NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Frank SA. Immunology and Evolution of Infectious Disease. Princeton (NJ): Princeton University Press; 2002.

Cover of Immunology and Evolution of Infectious Disease

Immunology and Evolution of Infectious Disease.

Show details


  1. Abraham J. M., Freitag C. S., Clements J. R., Eisenstein B. I. An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. Proceedings of the National Academy of Sciences. 1985;82:5724–5727. [PMC free article: PMC390624] [PubMed: 2863818]
  2. Abrams S. I., Schlom J. Rational antigen modification as a strategy to upregulate or downregulate antigen recognition. Current Opinion in Immunology. 2000;12:85–91. [PubMed: 10679405]
  3. Ada, G. 1999. The immunology of vaccination. In Plotkin, S. A., and Orenstein, W. A., eds., Vaccines, 3d ed., pp. 28–39. W. B. Saunders, Philadelphia.
  4. Agarwal A., Nayak B. P., Rao K. V. S. B cell responses to a peptide epitope. VII. Antigen-dependent modulation of the germinal center reaction. Journal of Immunology. 1998;161:5832–5841. [PubMed: 9834061]
  5. Agarwal A., Rao K. V. S. B cell responses to a peptide epitope. III. Differential T helper thresholds in recruitment of B cell fine specificities. Journal of Immunology. 1997;159:1077–1085. [PubMed: 9233600]
  6. Agarwal A., Sarkar S., Nazbal C., Balasundaram G., Rao K. V. S. B cell responses to a peptide epitope. I. The cellular basis for restricted recognition. Journal of Immunology. 1996;157:2779–2788. [PubMed: 8816380]
  7. Agarwal P., Oldenburg M. C., Czarneski J. E., Morse R. M., Hameed M. R., Cohen S., Fernandes H. Comparison study for identifying promoter allelic polymorphism in interleukin 10 and tumor necrosis factor alpha genes. Diagnostic Molecular Pathology. 2000;9:158–164. [PubMed: 10976723]
  8. Agur Z. Mathematical models for African trypanosomiasis. Parasitology Today. 1992;8:128–129. [PubMed: 15463592]
  9. Agur Z., Abiri D., van der Ploeg L. H. T. Ordered appearance of antigenic variants of African trypanosomes explained in a mathematical model based on a stochastic switch process and immune-selection against putative switch intermediates. Proceedings of the National Academy of Sciences USA. 1989;86:9626–9630. [PMC free article: PMC298551] [PubMed: 2594790]
  10. Ahmed R., Gray D. Immunological memory and protective immunity: understanding their relation. Science. 1996;272:54–60. [PubMed: 8600537]
  11. Alamgir A. S. M., Matsuzaki Y., Hongo S., Tsuchiya E., Sugawara K., Muraki Y., Nakamura K. Phylogenetic analysis of influenza C virus non-structural (NS) protein genes and identification of the NS2 protein. Journal of General Virology. 2000;81:1933–1940. [PubMed: 10900030]
  12. Albrecht P., Ennis F. A., Saltzmann E. J., Krugman S. Persistence of maternal antibody in infants beyond 12 months: mechanisms of measles vaccine failure. Journal of Hygiene. 1977;86:291–304. [PubMed: 909009]
  13. Alcami A., Koszinowski U. H. Viral mechanisms of immune evasion. Trends in Microbiology. 2000;8:410–418. [PMC free article: PMC7141568] [PubMed: 10989308]
  14. Allen T. M., O'Connor D. H., Jing P., Dzuris J. L., Mothé B. R., Vogel T. U., Dunphy E., Liebl M. E., Emerson C., Wilson N., Kunstman K. J., Wang X., Allison D. B., Hughes A. L., Desrosiers R. C., Altman J. D., Wolinsky S. M., Sette A., Watkins D. I. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature. 2000;407:386–390. [PubMed: 11014195]
  15. Almarri A., Batchelor J. R. HLA and hepatitis B infection. Lancet. 1994;344:1194–1195. [PubMed: 7934542]
  16. Altman J. D., Moss P. A. H., Goulder P. J. R., Barouch D. H., McHeyzer-Williams M. G., Bell J. I., McMichael A. J., Davis M. M. Phenotypic analysis of antigen-specific T lymphocytes. Science. 1996;274:94–96. [PubMed: 8810254]
  17. Anderson, R. M., and May, R. M. 1991. Infectious Diseases of Humans: Dynamics and Control. Oxford University Press, Oxford.
  18. Anderson T. J. C., Haubold B., Williams J. T., Estrada-Franco J. G., Richardson L., Mollinedo R., Bockarie M., Mikili J., Mharakurwa S., French N., Whitworth J., Velez I. D., Brockman A. H., Nosten F., Ferreira M. U., Day K. P. Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Molecular Biology and Evolution. 2000;17:1467–1482. [PubMed: 11018154]
  19. Andreasen V., Lin J., Levin S. A. The dynamics of cocirculating influenza strains conferring partial cross-immunity. Journal of Mathematical Biology. 1997;35:825–842. [PubMed: 9269738]
  20. Aslam N., Turner C. M. R. The relationship of variable antigen expression and population growth rates in Trypanosoma brucei. Parasitology Research. 1992;78:661–664. [PubMed: 1480602]
  21. Avrameas S. Natural autoantibodies: from horror autotoxicus to gnothi seauton. Immunology Today. 1991;12:154–159. [PubMed: 1715166]
  22. Awad-El-Kariem F. M. Does Cryptosporidium parvum have a clonal population structure? Parasitology Today. 1999;15:502–504. [PubMed: 10557152]
  23. Ayala F. J. The myth of Eve: molecular biology and human origins. Science. 1995;270:1930–1936. [PubMed: 8533083]
  24. Babiker H. A., Walliker D. Current views on the population structure of Plasmodium falciparum: implications for control. Parasitology Today. 1997;13:262–267. [PubMed: 15275063]
  25. Back N. K., Nijhuis M., Keulen W., Boucher C. A., Oude Essink B. O., van Kuilenburg A. B., van Gennip A. H., Berkout B. Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme. EMBO Journal. 1996;15:4040–4049. [PMC free article: PMC452124] [PubMed: 8670908]
  26. Badovinac V. P., Tvinnereim A. R., Harty J. T. Regulation of antigen-specific CD8+ T cell homeostasis by perforin and interferon-γ Science. 2000;290:1354–1357. [PubMed: 11082062]
  27. Banchereau J., Briere F., Caux C., Davoust J., Lebecque S., Liu Y.-J., Pulendran B., Palucka K. Immunobiology of dendritic cells. Annual Review of Immunology. 2000;18:767–811. [PubMed: 10837075]
  28. Baranowski E., Ruiz-Jarabo C. M., Sevilla N., Andreu D., Beck E., Domingo E. Cell recognition by foot-and-mouth disease virus that lacks the RGD integrin-binding motif: flexibility in aphthovirus receptor usage. Journal of Virology. 2000;74:1641–1647. [PMC free article: PMC111638] [PubMed: 10644333]
  29. Barbet A. F., Kamper S. M. The importance of mosaic genes to trypanosome survival. Parasitology Today. 1993;9:63–66. [PubMed: 15463711]
  30. Barbour A. G. Immunobiology of relapsing fever. Contributions to Microbiology and Immunology. 1987;8:125–137. [PubMed: 3304829]
  31. Barbour A. G. Linear DNA of Borrelia species and antigenic variation. Trends in Microbiology. 1993;1:236–239. [PubMed: 8137122]
  32. Barbour A. G., Bundoc V. In vitro and in vivo neutralization of the relapsing fever agent Borrelia hermsii with serotype-specific immunoglobulin M antibodies. Infection and Immunity. 2001;69:1009–1015. [PMC free article: PMC97981] [PubMed: 11159997]
  33. Barbour A. G., Burman N., Carter C. J., Kitten T., Bergstrom S. Variable antigen genes of the relapsing fever agent Borrelia hermsii are activated by promoter addition. Molecular Microbiology. 1991;5:489–493. [PubMed: 2041480]
  34. Barbour A. G., Hayes S. F. Biology of Borrelia species. Microbiological Reviews. 1986;50:381–400. [PMC free article: PMC373079] [PubMed: 3540570]
  35. Barbour, A. G., and Stoenner, H. G. 1985. Antigenic variation of Borrelia hermsii. In Herskowitz, I., and Simon, M. I., eds., Genome Rearrangement. UCLA Symposium on Molecular and Cellular Biology, New Series, Vol. 20. Alan Liss, Inc., New York.
  36. Barnabé C., Brisse S., Tibayrenc M. Population structure and genetic typing of Trypanosoma cruzi, the agent of Chagas disease: a multilocus enzyme electrophoretic approach. Parasitology. 2000;120:513–526. [PubMed: 10840981]
  37. Barnwell J. W. Malaria: a new escape and evasion tactic. Nature. 1999;398:562–563. [PubMed: 10217137]
  38. Barragan A., Kremsner P. G., Weiss W., Wahlgren M., Carlson J. Age-related buildup of humoral immunity against epitopes for rosette formation and agglutination in African areas of malaria endemicity. Infection and Immunity. 1998;66:4783–4787. [PMC free article: PMC108590] [PubMed: 9746579]
  39. Barry J. D. Antigenic variation during Trypanosoma vivax infections of different host species. Parasitology. 1986;92:51–65. [PubMed: 2421230]
  40. Barry J. D. The relative significance of mechanisms of antigenic variation in African trypanosomes. Parasitology Today. 1997;13:212–218. [PubMed: 15275073]
  41. Barry J. D., Peeling R. W., Brunham R. C. Analysis of the original antigenic sin antibody response to the major outer membrane protein of Chlamydia trachomatis. Journal of Infectious Diseases. 1999;179:180–186. [PubMed: 9841837]
  42. Barry J. D., Turner C. M. R. The dynamics of antigenic variation and growth of African trypanosomes. Parasitology Today. 1991;7:207–211. [PubMed: 15463498]
