI. 1994. Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses. Proc. Natl. Acad. Sci. USA 91:8388-8392.
15. ITO, T., Y. SUZUKI, A. TAKADA, A. KAWAMOTO, K. OTSUKI, H. MASUDA, M. YAMADA, T. SUZUKI, H. KIDA, and Y. KAWAOKA. 1997. Differences in sialic acid-galactose linkages in the chicken egg amnion and allantois influence human influenza virus receptor specificity and variant selection. J. Virol. 71:3357-3362.
16. LI, W.-H., C.-I. Wu, and C.-C. LUO. 1985. A new method for estimating synonymous and non-synonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
17. MESSIER, W., and C.-B. STEWART. 1997. Episodic adaptive evolution of primate lysosymes. Nature 385:151-154.
18. NAKAJIMA, S., K. NAKAJIMA, and A. P. KENDAL. 1983. Identification of the binding sites to monoclonal antibodies on A/USSR/90/77 (H1N1) hemagglutinin and their involvement in antigenic drift in H1N1 influenza viruses. Virology 131:116-127.
19. ROBERTSON, J. S. 1993. Clinical influenza virus and the embryonated hen's egg. Rev. Med. Virol. 3:97-106.
20. ROCHA, E. P., X. XU, H. E. HALL, J. R. ALLEN, H. L. REGNERY, and N. COX. 1993. Comparison of 10 influenza A (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell-and egg-grown viruses. J. Gen. Virol. 74:2513-2518.
21. ROGERS, G. N., J. C. PAULSON, R. S. DANIELS, J. J. SKEHEL, I. A. WILSON, and D. C. WILEY. 1983. Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity. Nature 304:76-78.
22. SAIKI, R. K., D. H. GELFAND, S. STOFFEL, S. J. SCHARF, R. HIGUCHI, G. T. HORN, K. B. MULLIS, and H. A. ERLICH. 1988. Primer-directed enzymatic amplification of DNA with a thermostabile DNA polymerase. Science 239:487-491.
23. SWOFFORD, D. L. 1993. PAUP (phylogenetic analysis using parsimony). Version 4.0.0d60. Illinois Natural History Survey, Champaign.
24. WEIS, W., J. H. BROWN, S. CUSACK, J. C. PAULSON, J. J. SKEHEL, and D. C. WILEY. 1988. Structure of the influenza virus haemagglutinin complexed with its receptor, sialic acid. Nature 333:426-431.
25. WILEY, D. C., and J. J. SKEHEL. 1987. The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu. Rev. Biochem. 56:365-394.
26. WILEY, D. C., I. A. WILSON, and J. J. SKEHEL. 1981. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature 289:373-378.
27. WILSON, I. A., and N. J. COX. 1990. Structural basis of immune recognition of influenza virus hemagglutinin. Annu. Rev. Immunol. 8:737-771.
28. YANG, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.