FEVERISHLY EVOLVING ANTIGENS
CASE STUDY IN MOLECULAR EVOLUTION NO. 4
Written by Harold B. White 8/93, Most recently revised 10/00
C-647 BIOCHEMICAL EVOLUTION, FALL 2002
Penicillin

Tetracycline

Erythromycin

Page 3
Warfare at the Molecular Level

Because human survival depends on disease resistance, it is natural to have an anthropocentric perspective on evolutionary changes in gene frequencies and neglect that pathogens also evolve (2). With modern techniques of immunology, biochemistry, and molecular biology, epidemiologists can monitor both the distribution of disease resistance genes and the evolution of virulence genes in infectious organisms. The picture is ominous. Most pathogenic bacteria have become resistant to one or more antibiotics and some appear to be resistant to all major antibiotics. Plasmids, containing multiple resistance genes, move from one bacterial species to another in a natural form of lateral gene transfer that creates transgenic pathogens. We promote this process by including antibiotics in animal feed. If bacteria evolution seems fast compared to human evolution, viral evolution is even faster.
 

Among human pathogens, influenza virus is remarkable. Its proteins evolve about one million times faster than typical human proteins (4), a rate that makes the influenza virus a model for evolutionary studies (5, 6, 7, 8). The spherical virus (6) is surrounded by a lipid bilayer in which two types of viral-encoded proteins, hemagglutinin (H) and neuraminidase (N), project as is shown in the figure at the left. Within the virus are eight separate RNA molecules, each of which encodes an mRNA for a different protein. Checkout the influenza sequence data base.

Influenza viruses evolve in two ways. Antigenic drift is the accumulation of acceptable amino acid replacements primarily in the H and N surface antigens that is driven in part by immune surveillance (9, 10, 11). These proteins play an important role in the infection and pathogenicity of various influenza strains (12) that have killed millions of people during periodic pandemics (5). Antigenic shift occurs when two different strains coinfect a cell and the resulting progeny virus contains a random combination of genes from each strain (6, 13). The sudden antigenic shift to a new strain usually occurs by recombination between a human and an avian or mammalian influenza virus (14, 15).

Because the three-dimensional structures of the H (16, 17, 18) and N (4, 19) antigens have been determined, it is possible to assess the role of human antibodies in viral protein evolution. By determining the nucleotide sequences of genes obtained from influenza A viruses isolated and preserved over the past fifty years, the molecular evolution of influenza virus has been reconstructed in some detail (20, 21). This virus evolves so rapidly that a fifty-year-old influenza virus is analogous to a 50-million-year-old fossil!

Assignment: Discuss all of the questions below in your groups. As a group, construct a Concept Map on the "Evolution of Viruses" that incorporates the issues and concepts highlighted by the questions below. This is the one of two assignments this semester for which a group grade will be given. The assignment is due Monday, October 28, 2002 at the beginning of class. Remember that a neat, well organized map will be more effective at communicating your understanding.

1. Familiarize yourself with the structure and epidemiology of influenza virus (6, 8) and its surface proteins (4, 16, 17, 18, 19). How does the evolutionary response of the pathogen play into the approach to treatment (22, 23)? Is there any point in trying to produce an influenza vaccine useful for more than a couple of years?

2. The survival strategy of the human influenza virus is to evolve rapidly (24), but in order to do so it must have a very high mutation rate. If the virus replicates within human cells, how can it have a vastly different mutation rate than the human genomic DNA?

3. Several authors have claimed that the rate of evolution of human influenza virus H antigen is due simply to the high mutation rate and not to natural selection (25, 26). Their basic argument is that the rate of evolution of the first and second codon positions was not very different from the third. Why would that imply little, if any, selection?

4. Fitch and coworkers (21) and others (27) attribute a majority of the nucleotide substitutions in the hemagglutinin gene to positive selection due to the immune system and provide tests to support their hypothesis over the neutrality hypothesis described above (25, 26). From the point of view of hypothesis testing, do these tests disprove the neutral evolution hypothesis in this case? Can one predict the evolutionary changes that might occur in future influenza outbreaks (35)?

5. HIV evolves at a rate similar to influenza virus. Rather than move from host to host, HIV evolves within a single host over a decade, producing several lineages (28, 29) and eventually swamping the host immune system before AIDS develops. Infection of new hosts occurs sporadically. Compendia of articles on AIDS can be found in refs. 30 and 31. Compared to the phylogeny of influenza virus isolates based on nucleotide sequence analysis, what would a phylogeny of contemporary HIV isolates look like? What implications does the natural history and evolution of HIV have for therapy (32)? When and where did the AIDS epidemic start (33, 34)?