  43. Barry J. D., Turner C. M. R. Mathematical models for African trypanosomiasis—reply. Parasitology Today. 1992;8:129.
  44. Barton N. H., Turelli M. Adaptive landscapes, genetic distance and the evolution of quantitative characters. Genetical Research. 1987;49:157–173. [PubMed: 3596236]
  45. Beaumont T., van Nuenen A., Broersen S., Blattner W. A., Lukashov V. V., Schuitemaker H. Reversal of human immunodeficiency virus type 1 IIIB to a neutralization-resistant phenotype in an accidentally infected laboratory worker with a progressive clinical course. Journal of Virology. 2001;75:2246–2252. [PMC free article: PMC114808] [PubMed: 11160728]
  46. Bednarek M. A., Sauma S. Y., Gammon M. C., Porter G., Tamhankar S., Williamson A. R., Zweerink H. J. The minimum peptide epitope from the influenza virus matrix protein: extra and intracellular loading of HLA-A2. Journal of Immunology. 1991;147:4047–4053. [PubMed: 1721637]
  47. Beekman N. J., van Veelen P. A., van Hall T., Neisig A., Sijts A., Camps M., Kloetzel P.-M., Neefjes J. J., Melief C. J., Ossendorp F. Abrogation of CTL epitope processing by single amino acid substitution flanking the C-terminal proteasome cleavage site. Journal of Immunology. 2000;164:1898–1905. [PubMed: 10657639]
  48. Belz G. T., Xie W., Altman J. D., Doherty P. C. A previously unrecognized H-2Db-restricted peptide prominent in the primary influenza A virus-specific CD8+ T-cell response is much less apparent following secondary challenge. Journal of Virology. 2000;74:3486–3493. [PMC free article: PMC111856] [PubMed: 10729122]
  49. Benjamin D. C., Berzofsky J. A., East I. J., Gurd F. R. N., Hannum C., Leach S. J., Margoliash E., Michael J. G., Miller A., Prager E. M., Reichlin M., Sercarz E. E., Smith-Gill S. J., Todd P. E., Wilson A. C. The antigenic structure of proteins: a reappraisal. Annual Review of Immunology. 1984;2:67–101. [PubMed: 6085753]
  50. Benjamin D. C., Perdue S. S. Site-directed mutagenesis in epitope mapping. Methods in Enzymology. 1996;9:508–515. [PubMed: 8812706]
  51. Bennett A. F., Lenski R. E. Experimental evolution and its role in evolutionary physiology. American Zoologist. 1999;39:346–362.
  52. Bennink J. R., Doherty P. C. The response to H-2-different virus-infected cells is mediated by long-lived T lymphocytes and is diminished by prior virus priming in a syngeneic environment. Cellular Immunology. 1981;61:220–224. [PubMed: 6973400]
  53. Berinstein A., Roivainen M., Hovi T., Mason P. W., Baxt B. Antibodies to the vitronectin receptor (integrin αv β3) inhibit binding and infection of foot-and-mouth disease virus to cultured cells. Journal of Virology. 1995;69:2664–2666. [PMC free article: PMC188951] [PubMed: 7533862]
  54. Bernard K. A., Klimstra W. B., Johnston R. E. Mutations in the E2 glycoprotein of Venezuelan equine encephalitis virus confer heparan sulfate interaction, low morbidity, and rapid clearance from blood of mice. Virology. 2000;276:93–103. [PubMed: 11021998]
  55. Bertoletti A., Sette A., Chisari F. V., Penna A., Levrero M., De Carli M., Fiaccadori F., Ferrari C. Natural variants of cytotoxic epitopes are T-cell receptor antagonists for antiviral cytotoxic T cells. Nature. 1994;369:407–410. [PubMed: 8196768]
  56. Bhattacharjee A. K., Glaudemans C. P. J. Dual binding specificities in MOPC 384 and 870 murine myeloma immunoglobulins. Journal of Immunology. 1978;120:411–413. [PubMed: 74386]
  57. Biozzi, G., Cabrera, W. H., Mouton, D., and Ibanez, D. M. 1982. Restricted and general polygenic regulation of antibody responsiveness. In Benacerraf, B., ed., Immunogenetics and Immune Regulation, p. 31. Masson Italia Editori, Milan.
  58. Bizebard T., Gigant B., Rigolet P., Rasmussen B., Diat O., Bösecke P., Wharton S. A., Skehel J. J., Knossow M. Structure of influenza virus haemagglutinin complexed with a neutralizing antibody. Nature. 1995;376:92–94. [PubMed: 7596443]
  59. Bobkov A., Cheingsong-Popov R., Salminen M., McCutchan F., Louwagie J., Ariyoshi K., Whittle H., Weber J. Complex mosaic structure of the partial envelope sequence from a Gambian HIV type 1 isolate. AIDS Research and Human Retroviruses. 1996;12:169–171. [PubMed: 8834467]
  60. Borre M. B., Owen C. A., Keen J. K., Sinha K. A., Holder A. A. Multiple genes code for high-molecular-mass rhoptry proteins of Plasmodium yoelii. Molecular and Biochemical Parasitology. 1995;70:149–155. [PubMed: 7637695]
  61. Borrow P., Shaw G. M. Cytotoxic T-lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? Immunological Reviews. 1998;164:37–51. [PMC free article: PMC7165923] [PubMed: 9795762]
  62. Borst P., Rudenko G., Blundell P. A., van Leeuwen F., Cross M. A., McCulloch R., Gerrits H., Chaves I. M. F. Mechanisms of antigenic variation in African trypanosomes. Behring Institute Mitteilungen. 1997;99:1–15. [PubMed: 9303197]
  63. Bousso P., Levraud J.-P., Kourilsky P., Abasado J.-P. The composition of a primary T cell response is largely determined by the timing of recruitment of individual T cell clones. Journal of Experimental Medicine. 1999;189:1591–1600. [PMC free article: PMC2193643] [PubMed: 10330438]
  64. Brannan L. R., Turner C. M. R., Phillips R. S. Malaria parasites undergo antigenic variation at high rates in vivo. Proceedings of the Royal Society of London Series B Biological Sciences. 1994;256:71–75. [PubMed: 8008760]
  65. Brisse S., Barnabé C., Tibayrenc M. Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis. International Journal for Parasitology. 2000a;30:35–44. [PubMed: 10675742]
  66. Brisse S., Dujardin J.-C., Tibayrenc M. Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers. Molecular and Biochemical Parasitology. 2000b;111:95–105. [PubMed: 11087920]
  67. Brown I. H., Ludwig S., Olsen C. W., Hannoun C., Scholtissek C., Hinshaw V. S., Harris P. A., McCauley J. W., Strong I. Antigenic and genetic analyses of H1N1 influenza A viruses from European pigs. Journal of General Virology. 1997;78:553–562. [PubMed: 9049404]
  68. Bruyere A., Wantroba M., Flasinski S., Dzianott A., Bujarski J. J. Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. Journal of Virology. 2000;74:4214–4219. [PMC free article: PMC111936] [PubMed: 10756034]
  69. Buonagurio D. A., Nakada S., Desselberger U., Krystal M., Palese P. Noncumulative sequence changes in the hemagglutinin genes of influenza C virus isolates. Virology. 1985;146:221–232. [PubMed: 3855244]
  70. Burch C. L., Chao L. Evolution by small steps and rugged landscapes in the RNA virus variant ϕ6. Genetics. 1999;151:921–927. [PMC free article: PMC1460516] [PubMed: 10049911]
  71. Burkhart C., Freer G., Castro R., Adorini L., Wiesmuller K. H., Zinkernagel R. M., Hengartner H. Characterization of T helper epitopes of the glycoprotein of vesicular stomatitis virus. Journal of Virology. 1994;68:1573–1580. [PMC free article: PMC236614] [PubMed: 7508998]
  72. Burrows S. R., Khanna R., Burrows J. M., Moss D. J. An alloresponse in humans is dominated by cytotoxic T lymphocytes (CTL) cross-reactive with a single Epstein-Barr virus CTL epitope: implications for graft-versus-host disease. Journal of Experimental Medicine. 1994;179:1155–1161. [PMC free article: PMC2191444] [PubMed: 7511682]
  73. Burrows S. R., Silins S. L., Moss D. J., Khanna R., Misko I. S., Argaet V. P. T cell receptor repertoire for a viral epitope in humans is diversified by tolerance to a background major histocompatibility complex antigen. Journal of Experimental Medicine. 1995;182:1703–1715. [PMC free article: PMC2192251] [PubMed: 7500015]
  74. Busch D. H., Pilip I. M., Vijh S., Pamer E. G. Coordinate regulation of complex T cell populations responding to bacterial infection. Immunity. 1998;8:353–362. [PubMed: 9529152]
  75. Bush R. M. Predicting adaptive evolution. Nature Reviews Genetics. 2001;2:387–392. [PubMed: 11331905]
  76. Bush R. M., Bender C. A., Subbarao K., Cox N. J., Fitch W. M. Predicting the evolution of influenza A. Science. 1999;286:1921–1925. [PubMed: 10583948]
  77. Buss, L. W. 1987. The Evolution of Individuality. Princeton University Press, Princeton, New Jersey.
  78. Butz E. A., Bevan M. J. Massive expansion of antigen-specific CD8+ T cells during an acute virus infection. Immunity. 1998;8:167–175. [PMC free article: PMC2776648] [PubMed: 9491998]
  79. Buus S. Description and prediction of peptide-MHC binding: the 'human MHC project'. Current Opinion in Immunology. 1999;11:209–213. [PubMed: 10322158]
  80. Byers V. S., Sercarz E. E. The x-y-z scheme of immunocyte maturation. Journal of Experimental Medicine. 1968;128:715–728. [PMC free article: PMC2138541] [PubMed: 5691983]
  81. Byrnes A. P., Griffin D. E. Large-plaque mutants of Sindbis virus show reduced binding to heparan sulfate, heightened viremia, and slower clearance from the circulation. Journal of Virology. 2000;74:644–651. [PMC free article: PMC111583] [PubMed: 10623725]
  82. Cadavid D., Pachner A. R., Estanislao L., Patalapati R., Barbour A. G. Isogenic serotypes of Borrelia turnicatae show different localization in the brain and skin of mice. Infection and Immunity. 2001;69:3389–3397. [PMC free article: PMC98298] [PubMed: 11292762]
  83. Calisher C. H., Karabatsos N., Dalrymple J. M., Shope R. E., Porterfield J. S., Westaway E. G., Brandt W. E. Antigenic relationships between flaviviruses as determined by cross-neutralization tests with polyclonal antisera. Journal of General Virology. 1989;70:37–43. [PubMed: 2543738]
  84. Callan M. F. C., Tan L., Annels N., Ogg G. S., Wilson J. D. K., O'Callaghan C. A., Steven N., McMichael A. J., Rickinson A. B. Direct visualization of antigen-specific CD8+ T cells during the primary immune response to Epstein-Barr virus in vivo. Journal of Experimental Medicine. 1998;187:1395–1402. [PMC free article: PMC2212279] [PubMed: 9565632]
  85. Caporale L. H. Chance favors the prepared genome. Annals of the New York Academy of Sciences. 1999;870:1–21. [PubMed: 10415469]
  86. Carrillo C., Borca M., Moore D. M., Morgan D. O., Sobrino F. In vivo analysis of the stability and fitness of variants recovered from foot-and-mouth disease virus quasispecies. Journal of General Virology. 1998;79:1699–1706. [PubMed: 9680133]
  87. Caton A. J., Brownlee G. G., Yewdell J. W., Gerhard W. The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell. 1982;31:417–427. [PubMed: 6186384]
  88. Chackerian B., Rudensey L. M., Overbaugh J. Specific N-linked and O-linked glycosylation modifications in the envelope V1 domain of simian immunodeficiency virus variants that evolve in the host after recognition by neutralizing antibodies. Journal of Virology. 1997;71:7719–7727. [PMC free article: PMC192123] [PubMed: 9311856]
  89. Chao L., Cox E. C. Competition between high and low mutating strains of Escherichia coli. Evolution. 1983;37:125–134. [PubMed: 28568016]
  90. Chapman B. A., Burt M. J., Frampton C. M., Collett J. A., Yeo K. H., Wilkinson I. D., Cook H. B., Barclay M. J., Ross A. G., George P. M. The prevalence of viral hepatitis (HAV, HBC and HCV) in the Christchurch community. New Zealand Medical Journal. 2000;113:394–396. [PubMed: 11062814]
  91. Charlesworth B., Sniegowski P., Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature. 1994;371:215–220. [PubMed: 8078581]
  92. Chen Q., Fernandez V., Sundström A., Schlichtherle M., Datta S., Hagblom P., Wahlgren M. Developmental selection of var gene expression in Plasmodium falciparum. Nature. 1998;394:392–395. [PubMed: 9690477]
  93. Chen W., Antón L. C., Bennink J. R., Yewdell J. W. Dissecting the multifactorial causes of immunodominance in class I–restricted T cell responses to viruses. Immunity. 2000;12:83–93. [PubMed: 10661408]
  94. Chen W., Khilko S., Fecondo J., Margulies D. H., McLuskey J. Determinant selection of major histocompatibility complex class I–restricted antigenic peptides is explained by class I–peptide affinity and is strongly influenced by nondominant anchor residues. Journal of Experimental Medicine. 1994;180:1471–1483. [PMC free article: PMC2191679] [PubMed: 7523572]
  95. Chen Z. J., Wheeler C. J., Shi W., Wu A. J., Yarboro C. H., Gallagher M., Notkins A. L. Polyreactive antigen-binding B cells are the predominant cell type in the newborn B cell repertoire. European Journal of Immunology. 1998;28:989–994. [PubMed: 9541594]
  96. Chen Z. W., Craiu A., Shen L., Kuroda M. J., Iroku U. C., Watkins D. I., Voss G., Letvin N. L. Simian immunodeficiency virus evades a dominant epitope-specific cytotoxic T lymphocyte response through mutation resulting in the accelerated dissociation of viral peptide and MHC class I. Journal of Immunology. 2000;164:6474–6479. [PubMed: 10843704]
  97. Chisari F. V. Hepatitis B virus immunopathogenesis. Annual Review of Immunology. 1995;13:29–60. [PubMed: 7612225]
  98. Ciurea A., Klenerman P., Hunziker L., Horvath E., Senn B. M., Ochsenbein A. F., Hengartner H., Zinkernagel R. M. Viral persistence in vivo through selection of neutralizing antibody-escape variants. Proceedings of the National Academy of Sciences USA. 2000;97:2749–2754. [PMC free article: PMC16001] [PubMed: 10688894]
  99. Cleghorn F. R., Jack N., Carr J. K., Edwards J., Mahabir B., Sill A., McDanal C. B., Connolly S. M., Goodman D., Bennetts R. Q., O'Brien T. R., Weinhold K. J., Bartholomew C., Blattner W. A., Greenberg M. L. A distinctive clade B HIV type 1 is heterosexually transmitted in Trinidad and Tobago. Proceedings of the National Academy of Sciences USA. 2000;97:10532–10537. [PMC free article: PMC27059] [PubMed: 10984542]
  100. Cleveland S. M., Taylor H. P., Dimmock N. J. Selection of neutralizing antibody escape mutants with type A influenza virus HA-specific polyclonal antisera: possible significance for antigenic drift. Epidemiology and Infection. 1997;118:149–154. [PMC free article: PMC2808776] [PubMed: 9129591]
  101. Coffin J. M. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995;267:483–489. [PubMed: 7824947]
  102. Coffin, J. M. 1996. Retroviridae: the viruses and their replication. In Fields, B. N., Knipe, D. M., and Howley, P. M., eds., Fields Virology, 3d ed., pp. 763–843. Lippincott-Raven, Philadelphia.
  103. Coffman, R. L., and Beebe, A. M. 1998. Genetic control of the T cell response to Leishmania major infection. In Gupta, S., Sher, A., and Ahmed, R., eds., Mechanisms of Lymphocyte Activitation and Immune Regulation VII: Molecular Determinants of Microbial Immunity, pp. 61–66. Plenum Press, New York.
  104. Cohen, S., and Lambert, P. H. 1982. Malaria. In Cohen, S., and Warren, D., eds., Immunology of Parasitic Infections, 2d ed., pp. 422–438. Blackwell, London.
  105. Cole G. A., Hogg T. L., Coppola M. A., Woodland D. L. Efficient priming of CD8+ memory T cells specific for a subdominant epitope following Sendai virus infection. Journal of Immunology. 1997;158:4301–4309. [PubMed: 9126992]
  106. Colman, P. M. 1998. Structure and function of the neuraminidase. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 65–73. Blackwell Science, Oxford.
  107. Connor R. I., Sheridan K. E., Ceradini D., Choe S., Landau N. R. Change in coreceptor use correlates with disease progression in HIV-1-infected individuals. Journal of Experimental Medicine. 1997;185:621–628. [PMC free article: PMC2196142] [PubMed: 9034141]
  108. Connor R. J., Kawaoka Y., Webster R. G., Paulson J. C. Receptor specificity in human, avian, and equine H2 and H3 influenza virus isolates. Virology. 1994;205:17–23. [PubMed: 7975212]
  109. Constant S. L., Bottomly K. Induction of Th1 and Th2 CD4+ T cell responses: the alternative approaches. Annual Review of Immunology. 1997;15:297–322. [PubMed: 9143690]
  110. Conway D. J. Natural selection on polymorphic malaria antigens and the search for a vaccine. Parasitology Today. 1997;13:26–29. [PubMed: 15275163]
  111. Conway D. J., Cavanagh D. R., Tanabe K., Roper C., Mikes Z. S., Sakihama N., Bojang K. A., Oduola A. M. J., Kremsner P. G., Arnot D. E., Greenwood B. M., McBride J. S. A principal target of human immunity to malaria identified by molecular population genetic and immunological analyses. Nature Medicine. 2000;6:689–692. [PubMed: 10835687]
  112. Conway D. J., Roper C., Oduola A. M. J., Arnot D. E., Kremsner P. G., Grobusch M. P., Curtis C. F., Greenwood B. M. High recombination rate in natural populations of Plasmodium falciparum. Proceedings of the National Academy of Sciences USA. 1999;96:4506–4511. [PMC free article: PMC16362] [PubMed: 10200292]
  113. Cooper L. A., Scott T. W. Differential evolution of eastern equine encephalitis virus populations in response to host cell type. Genetics. 2001;157:1403–1412. [PMC free article: PMC1461603] [PubMed: 11290699]
  114. Cornelissen M., Kampinga G., Zorgdrager F., Goudsmit J. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. Journal of Virology. 1996;70:8209–8212. [PMC free article: PMC190904] [PubMed: 8892955]
  115. Couceiro J. N., Paulson J. C., Baum L. G. Influenza virus strains selectively recognize sialyloligosaccharides on human respiratory epithelium: the role of the host cell in selection of hemagglutinin receptor specificity. Virus Research. 1993;29:155–165. [PubMed: 8212857]
  116. Cowell L., Kepler T. B., Janitz M., Lauster R., Mitchison N. A. The distribution of variation in regulatory gene segments as present in MHC class II promoters. Genome Research. 1998;8:124–134. [PubMed: 9477340]
  117. Cox N. J., Bender C. A. The molecular epidemiology of influenza viruses. Seminars in Virology. 1995;6:359–370.
  118. Cox N. J., Subbarao K. Global epidemiology of influenza: past and present. Annual Review of Medicine. 2000;51:407–421. [PubMed: 10774473]
  119. Crandall, K. A., ed. 1999. The Evolution of HIV. Johns Hopkins University Press, Baltimore, Maryland.
  120. Crill W. D., Wichman H. A., Bull J. J. Evolutionary reversals during viral adaptation to alternating hosts. Genetics. 2000;154:27–37. [PMC free article: PMC1460906] [PubMed: 10628966]
  121. Croft M., Swain S. L. Analysis of CD4+ T cells that provide contact-dependent bystander help to B cells. Journal of Immunology. 1992;149:3157–3165. [PubMed: 1358966]
  122. Crow, J. F., and Kimura, M. 1970. An Introduction to Population Genetics Theory. Burgess, Minneapolis, Minnesota.
  123. Daser A., Mitchison H., Mitchison A., Müller B. Non-classical-MHC genetics of immunological disease in man and mouse. The key role of pro-inflammatory cytokine genes. Cytokine. 1996;8:593–597. [PubMed: 8894433]
  124. Davis M. M., Boniface J. J., Reich Z., Lyons D., Hampl J., Arden B., Chien Y. Ligand recognition by αβ T cell receptors. Annual Review of Immunology. 1998;16:523–544. [PubMed: 9597140]
  125. de Lana M., da Silveira A., Bastrenta B., Barnabé C., Noël S., Tibayrenc M. Trypanosoma cruzi: infectivity of clonal genotype infections in acute and chronic phases in mice. Experimental Parasitology. 2000;96:61–66. [PubMed: 11052864]
  126. Deitsch K. W., Moxon E. R., Wellems T. E. Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections. Microbiology and Molecular Biology Reviews. 1997;61:281–293. [PMC free article: PMC232611] [PubMed: 9293182]
  127. Deitsch K. W., Wellems T. E. Membrane modifications in erythrocytes parasitized by Plasmodium falciparum. Molecular and Biochemical Parasitology. 1996;76:1–10. [PubMed: 8919990]
  128. del Portillo H. A., Fernandez-Becerra C., Bowman S., Oliver K., Preuss M., Sanchez C. P., Schneider N. K., Villalobos J. M., Rajandream M.-A., Harris D., Perera da Silva L. H., Barrell B., Lanzer M. A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax. Nature. 2001;410:839–842. [PubMed: 11298455]
  129. Deng Y., Yewdell J. W., Eisenlohr L. C., Bennink J. R. MHC affinity, peptide liberation, T cell repertoire, and immunodominance all contribute to the paucity of MHC class I–restricted peptides recognized by antiviral CTL. Journal of Immunology. 1997;158:1507–1515. [PubMed: 9029084]
  130. Dick L. R., Aldrich C., Jameson S. C., Moomaw C. R., Pramanik B. C., Doyle C. K., Demartino G. N., Bevan M. J., Forman J. M., Slaughter C. A. Proteolytic processing of ovalbumin and beta-galactosidase by the proteasome to yield antigenic peptides. Journal of Immunology. 1994;152:3884–3894. [PMC free article: PMC2778727] [PubMed: 8144958]
  131. Dimmock N. J. Neutralization of animal viruses. Current Topics in Microbiology and Immunology. 1993;183:1–149. [PubMed: 8354080]