Return to Page 1: The Black Death
Return to Page 2: A World of Different People

 References

1. Zinsser, H. (1933) Rats, Lice and History, Little, Brown and Co., Boston.
2. Burnet, M. and White, D. O. (1972) Natural History of Infectious Disease, 4th edition, Cambridge University Press, Cambridge, U.K.
Note: Refs. 1 and 2 are classics and are highly recommended reading for anyone aspiring to be a physician. In particular they show the importance of an evolutionary perspective on disease.
3. Anderson, R. M. and May, R. M. (1992) Understanding the AIDS epidemic. Scientific American 266 (5), 58-66.
4. Colman, P. M., Varghese, J. N. and Laver, W. G. (1983) Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature 303, 41-44.
5. Krug, R. M. (editor) (1989) The Influenza Viruses, Plenum, New York. [Review by R. G. Webster in Nature 344, 208 (1990)]
6. Kaplan, M. M. and Webster, R. G. (1977) The epidemiology of influenza. Scientific American 237 (6), 88-106.
7. Palese, P. (1980) Genetic variation of human influenza viruses. TIBS, March 1980, pp. iii-v.
8. Stuart-Harris, C. (1981) The epidemiology and prevention of influenza. American Scientist 69, 166-172.
9. Young, J. F., Desselberger, U. and Palese, P. (1979) Evolution of human influenza A viruses in nature: Sequential mutations in the genomes of new H1N1 isolates. Cell 18, 73-83.
10. Webster, R. G., Laver, W. G., Air, G. M. and Schild, G. C. (1982) Molecular mechanisms of variation in influenza viruses. Nature 296, 115-121.
11. Laver, W. G., Air, G. M. and Webster, R. G. (1981) The mechanism of antigenic drift in influenza virus. J. Mol. Biol. 145, 339-361.
12. Rott, R. (1982) Determinants of influenza virus pathogeneity. Hoppe-Seyler's Z. Physiol. Chem. 363, 1273-1282.
13. Young, J. F. and Palese, P. (1979) Evolution of human influenza A viruses in nature: Recombination contributes to genetic variation in H1N1 strains. Proc. Natl. Acad. Sci. USA 76, 6547-6551.
14. Ward, C. W. and Copheide, T. A. (1981) Evolution of the Hong Kong influenza A subtype. Biochem. J. 195, 337-340.
15. Hall, S. S. (1983) The flu. Science 83, November, 56-63.
16. Wilson, I. A., Skehel, J. J. and Wiley, D. C. (1981) Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature 289, 366-373.
17. Wiley, D. C., Wilson, I. A. and Skehel, J. J. (1981) Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature  289, 373-378.
18. Bullough, P. A., Hughson, F. M., Skehel, J. J. & Wiley, D. C. (1994) Structure of influenza hemagglutinin at the pH of membrane fusion. Nature 371, 37-43. (See also the commentary on page 19 of the same issue.)
19. Varghese, J. N., Laver, W. G. and Colman, P. M. (1983) Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature 303, 35-40.
20. Buonagurio, D., Nakada, S., Parvin, J. D., Krystal, M., Palese, P. and Fitch, W. M. (1986) Evolution of human influenza A viruses over 50 years: Rapid, uniform rate of change in the NS gene. Science 282, 980-982.
21. Fitch, W. M., Leiter, J.M.E., Li, X., and Palese, P. (1991) Positive Darwinian evolution in human influenza A viruses. Proc. Natl. Acad. Sci. USA 88, 4270-4274.
22. Amábile-Cuevas, C. F., Cárdenas-García, M. and Ludgar, M. (1995) Antibiotic resistance. American Scientist 83, 320-329.
23. Evolution of antibiotic resistance is discussed in several articles in Science 257, 1050-1082 (1994).
24. Clarke, D. K., Duarte, E. A., Elena, S. F., Moya, A., Domingo, E. & Holland, J. (1994) The red queen reigns in the kingdom of RNA viruses. Proc. Natl. Acad. Sci. USA. 91, 4821-4824.
25. Saitou, N. and Nei, M. (1986) Polymorphism and evolution of influenza A virus genes. Mol. Biol. Evol. 3, 57-74.
26. Sugita, S., Yoshioka, Y., Iamura, S., Kanague, Y., Oguchi, K., Gojobori, T., Nerome, K. and Oya, A. (1991) Molecular evolution of hemagglutinin gene of H1N1 swine and human influenza A viruses. J. Mol. Evol. 32, 16-23.
27. Ina, Y. & Gojobori, T. (1994) Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses. Proc. Natl. Acad. Sci. USA. 91, 8388-8392.
28. Holmes, E. C., Zhang, L. Q., Simmonds, P., Ludlam, C. A., and Leigh Brown, A. J. (1992) Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89, 4835-4839.
29. Ewald, P. W. (1994) Evolution of Infectious Disease. Oxford University Press.
30. What science knows about AIDS. Scientific American (October 1988).
31. AIDS: 10 years later. FASEB Journal (July 1991).
32. Coffin, J. M. (1995) HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy. Science 267, 483-489.
33. Korber, B. et al. (2000) Timing the ancestor of the HIV-1 pandemic strains Science 288, 1789 - 1796. See also the commentary by D. M. Hillis on page 1757-8 of the same issue.
34.  Hahn B. H., Shaw, G. M., DeCock, K. M., and Sharp, P. M. (2000) AIDS as a zoonosis: Scientific and public health implications. Science 287, 607 - 614.
35. Bush, R. M., Bender, C. A., Subbarao, K., Cox, N. J., and Fitch, W. M. (1999) Predicting the evolution of human influenza A. Science 286, 1921 - 1925.


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Created 3 October 2000. Last updated 11 October 2002 by Hal White
Copyright 2002, Harold B. White, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716