  132. Dimmock N. J. Update on the neutralization of animal viruses. Reviews in Medical Virology. 1995;5:165–179.
  133. Doherty P. C., Biddison W. E., Bennink J. R., Knowles B. B. Cytotoxic T-cell responses in mice infected with influenza and vaccinia viruses vary in magnitude with H-2 genotype. Journal of Experimental Medicine. 1978;148:534–543. [PMC free article: PMC2184940] [PubMed: 100569]
  134. Doherty P. C., Christensen J. P. Accessing complexity: the dynamics of virus-specific T cell responses. Annual Review of Immunology. 2000;18:561–592. [PubMed: 10837069]
  135. Dougan D. A., Malby R. L., Gruen L. C., Kortt A. A., Hudson P. J. Effects of substitutions in the binding surface of an antibody on antigen affinity. Protein Engineering. 1998;11:65–74. [PubMed: 9579662]
  136. Dowdle W. R. Influenza A virus recycling revisited. Bulletin of the World Health Organization. 1999;77:820–828. [PMC free article: PMC2557748] [PubMed: 10593030]
  137. Drake J. W., Charlesworth B., Charlesworth D., Crow J. F. Rates of spontaneous mutation. Genetics. 1998;148:1667–1686. [PMC free article: PMC1460098] [PubMed: 9560386]
  138. Drake J. W., Holland J. J. Mutation rates among RNA viruses. Proceedings of the National Academy of Sciences USA. 1999;96:13910–13913. [PMC free article: PMC24164] [PubMed: 10570172]
  139. Drescher J., Aron R. Influence of the amino acid differences between the hemagglutinin HA1 domains of influenza virus H1N1 strains on their reaction with antibody. Journal of Medical Virology. 1999;57:397–404. [PubMed: 10089053]
  140. Dutton R. W., Bradley L. M., Swain S. L. T cell memory. Annual Review of Immunology. 1998;16:201–223. [PubMed: 9597129]
  141. Earn D. J. D., Rohani P., Bolker B. M., Grenfell B. T. A simple model for complex dynamical transitions in epidemics. Science. 2000;287:667–670. [PubMed: 10650003]
  142. Edfors-Lilja I., Wattrang E., Marklund L., Moller M., Andersson-Eklund L., Andersson L., Fossum C. Mapping quantitative trait loci for immune capacity in the pig. Journal of Immunology. 1998;161:829–835. [PubMed: 9670960]
  143. Edwards M. J., Dimmock N. J. Two influenza A virus-specific Fabs neutralize by inhibiting virus attachment to target cells, while neutralization by their IgGs is complex and occurs simultaneously through fusion inhibition and attachment inhibition. Virology. 2000;278:423–435. [PubMed: 11118365]
  144. El-Omar E. M., Carrington M., Chow W.-H., McColl K. E. L., Bream J. H., Young H. A., Herrera J., Lissowska J., Yuan C.-C., Rothman N., Lanyon G., Martin M., Fraumeni J. F. Jr, Rabkin C. S. Interleukin-1 polymorphisms associated with increased risk of gastric cancer. Nature. 2000;404:398–402. [PubMed: 10746728]
  145. Endo T., Ikeo K., Gojobori T. Large-scale search for genes on which positive selection may operate. Molecular Biology and Evolution. 1996;13:685–690. [PubMed: 8676743]
  146. Engelhard V. H., Lacy E., Ridge J. P. Influenza A–specific, HLA-A2.1–restricted cytotoxic T lymphocytes from HLA-A2.1 transgenic mice recognize fragments of the M1 protein. Journal of Immunology. 1991;146:1226–1232. [PubMed: 1704033]
  147. Enright M. C., Spratt B. G. Multilocus sequence typing. Trends in Microbiology. 1999;7:482–487. [PubMed: 10603483]
  148. Evans D. T., O'Connor D. H., Jing P., Dzuris J. L., Sidney J., da Silva J., Allen T. M., Horton H., Venham J. E., Rudersdorf R. A., Vogel T., Pauza C. D., Bontrop R. E., DeMars R., Sette A., Hughes A. L., Watkins D. I. Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nature Medicine. 1999;5:1270–1276. [PubMed: 10545993]
  149. Farber D. L. T cell memory: heterogeneity and mechanisms. Clinical Immunology. 2000;95:173–181. [PubMed: 10866123]
  150. Farci P., Shimoda A., Coiana A., Diaz G., Peddis G., Melpolder J. C., Strazzera A., Chien D. Y., Munoz S. J., Balestrieri A., Purcell R. H., Alter H. J. The outcome of acute hepatitis C predicted by the evolution of viral quasispecies. Science. 2000;288:339–344. [PubMed: 10764648]
  151. Fazekas de St. Groth S., Webster R. G. Disquisitions on original antigenic sin. I. Evidence in man. Journal of Experimental Medicine. 1966a;124:331–345. [PMC free article: PMC2138235] [PubMed: 5922742]
  152. Fazekas de St. Groth S., Webster R. G. Disquisitions on original antigenic sin. II. Proof in lower creatures. Journal of Experimental Medicine. 1966b;124:347–361. [PMC free article: PMC2138229] [PubMed: 5926092]
  153. Feavers I. M., Fox A. J., Gray S., Jones D. M., Maiden M. C. J. Antigenic diversity of meningococcal outer membrane protein PorA has implications for epidemiological analysis and vaccine design. Clinical and Diagnostic Laboratory Immunology. 1996;3:444–450. [PMC free article: PMC170365] [PubMed: 8807211]
  154. Feigelstock D. A., Mateu M. G., Valero M. L., Andreu D., Domingo E., Palma E. L. Emerging foot-and-mouth disease virus variants with antigenically critical amino acid substitutions predicted by model studies using reference viruses. Vaccine. 1996;14:97–102. [PubMed: 8852403]
  155. Ferguson N., Anderson R., Gupta S. The effect of antibody-dependent enhancement on the transmission dynamics and persistence of multiple-strain pathogens. Proceedings of the National Academy of Sciences USA. 1999;96:790–794. [PMC free article: PMC15215] [PubMed: 9892712]
  156. Fischetti V. A. Streptococcal M protein. Scientific American. 1991;264(6):32–39. [PubMed: 1857955]
  157. Fish S., Zenowich E., Fleming M., Manser T. Molecular analysis of original antigenic sin. I. Clonal selection, somatic mutation, and isotype switching during a memory B cell response. Journal of Experimental Medicine. 1989;170:1191–1209. [PMC free article: PMC2189480] [PubMed: 2477487]
  158. Fleury D., Barrère B., Bizebard T., Daniels R. S., Skehel J. J., Knossow M. A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site. Nature Structural Biology. 1999;6:530–534. [PubMed: 10360354]
  159. Fleury D., Wharton S. A., Skehel J. J., Knossow M., Bizebard T. Antigen distortion allows influenza virus to escape neutralization. Nature Structural Biology. 1998;5:119–123. [PubMed: 9461077]
  160. Forsyth K. P., Philip G., Smith T., Kum E., Southwell B., Brown G. V. Diversity of antigens expressed on the surface of the erythrocytes infected with mature Plasmodium falciparum parasites in Papua New Guinea. American Journal of Tropical Medicine and Hygiene. 1989;41:259–265. [PubMed: 2679156]
  161. Foster C. B., Lehrnbecher T., Samuels S., Stein S., Mol F., Metcalf J. A., Wyvill K., Steinberg S. M., Kovacs J., Blauvelt A., Yarchoan R., Chanock S. J. An IL6 promoter polymorphism is associated with a lifetime risk of development of Kaposi sarcoma in men infected with human immunodeficiency virus. Blood. 2000;96:2562–2567. [PubMed: 11001912]
  162. Fox G., Parry N. R., Barnett P. V., McGinn B., Rowlands D. J., Brown F. The cell attachment site on foot-and-mouth disease virus includes the amino acid sequence RGD (arginine-glycine-aspartic acid). Journal of General Virology. 1989;70:625–637. [PubMed: 2543752]
  163. Francis T. The newe acquayantance. Annals of Internal Medicine. 1953;39:203–212. [PubMed: 13080880]
  164. Franco A., Ferrari C., Sette A., Chisari F. V. Viral mutations, TCR antagonism and escape from the immune response. Current Opinion in Immunology. 1995;7:524–531. [PubMed: 7495517]
  165. Frank S. A. Coevolutionary genetics of plants and pathogens. Evolutionary Ecology. 1993;7:45–75.
  166. Frank S. A. Recognition and polymorphism in host-parasite genetics. Philosophical Transactions of the Royal Society of London B. 1994;346:283–293. [PubMed: 7708825]
  167. Frank S. A. Models of parasite virulence. Quarterly Review of Biology. 1996;71:37–78. [PubMed: 8919665]
  168. Frank S. A. A model for the sequential dominance of antigenic variants in African trypanosome infections. Proceedings of the Royal Society of London B. 1999;266:1397–1401. [PMC free article: PMC1690072] [PubMed: 10445294]
  169. Frank S. A. Multiplicity of infection and the evolution of hybrid incompatibility in segmented viruses. Heredity. 2001;87:522–529. [PubMed: 11869342]
  170. Fry E. E., Lea S. M., Jackson T., Newman J. W. I., Ellard F. M., Blakemore W. E., Abu-Ghazaleh R., Samuel A., King A. M. Q., Stuart D. I. The structure and function of foot-and-mouth disease virus-oligosaccharide receptor complex. EMBO Journal. 1999;18:543–554. [PMC free article: PMC1171147] [PubMed: 9927414]
  171. Fujita K., Maeda K., Yokoyama N., Miyazawa T., Kai C., Mikami T. In vitro recombination of feline herpesvirus type 1. Archives of Virology. 1998;143:25–34. [PubMed: 9505964]
  172. Fussenegger M. Different lifestyles of human pathogenic procaryotes and their strategies for phase and antigenic variation. Symbiosis. 1997;22:85–153.
  173. Fussenegger M., Rudel T., Barten R., Ryll R., Meyer T. F. Transformation competence and type-1 pilus biogenesis in Neisseria gonorrhoeae: a review. Gene. 1997;192:125–134. [PubMed: 9224882]
  174. Gao P., Robertson D. L., Carruthers C. D., Li Y., Bailes E., Kosrikis L. G., Salminen M. O., Bibollet-Ruche F., Peeters M., Ho D. D., Shaw G. M., Sharp P. M., Hahn B. H. An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). Journal of Virology. 1998;72:10234–10241. [PMC free article: PMC110605] [PubMed: 9811767]
  175. Germain R. N., Štefanová I. The dynamics of T cell receptor signaling: complex orchestration and the key roles of tempo and cooperation. Annual Review of Immunology. 1999;17:467–522. [PubMed: 10358766]
  176. Ghany M. G., Ayola B., Villamil F. G., Gish R. G., Rojter S., Vierling J. M., Lok A. S. F. Hepatitis B virus S mutants in liver transplant recipients who were reinfected despite hepatitis B immune globulin prophylaxis. Hepatology. 1998;27:213–222. [PubMed: 9425940]
  177. Gianfrani C., Oseroff C., Sidney J., Chesnut R. W., Sette A. Human memory CTL response specific for influenza A virus is broad and multispecific. Human Immunology. 2000;61:438–452. [PubMed: 10773346]
  178. Gilbert S. C., Plebanski M., Gupta S., Morris J., Cox M., Aidoo M., Kwiatkowski D., Greenwood B. M., Whittle H. C., Hill A. V. S. Association of malaria parasite population structure, HLA, and immunological antagonism. Science. 1998;279:1173–1177. [PubMed: 9469800]
  179. Golub, E. S., and Green, D. R. 1991. Immunology: A Synthesis, 2d ed. Sinauer Associates, Sunderland, Massachusetts.
  180. Good M. F., Zevering Y., Currier J., Bilsborough J. Original antigenic sin, T cell memory, and malaria sporozoite immunity: an hypothesis for immune evasion. Parasite Immunology. 1993;15:187–193. [PubMed: 7685075]
  181. Goulder P. J. R., Brander C., Tang Y., Tremblay C., Colbert R. A., Addo M. M., Rosenberg E. S., Nguyen T., Allen R., Trocha A., Altfeld M., He S., Bunce M., Funkhouser R., Pelton S. I., Burchett S. K., McIntosh K., Korber B. T. M., Walker B. D. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature. 2001;412:334–338. [PubMed: 11460164]
  182. Gow P. J., Mutimer D. Mechanisms of hepatitis B virus escape after immunoglobulin therapy. Current Opinion in Infectious Disease. 2000;13:643–646. [PubMed: 11964835]
  183. Gras-Masse H., Georges B., Estaquier J., Tranchand-Bunel D., Tartar A., Druilhe P., Auriault C. Convergent peptide libraries, or mixotopes, to elicit or to identify specific immune responses. Current Opinion in Immunology. 1999;11:223–228. [PubMed: 10322149]
  184. Gravenor M. B., Lloyd A. L. Reply to: models for the in-host dynamics of malaria revisited: errors in some basic models lead to large over-estimates of growth rates. Parasitology. 1998;117:409–410. [PubMed: 9836304]
  185. Gravenor M. B., McLean A. R., Kwiatkowski D. The regulation of malaria parasitaemia: parameter estimates for a population model. Parasitology. 1995;110:115–122. [PubMed: 7885729]
  186. Gray A. R. Antigenic variation in a strain of Trypanosoma brucei transmitted by Glossina morsitans and G. palpalis. Journal of General Microbiology. 1965;41:195–214. [PubMed: 5866129]
  187. Gray D. Thanks for the memory. Nature Immunology. 2000;1:11–12. [PubMed: 10881165]
  188. Gray-Owen S. D., Lorenzen D. R., Haude A., Meyer T. F., Dehio C. Differential Opa specificities for CD66 receptors influence tissue interactions and cellular response to Neisseria gonorrhoeae. Molecular Microbiology. 1997;26:971–980. [PubMed: 9426134]
  189. Griffin, D. E. 2001. Measles virus. In Knipe, D. M., and Howley, P. M., eds., Fields Virology, 4th ed., pp. 1401–1441. Lippincott-Raven, Philadelphia.
  190. Gross M. D., Siegel E. C. Incidence of mutator strains in Escherichia coli and coliforms in nature. Mutation Research. 1981;91:107–110. [PubMed: 7019693]
  191. Guardiola J., Maffei A., Lauster R., Mitchison N. A., Accolla R. S., Sartoris S. Functional significance of polymorphism among MHC class II gene promoters. Tissue Antigens. 1996;48:615–625. [PubMed: 9008303]
  192. Gubbels M.-J., Katzer F., Hide G., Jongejan F., Shiels B. R. Generation of a mosaic pattern of diversity in the major merozoite-piroplasm surface antigen of Theileria annulata. Molecular and Biochemical Parasitology. 2000;110:23–32. [PubMed: 10989142]
  193. Guillot S., Caro V., Cuervo N., Korotkova E., Combiescu M., Persu A., Aubert-Combiescu A., Delpeyroux F., Crainic R. Natural genetic exchanges between vaccine and wild poliovirus strains in humans. Journal of Virology. 2000;74:8434–8443. [PMC free article: PMC116354] [PubMed: 10954543]
  194. Gupta S., Day K. P. A strain theory of malaria transmission. Parasitology Today. 1994;10:476–481. [PubMed: 15275516]
  195. Gupta S., Ferguson N., Anderson R. Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents. Science. 1998;280:912–915. [PubMed: 9572737]
  196. Gupta S., Maiden M. C. J., Anderson R. M. Population structure of pathogens: the role of immune selection. Parasitology Today. 1999;15:497–501. [PubMed: 10557151]
  197. Gupta S., Maiden M. C. J., Feavers I. M., Nee S., May R. M., Anderson R. M. The maintenance of strain structure in populations of recombining infectious agents. Nature Medicine. 1996;2:437–442. [PubMed: 8597954]
  198. Gupta S. C., Hengartner H., Zinkernagel R. M. Primary antibody responses to a well-defined and unique antigen are not enhanced by preimmunization with carrier: analysis in a viral model. Proceedings of the National Academy of Sciences USA. 1986;83:2604–2608. [PMC free article: PMC323347] [PubMed: 3010314]
  199. Gutjahr T. S., O'Rourke M., Ison C. A., Spratt B. G. Arginine-, hypoxanthine-, uracil-requiring isolates of Neisseria gonorrhoeae are a clonal lineage within a non-clonal population. Microbiology. 1997;143:633–640. [PubMed: 9043139]
  200. Guttman D. S. Recombination and clonality in natural populations of Escherichia coli. Trends in Ecology and Evolution. 1997;12:16–22. [PubMed: 21237956]
  201. Haanen J. B. A. G., Wolkers M. C., Kruisbeek A. M., Schumacher T. N. M. Selective expansion of cross-reactive CD8+ memory T cells by viral variants. Journal of Experimental Medicine. 1999;190:1319–1328. [PMC free article: PMC2195685] [PubMed: 10544203]
  202. Hackstadt, T. 1999. Cell biology. In Stephens, R. S., ed., Chlamydia: Intracellular Biology, Pathogenesis, and Immunity, pp. 101–138. American Society for Microbiology, Washington, D.C.
  203. Hajós J. P., Pijnenburg J., Usmany M., Zuidema D., Závadszky P., Vlak J. M. High frequency recombination between homologous baculoviruses in cell culture. Archives of Virology. 2000;145:159–164. [PubMed: 10664413]
  204. Harindranath N., Ikematsu H., Notkins A. L., Casali P. Structure of the VH and VL segments of polyreactive and monoreactive human natural antibodies to HIV-1 and Escherichia coli β-galactosidase. International Immunology. 1993;5:1523–1533. [PMC free article: PMC4638119] [PubMed: 8312222]
  205. Harrigan P. R., Bloor S., Larder B. A. Relative replicative fitness of zidovudine-resistant human immunodeficiency virus type 1 isolates in vitro. Journal of Virology. 1998;72:3773–3778. [PMC free article: PMC109599] [PubMed: 9557659]
  206. Harrison S. C. Picornaviruses: finding the receptors. Nature. 1989;338:205–206. [PubMed: 2466201]
  207. Hartl, D. L., and Clark, A. G. 1997. Principles of Population Genetics, 3d ed. Sinauer Associates, Sunderland, Massachusetts.
  208. Hartl D. L., Taubes C. H. Compensatory nearly neutral mutations: selection without adaptation. Journal of Theoretical Biology. 1996;182:303–309. [PubMed: 8944162]
  209. Hasegawa M., Di Rienzo A., Kocher T. D., Wilson A. C. Toward a more accurate time scale for the human mitochondrial DNA tree. Journal of Molecular Evolution. 1993;37:347–354. [PubMed: 8308904]
  210. Hastings I. M., Wedgwood-Oppenheim B. Sex, strains and virulence. Parasitology Today. 1997;13:375–383. [PubMed: 15275150]
  211. Hauser S. L. T-cell receptor genes. Annals of the New York Academy of Sciences. 1995;756:233–240. [PubMed: 7645843]
  212. Haydon D. T., Bastos A. D., Knowles N. J., Samuel A. R. Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. Genetics. 2001;157:7–15. [PMC free article: PMC1461471] [PubMed: 11139487]
  213. Haydon D. T., Woolhouse M. E. J. Immune avoidance strategies in RNA viruses: fitness continuums arising from trade-offs between immunogenicity and antigenic variability. Journal of Theoretical Biology. 1998;193:601–612. [PubMed: 9745756]
  214. Haywood A. M. Virus receptors: binding, adhesion strengthening, and changes in viral structure. Journal of Virology. 1994;68:1–5. [PMC free article: PMC236257] [PubMed: 8254718]
  215. Hedrick, P. W. 2000. Genetics of Populations, 2d ed. Jones and Bartlett, Boston.
  216. Hetzel C., Anderson R. M. The within-host cellular dynamics of bloodstage malaria: theoretical and experimental studies. Parasitology. 1996;113:25–38. [PubMed: 8710412]
  217. Hide G., Welburn S. C., Tait A., Maudlin I. Epidemiological relationships of Trypanosoma brucei stocks from south east Uganda: evidence for different population structures in human infective and non-human infective isolates. Parasitology. 1994;109:95–111. [PubMed: 7914692]
  218. Hill A. V. S. The immunogenetics of human infectious diseases. Annual Review of Immunology. 1998;16:593–617. [PubMed: 9597143]
  219. Hillis, D. M., Moritz, C., and Mable, B. K., eds. 1996. Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts.
  220. Hiromoto Y., Saito T., Lindstrom S. E., Li Y., Nerome R., Sugita S., Shinjoh M., Nerome K. Phylogenetic analysis of the three polymerase genes (PB1, PB2 and PA) of the influenza B virus. Journal of General Virology. 2000;81:929–937. [PubMed: 10725418]
  221. Hoe N. P., Nakashima K., Lukomski S., Grigsby D., Liu M., Kordari P., Dou S.-J., Pan X., Vuopio-Varkila J., Salmelinna S., McGeer A., Low D. E., Schwartz B., Schuchat A., Naidich S., de Lorenzo D., Fu Y.-X., Musser J. M. Rapid selection of complement-inhibiting protein variants in group A strepococcus epidemic waves. Nature Medicine. 1999;5:924–929. [PubMed: 10426317]
  222. Hohler T., Gerken G., Notghi A., Lubjuhn R., Taheri H., Protzer U., Lohr H. F., Schneider P. M., Meyer zum Buschenfelde K. H., Rittner C. HLA-DRB1*1301 and *1302 protect against chronic hepatitis B. Journal of Hepatology. 1997;26:503–507. [PubMed: 9075656]
  223. Holland, J. J., ed. 1992. Genetic Diversity of RNA Viruses. Springer-Verlag, New York.
  224. Hollingshead S. K., Fischetti V. A., Scott J. R. Complete nucleotide sequence of type 6 M protein of the group A streptococcus: repetitive structure and membrane anchor. Journal of Biological Chemistry. 1986;261:1677–1686. [PubMed: 3511046]
  225. Hollingshead S. K., Fischetti V. A., Scott J. R. Size variation in group A streptococcal protein is generated by homologous recombination between intragenic repeats. Molecular and General Genetics. 1987;207:196–203. [PubMed: 3039291]
  226. Holmes E. C., Zhang L. Q., Simmonds P., Ludlam C. A., Leigh Brown A. J. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proceedings of the National Academy of Sciences. 1992;89:4835–4839. [PMC free article: PMC49182] [PubMed: 1594583]
  227. Housworth W. J., Spoon M. M. The age distribution of excess mortality during A2 Hong Kong influenza outbreaks. American Journal of Epidemiology. 1971;94:348–350. [PubMed: 5110551]
  228. Hughes A. L. Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. Molecular Biology and Evolution. 1992;9:381–393. [PubMed: 1584009]
  229. Hughes, A. L. 1999. Adaptive Evolution of Genes and Genomes. Oxford University Press, Oxford.
  230. Hughes A. L., Verra F. Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum. Proceedings of the Royal Society of London Series B Biological Sciences. 2001;268:1855–1860. [PMC free article: PMC1088819] [PubMed: 11522206]
  231. Hughes M. K., Hughes A. L. Natural selection on Plasmodium surface proteins. Molecular and Biochemical Parasitology. 1995;71:99–113. [PubMed: 7630387]
  232. Hulst M. M., van Gennip H. G. P., Moormann R. J. M. Passage of classical swine fever virus in cultured swine kidney cells selects virus variants that bind to heparan sulfate due to a single amino acid change in envelope protein Erns. Virology. 2000;276:93–103. [PMC free article: PMC112386] [PubMed: 11000226]
  233. Hurwitz J. L., Heber-Katz E., Hackett C. J., Gerhard W. Characterization of the murine TH response to influenza virus hemagglutinin: evidence for three major specificities. Journal of Immunology. 1984;133:3371–3377. [PubMed: 6208279]
  234. Hynes R. O. Integrins: versatility, modulation, and signaling in cell adhesion. Cell. 1992;69:11–25. [PubMed: 1555235]
  235. Icenogle J. C., Shiwen H., Duke G., Gilbert S., Rueckert R., Anderegg J. Neutralization of poliovirus by a monoclonal antibody: kinetics and stoichiometry. Virology. 1983;127:412–425. [PubMed: 6306918]
  236. Iida S., Meyer J., Kennedy K. E., Arber W. A site-specific, conservative recombination system carried by bacteriophage P1: mapping the recombinase gene cin and the crossover sites cix for the inversion of the C-segment. EMBO Journal. 1982;1:1445–1453. [PMC free article: PMC553230] [PubMed: 6327269]
  237. Iqbal J., Perlmann P., Berzins K. Serologic diversity of antigens expressed on the surface of Plasmodium falciparum infected erythrocytes in Punjab (Pakistan). Transactions of the Royal Society of Tropical Medicine and Hygiene. 1993;87:583–588. [PubMed: 8266416]
  238. Jackson T., Blakemore W., Newman J. W. I., Knowles N. J., Mould A. P., Humphries M. J., King A. M. Q. Foot-and-mouth disease virus is a ligand for the high-affinity binding conformation of integrin α5β1: influence of the leucine residue within the RGDL motif on selectivity of integrin binding. Journal of General Virology. 2000;81:1383–1391. [PubMed: 10769082]
  239. Jackson T., Ellard F. M., Abu-Ghazaleh R., Brookes S. M., Blakemore W. E., Corteyn A. H., Stuart D. I., Newman J. W. I., King A. M. Q. Efficient infection of cells in culture by type O foot-and-mouth disease virus requires binding to cell surface heparan sulfate. Journal of Virology. 1996;70:5282–5287. [PMC free article: PMC190485] [PubMed: 8764038]
  240. Jackson T., Sheppard D., Denyer M., Blakemore W. E., King A. M. Q. The epithelial integrin ανβ6 is a receptor for foot-and-mouth disease virus. Journal of Virology. 2000;74:4949–4956. [PMC free article: PMC110846] [PubMed: 10799568]
  241. Jameson S. C., Bevan M. J. T cell receptor antagonists and partial agonists. Immunity. 1995;2:1–11. [PubMed: 7600296]
  242. Jamieson B. D., Ahmed R. T cell memory: long-term persistence of virus-specific cytotoxic T cells. Journal of Experimental Medicine. 1989;169:1993–2005. [PMC free article: PMC2189353] [PubMed: 2471771]
  243. Janeway C. A. Jr. How the immune system recognizes invaders. Scientific American. 1993;269(3):73–79. [PubMed: 8211093]
  244. Janeway, Jr., C. A., Travers, P., Capra, J. D., and Walport, M. J. 1999. Immunobiology: The Immune System in Health and Disease. Garland Publishers, New York.
  245. Jaulin C., Casanova J.-L., Romero P., Luescher I., Cordey A.-S., Maryanski J. L., Kourilsky P. Highly diverse T cell recognition of a single Plasmodium berghei peptide presented by a series of mutant H-2 Kd molecules. Immunity. 1992;4:47–55. [PubMed: 1281196]
  246. Jenni L., Marti S., Schweizer J., Betschart B., Le Page R. W. F., Wells J. M., Tait A., Paindavoine P., Pays E., Steinert M. Hybrid formation between trypanosomes during cyclical transmission. Nature. 1986;322:173–175. [PubMed: 3724860]
  247. Jensen L. T., Laderoged S., Birkelund S., Christiansen G. Selection of Mycoplasma hominis PG21 deletion mutants by cultivation in the presence of monoclonal antibody 552. Infection and Immunity. 1995;63:3336–3347. [PMC free article: PMC173459] [PubMed: 7543881]
  248. Jetzt A. E., Yu H., Klarmann G. J., Ron Y., Preston B. D., Dougherty J. P. High rate of recombination throughout the human immunodeficiency virus type 1 genome. Journal of Virology. 2000;74:1234–1240. [PMC free article: PMC111457] [PubMed: 10627533]
  249. Jung H. C., Kim J. M., Song I. S., Kim C. Y. Heliobacter pylori induces an array of pro-inflammatory cytokines in human gastric epithelial cells: quantification of mRNA for interleukin-8, -1 α/β, granulocyte-macrophage colony-stimulating factor, monocyte chemoattractant protein-1 and tumour necrosis factor-alpha. Journal of Gastroenterology and Hepatology. 1997;12:473–480. [PubMed: 9257236]
  250. Jyssum K. Observations on two types of genetic instability in Escherichia coli. Acta Pathologica et Microbiologica Scandinavica. 1960;48:113–120. [PubMed: 14408281]
  251. Kamp D., Kahmann R., Zipser D., Broker T. R., Chow L. T. Inversion of the G DNA segment of phage Mu controls phage infectivity. Nature. 1978;271:577–580. [PubMed: 622196]
  252. Kaverin N. V., Smirnov Y. A., Govorkova E. A., Rudneva I. A., Gitelman A. K., Lipatov A. S., Varich N. L., Yamnikova S. S., Makarova N. V., Webster R. G., Lvov D. K. Cross-protection and reassortment studies with avian H2 influenza viruses. Archives of Virology. 2000;145:1059–1066. [PubMed: 10948982]
  253. Kawaoka Y., Krauss S., Webster R. G. Avian-to-human tranmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics. Journal of Virology. 1989;63:4603–4608. [PMC free article: PMC251093] [PubMed: 2795713]
  254. Keitel T., Kramer A., Wessner H., Scholz C., Schneider-Mergener J., Höhne W. Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity. Cell. 1997;91:811–820. [PubMed: 9413990]
  255. Kilbourne E. D., Laver W. G., Schulman J. L., Webster R. G. Antiviral activity of antiserum specific for an influenza virus neuraminidase. Journal of Virology. 1968;2:281–288. [PMC free article: PMC375612] [PubMed: 4911843]
  256. Kimata J. T., Kuller L., Anderson D. B., Dailey P., Overbaugh J. Emerging cytopathic and antigenic simian immunodeficiency virus variants influence AIDS progression. Nature Medicine. 1999;5:535–541. [PubMed: 10229230]
  257. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
  258. Klenerman P., Rowland-Jones S., McAdam S., Edwards J., Daenke S., Lalloo D., Koppe B., Rosenberg W., Boyd D., Edwards A. Cytotoxic T-cell activity antagonized by naturally occurring HIV-1 Gag variants. Nature. 1994;369:403–407. [PubMed: 7515165]
  259. Klenerman P., Zinkernagel R. M. Original antigenic sin impairs cytotoxic T lymphocyte responses to viruses bearing variant epitopes. Nature. 1998;394:482–485. [PubMed: 9697771]
  260. Klimstra W. B., Ryman K. D., Johnston R. E. Adaptation of Sindbis virus to BHK cells selects for use of heparan sulfate as an attachment receptor. Journal of Virology. 1998;72:7357–7366. [PMC free article: PMC109960] [PubMed: 9696832]
  261. Knipe, D. M., and Howley, P. M., eds. 2001. Fields Virology, 4th ed. Lippincott-Raven, Philadelphia.
  262. Kollmann T. R., Pettoello-Mantovani M., Katopodis N. F., Hachamvitch M., Rubinstein A., Kim A., Goldstein H. Inhibition of acute in vivo human immunodeficiency virus infection by human interleukin 10 treatment of SCID mice implanted with human fetal thymus and liver. Proceedings of the National Academy of Sciences USA. 1996;93:3126–3131. [PMC free article: PMC39773] [PubMed: 8610180]
  263. Korber B., Muldoon M., Theiler J., Gao F., Gupta R., Lapedes A., Hahn B. H., Wolinsky S., Bhattacharya T. Timing the ancestor of the HIV-1 pandemic strains. Science. 2000;288:1789–1796. [PubMed: 10846155]
  264. Kosinski R. J. Antigenic variation in trypanosomes: a computer analysis of variant order. Parasitology. 1980;80:343–357. [PubMed: 6768048]
  265. Kostolanský F., Varečková E., Betáková T., Mucha V., Russ G., Wharton S. A. The strong positive correlation between effective affinity and infectivity neutralization of highly cross-reactive monoclonal antibody IIB4, which recognizes antigenic site B on influenza A virus haemagglutinin. Journal of General Virology. 2000;81:1727–1735. [PubMed: 10859378]
  266. Kramer A., Keitel T., Winkler K., Stöcklein W., Höhne W., Schneider-Mergener J. Molecular basis for the binding promiscuity of an anti-p24 (HIV-1) monoclonal antibody. Cell. 1997;91:799–809. [PubMed: 9413989]
  267. Kropshofer H., Hämmerling G. J., Vogt A. B. The impact of the non-classical MHC proteins HLA-DM and HLA-DO on loading of MHC class II molecules. Immunological Reviews. 1999;172:267–278. [PubMed: 10631952]
  268. Kumar V., Bansal V. J., Rao K. V. S., Jameel S. Hepatitis B virus envelope epitopes: gene assembly and expression in Escherichia coli of an immunologically reactive novel multiple-epitope polypeptide 1 (MEP-1). Gene. 1992;110:137–144. [PubMed: 1371488]
  269. Kuno G., Chang G.-J., Tsuchiya K. R., Karabatsos N., Cropp C. B. Phylogeny of the genus Flavivirus. Journal of Virology. 1998;72:73–83. [PMC free article: PMC109351] [PubMed: 9420202]
  270. Laeeq S., Smith C. A., Wagner S. D., Thomas D. B. Preferential selection of receptor-binding variants of influenza virus hemagglutinin by the neutralizing antibody repertoire of transgenic mice expressing a human immunoglobulin μ minigene. Journal of Virology. 1997;71:2600–2605. [PMC free article: PMC191380] [PubMed: 9060611]
  271. Lamb, R. A., and Krug, R. M. 2001. Orthomyxoviridae: the viruses and their replication. In Knipe, D. M., and Howley, P. M., eds., Fields Virology, 4th ed., pp. 1487–1531. Lippincott-Raven, Philadelphia.
  272. Lambkin R., Dimmock N. J. Longitudinal study of an epitope-biased serum haemagglutinin-inhibition antibody response in rabbits immunized with type A influenza virions. Vaccine. 1996;14:212–218. [PubMed: 8920702]
  273. Lambkin R., McLain L., Jones S. E., Aldridge S. L., Dimmock N. J. Neutralization escape mutants of type A influenza virus are readily selected by antisera from mice immunized with whole virus: a possible mechanism for antigenic drift. Journal of General Virology. 1994;75:3493–3502. [PubMed: 7527838]
  274. Lancefield R. C. Current knowledge of type-specific M antigens of group A streptococci. Journal of Immunology. 1962;89:307–313. [PubMed: 14461914]
  275. Landweber L. F. Experimental RNA evolution. Trends in Ecology and Evolution. 1999;14:353–358. [PubMed: 10441309]
  276. Larsen O., Andersson S., da Silva Z., Hedegaard K., Sandstrom A., Naucler A., Dias F., Melbye M., Aaby P. Prevalences of HTLV-1 infection and associated risk determinants in an urban population in Guinea–Bissau, West Africa. Journal of Acquired Immune Deficiency Syndrome. 2000;25:157–163. [PubMed: 11103046]
  277. Latek R. R., Unanue E. R. Mechanisms and consequences of peptide selection by the I-Ak class II molecule. Immunological Reviews. 1999;172:209–228. [PubMed: 10631948]
  278. Latham, J. L., and Burgess, A. E. 1977. Elementary Reaction Kinetics, 3d ed. Butterworths, London.
  279. Laukkanen T., Carr J. K., Janssens W., Liitsola K., Gotte D., McCutchan F. E., de Coul E. O., Cornelissen M., Heyndrickx L., van der Groen G. Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America. Virology. 2000;269:95–104. [PubMed: 10725202]
  280. Lavoie T. B., Mohan S., Lipschultz C. A., Grivel J.-C., Li Y., Mainhart C. R., Kam-Morgan L. N. W., Drohan W. N., Smith-Gill S. J. Structural differences among monoclonal antibodies with distinct fine specificities and kinetic properties. Molecular Immunology. 1999;36:1189–1205. [PubMed: 10698321]
  281. Layne S. P., Beugelsdijk T. J., Patel C. K., Taubenberger J. K., Cox N. J., Gust I. D., Hay A. J., Tashiro M., Lavanchy D. A global lab against influenza. Science. 2001;293:1729. [PubMed: 11546841]
  282. LeClerc J. E., Li B., Payne W. L., Cebula T. A. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science. 1996;274:1208–1211. [PubMed: 8895473]
  283. Leigh E. G. Natural selection and mutability. American Naturalist. 1970;104:301–305.
  284. Lescar J., Pellegrini M., Souchon H., Tello D., Poljak R. J., Peterson N., Greene M., Alzari P. M. Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea fowl lysozyme. Journal of Biological Chemistry. 1995;270:18067–18076. [PubMed: 7629116]
  285. Levin B. R., Bull J. J. Short-sighted evolution and the virulence of pathogenic microorganisms. Trends in Microbiology. 1994;2:76–81. [PubMed: 8156275]
  286. Levinson G., Gutman G. A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution. 1987;4:203–221. [PubMed: 3328815]
  287. Li, C. C. 1976. First Course in Population Genetics. Boxwood Press, Pacific Grove, California.
  288. Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Sunderland, Massachusetts.
  289. Liang S., Mozdzanowska K., Palladino G., Gerhard W. Heterosub-typic immunity to influenza type A virus in mice. Journal of Immunology. 1994;152:1653–1661. [PubMed: 8120375]
  290. Liebert U. G., Flanagan S. G., Loffler S., Baczko K., ter Meulen V., Rima B. K. Antigenic determinants of measles virus hemagglutinin associated with neurovirulence. Journal of Virology. 1994;68:1486–1493. [PMC free article: PMC236604] [PubMed: 7508996]
  291. Lin J., Andreasen V., Levin S. A. Dynamics of influenza A drift: the linear three-strain model. Mathematical Biosciences. 1999;162:33–51. [PubMed: 10616279]
  292. Lindstrom S. E., Hiromoto Y., Nerome R., Omoe K., Sugita S., Yamazaki Y., Takahashi T., Nerome K. Phylogenetic analysis of the entire genome of influenza A (H3N2) viruses from Japan: evidence for genetic reassortment of the six internal genes. Journal of Virology. 1998;72:8021–8031. [PMC free article: PMC110138] [PubMed: 9733841]
  293. Lindstrom S. E., Hiromoto Y., Nishimura H., Saito T., Nerome R., Nerome K. Comparative analysis of evolutionary mechanisms of the hemagglutinin and three internal protein genes of inflenza B virus: multiple cocirculating lineages and frequent reassortment of the NP, M, and NS genes. Journal of Virology. 1999;73:4413–4426. [PMC free article: PMC104222] [PubMed: 10196339]
  294. Llorente M., Sánchez-Palomino S., Mañes S., Luca P., Kremer L., de Alborán I. M., Torán J. L., Alcamí J., del Real G., Martínez-A. C. Natural human antibodies retrieved by phage display libraries from healthy donors: polyreactivity and recognition of human immunodeficiency virus type 1 gp120 epitopes. Scandinavian Journal of Immunology. 1999;50:270–279. [PubMed: 10447936]
  295. Lord C. C., Barnard B., Day K., Hargrove J. W., McNamara J. J., Paul R. E. L., Trenholme K., Woolhouse M. E. J. Aggregation and distribution of strains in microparasites. Philosophical Transactions of the Royal Society of London B. 1999;354:799–807. [PMC free article: PMC1692560] [PubMed: 10365405]
  296. Louis P., Eliaou J.-F., Kerlan-Candon S., Pinet V., Vincent R., Clot J. Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution. Immunogenetics. 1993;38:21–26. [PubMed: 8462990]
  297. Louis P., Vincent R., Cavadore P., Clot J., Eliaou J.-F. Differential transcriptional activities of HLA-DR genes in the various haplotypes. Journal of Immunology. 1994;153:5059–5067. [PubMed: 7963565]
  298. MacLeod A., Turner C. M. R., Tait A. A high level of mixed T. brucei infections in tsetse flies detected by three hypervariable minisatellites. Molecular and Biochemical Parasitology. 1999;102:237–248. [PubMed: 10498180]
  299. MacLeod A., Tweedie A., Welburn S. C., Maudlin I., Turner C. M. R., Tait A. Minisatellite marker analysis of Trypanosoma brucei: reconciliation of clonal, panmictic, and epidemic population genetic structures. Proceedings of the National Academy of Sciences USA. 2000;97:13442–13447. [PMC free article: PMC27243] [PubMed: 11078512]
  300. Madrenas J. Differential signalling by variant ligands of the T cell receptor and the kinetic model of T cell activation. Life Sciences. 1999;64:717–731. [PubMed: 10075104]
  301. Malorny B., Morelli G., Kusecek B., Kolberg J., Achtman M. Sequence diversity, predicted two-dimensional protein structure, and epitope mapping of neisserial Opa proteins. Journal of Bacteriology. 1998;180:1323–1330. [PMC free article: PMC107023] [PubMed: 9495774]
  302. Man S., Newberg M. H., Crotzer V. L., Luckey C. J., Williams N. S., Chen Y., Huczko E. L., Ridge J. P., Engelhard V. H. Definition of a human T cell epitope from influenza A non-structural protein 1 using HLA-A2.1 transgenic mice. International Immunology. 1995;7:597–605. [PubMed: 7547687]
  303. Man S., Ridge J. P., Engelhard V. H. Diversity and dominance among TCR recognizing HLA-A2.1(+) influenza matrix peptide in human MHC class I transgenic mice. Journal of Immunology. 1994;153:4458–4467. [PubMed: 7963521]
  304. Manz R. A., Löhning M., Cassese G., Theil A., Radbruch A. Survival of long-lived plasma cells is independent of antigen. International Immunology. 1998;10:1703–1711. [PubMed: 9846699]
  305. Mao E. F., Lane L., Lee J., Miller J. H. Proliferation of mutators in a cell population. Journal of Bacteriology. 1997;179:417–422. [PMC free article: PMC178711] [PubMed: 8990293]
  306. Marrs C. F., Reuhl W. W., Schoolnik G. K., Falkow S. Pilin gene phase variation of Moraxella bovis is caused by an inversion of the pilin gene. Journal of Bacteriology. 1988;170:3032–3039. [PMC free article: PMC211245] [PubMed: 2898471]
  307. Marsh K., Howard R. J. Antigens induced on erythrocytes by P. falciparum: expression of diverse and conserved determinants. Science. 1986;231:150–153. [PubMed: 2417315]
  308. Marsh, S. G. E., Parham, P., and Barber, L. D. 2000. The HLA FactsBook. Academic Press, San Diego.
  309. Marshall D., Sealy R., Sangster M., Coleclough C. TH cells primed during influenza virus infection provide help for qualitatively distinct antibody responses to subsequent immunization. Journal of Immunology. 1999;163:4673–4682. [PubMed: 10528164]
  310. Martin D. R., Single L. A. Molecular epidemiology of group A streptococcus-M type-1 infections. Journal of Infectious Diseases. 1993;167:1112–1117. [PubMed: 8098053]
  311. Martin D. W., Weber P. C. DNA replication promotes high-frequency homologous recombination during Autograha californica multiple nuclear polyhedrosis virus infection. Virology. 1997;232:300–309. [PubMed: 9191843]
  312. Martín J., Wharton S. A., Lin Y. P., Takemoto D. K., Skehel J. J., Wiley D. C., Steinhauer D. A. Studies of the binding properties of influenza hemagglutinin receptor-site mutants. Virology. 1998;241:101–111. [PubMed: 9454721]
  313. Martínez M. A., Verdaguer N., Mateu M. G., Domingo E. Evolution subverting essentiality: dispensability of the cell attachment Arg-Gly-Asp motif in multiply passaged foot-and-mouth disease virus. Proceedings of the National Academy of Sciences USA. 1997;94:6798–6802. [PMC free article: PMC21238] [PubMed: 9192645]
  314. Martinson J. J., Chapman N. H., Rees D. C., Liu Y.-T., Clegg J. B. Global distribution of the CCR5 gene 32-basepair deletion. Nature Genetics. 1997;16:100–103. [PubMed: 9140404]
  315. Maryanski J. L., Attuil V., Bucher P., Walker P. R. A quantitative, single-cell PCR analysis of an antigen-specific TCR repertoire selected during an in vivo CD8 response: direct evidence for a wide range of clone sizes with uniform tissue distribution. Molecular Immunology. 1999;36:745–753. [PubMed: 10593513]
  316. Maryanski J. L., Casanova J.-L., Falk K., Gournier H., Jaulin C., Kourilsky P., Lemonier F. A., Luthy R., Rammensee H. G., Rotzschke O., Servis C., Lopez J. A. The diversity of antigen-specific TCR repertoires reflects the relative complexity of epitopes recognized. Human Immunology. 1997;54:117–128. [PubMed: 9297530]
  317. Maryanski J. L., Jongeneel C. V., Bucher P., Casanova J.-L., Walker P. R. Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones. Immunity. 1996;4:47–55. [PubMed: 8574851]
  318. Mason D. A very high level of crossreactivity is an essential feature of the T-cell receptor. Immunology Today. 1999;19:395–404. [PubMed: 9745202]
  319. Masurel N. Serological characteristics of a `new' serotype of influenza A virus: the Hong Kong strain. Bulletin of the World Health Organization. 1969;41:461–468. [PMC free article: PMC2427714] [PubMed: 5309456]
  320. Masurel N. Swine influenza virus and the recycling of influenza A viruses in man. Lancet. 1976;22:244–247. [PubMed: 59252]
  321. Mateu M. G. Antibody recognition of picornaviruses and escape from neutralization: a structural view. Virus Research. 1995;38:1–24. [PubMed: 8546007]
  322. Mateu M. G., Escarmís C., Domingo E. Mutational analysis of discontinuous epitopes of foot-and-mouth disease virus using an unprocessed capsid promoter precursor. Virus Research. 1998;53:27–37. [PubMed: 9617767]
  323. Mateu M. G., Hernández J., Martínez M. A., Feigelstock D., Lea S., Peréz J. J., Giralt E., Stuart D., Palma E. L., Domingo E. Antigenic heterogeneity of a foot-and-mouth disease virus serotype in the field is mediated by very limited sequence variation at several antigenic sites. Journal of Virology. 1994;68:1407–1417. [PMC free article: PMC236594] [PubMed: 8107204]
  324. Mateu M. G., Silva D. A., Rocha E., De Brum D. L., Alonso A., Enjuanes L., Domingo E., Barahona H. Extensive antigenic heterogeneity of foot-and-mouth disease virus of serotype C. Virology. 1988;167:113–124. [PubMed: 2460992]
  325. Matrosovich M., Gao P., Kawaoka Y. Molecular mechanisms of serum resistance of human influenza H3N2 virus and their involvement in virus adaptation in a new host. Journal of Virology. 1998;72:6373–6380. [PMC free article: PMC109785] [PubMed: 9658077]
  326. Matrosovich M., Zhou N., Kawaoka Y., Webster R. The surface glycoproteins of H5 influenza viruses isolated from humans, chickens, and wild aquatic birds have distinguishable properties. Journal of Virology. 1999;73:1146–1155. [PMC free article: PMC103935] [PubMed: 9882316]
  327. Matrosovich M. N., Gambaryan A. S., Teneberg S., Piskarev V. E., Yamnikova S. S., Lvov D. K., Robertson J. S., Karlsson K.-A. Avian influenza A viruses differ from human viruses by recognition of sialyloligosaccharides and gangliosides and by a higher conservation of the HA receptor-binding site. Virology. 1997;233:224–234. [PubMed: 9201232]
  328. Maynard Smith J., Smith N. H., O'Rourke M., Spratt B. G. How clonal are bacteria? Proceedings of the National Academy of Sciences USA. 1993;90:4384–4388. [PMC free article: PMC46515] [PubMed: 8506277]
  329. McCutchan, F. E. 1999. Global diversity in HIV. In Crandall, K. A., ed., The Evolution of HIV, pp. 41–101. Johns Hopkins University Press, Baltimore, Maryland.
  330. McLain L., Dimmock N. J. Single- and multi-hit kinetics of immunoglobulin G neutralization of human immunodeficiency virus type 1 by monoclonal antibodies. Journal of General Virology. 1994;75:1457–1460. [PubMed: 8207410]
  331. McMichael A. J., Doherty P. C. Introduction. Philosophical Transactions of the Royal Society of London B. 2000;355:315–316.
  332. McMichael A. J., Gotch F. M., Dongworth D. W., Clark A., Potter C. W. Declining T-cell immunity to influenza, 1977–1982. Lancet. 1983a;2:762–764. [PubMed: 6137602]
  333. McMichael A. J., Gotch F. M., Noble G. R., Beare P. S. Cytotoxic T-cell immunity to influenza. New England Journal of Medicine. 1983b;309:13–17. [PubMed: 6602294]
  334. McMichael A. J., Phillips R. E. Escape of human immunodeficiency virus from immune control. Annual Review of Immunology. 1997;15:271–296. [PubMed: 9143689]
  335. Menon J. N., Bretscher P. A. Parasite dose determines the Th1/Th2 nature of the response to Leishmania major independently of infection route and strain of host or parasite. European Journal of Immunology. 1998;28:4020–4028. [PubMed: 9862338]
  336. Meyer S., Weiss G., von Haeseler A. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics. 1999;152:1103–1110. [PMC free article: PMC1460673] [PubMed: 10388828]
  337. Meyer T. F. Molecular basis of surface antigen variation in Neisseria. Trends in Genetics. 1987;3:319–324.
  338. Michod R. E. Cooperation and conflict in the evolution of individuality. I. Multilevel selection of the organism. American Naturalist. 1997;149:607–645.
  339. Mills K., Skehel J., Thomas B. Extensive diversity in the recognition of influenza virus hemagglutinin by murine T helper clones. Journal of Experimental Medicine. 1986;163:1477–1490. [PMC free article: PMC2188120] [PubMed: 2423631]
  340. Mims, C., Nash, A., and Stephen, J. 2001. Mims Pathogenesis of Infectious Disease, 5th ed. Academic Press, San Diego.
  341. Mims, C., Playfair, J., Roitt, I., Wakelin, D., and Williams, R. 1998. Medical Microbiology, 2d ed. Mosby, London.
  342. Mims, C. A. 1987. The Pathogenesis of Infectious Disease, 3d ed. Academic Press, London.
  343. Mims, C. A., Playfair, J. H. L., Roitt, I. M., Wakelin, D., and Williams, R. 1993. Medical Microbiology. Mosby, St. Louis, Missouri.
  344. Mitchison A. Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins. Immunogenetics. 1997;46:46–52. [PubMed: 9148788]
  345. Mitchison N. A., Muller B., Segel R. M. Natural variation in immune responsiveness, with special reference to immunodeficiency and promoter polymorphism in class II MHC genes. Human Immunology. 2000;61:177–181. [PubMed: 10717812]
  346. Modrow S., Hahn B. H., Shaw G. M., Gallo R. C., Wong-Staal F., Wolf H. Computer-assisted analysis of envelope protein sequences of seven human immunodeficiency isolates: predictions of antigenic epitopes in conserved and variable regions. Journal of Virology. 1987;61:570–578. [PMC free article: PMC253982] [PubMed: 2433466]
  347. Moffatt M. F., Schou C., Faux J. A., Cookson W. O. C. M. Germline TCR-A restriction of immunoglobulin E responses to allergen. Immunogenetics. 1997;46:226–230. [PubMed: 9211749]
  348. Mohan, K., and Stevenson, M. M. 1998. Acquired immunity to asexual blood stages. In Sherman, I. W., ed., Malaria: Parasite Biology, Pathogenesis, and Protection, pp. 467–493. American Society for Microbiology, Washington, D.C.
  349. Montgomery A. M. P., Reisfeld R. A., Cheresh D. A. Integrin ανβ3 rescues melanoma cells from apoptosis in three-dimensional dermal collagen. Proceedings of the National Academy of Sciences USA. 1994;91:8856–8860. [PMC free article: PMC44705] [PubMed: 7522323]
  350. Moody A. M., Reyburn H., Willcox N., Newsom-Davis J. New polymorphism of the human T-cell receptor AV28S1 gene segment. Immunogenetics. 1998;48:62–64. [PubMed: 9601945]
  351. Morrison J., Elvin J., Latron F., Gotch F., Moots R., Strominger J. L., McMichael A. Identification of the nonamer peptide from influenza A matrix protein and the role of pockets of HLA-A2 in its recognition by cytotoxic T lymphocytes. European Journal of Immunology. 1992;22:903–907. [PubMed: 1372560]
  352. Moskophidis D., Zinkernagel R. M. Immunobiology of cytotoxic T-cell escape mutants of lymphocytic choriomeningitis virus. Journal of Virology. 1995;69:2187–2193. [PMC free article: PMC188887] [PubMed: 7533851]
  353. Mosser, A. G., Leippe, D., and Rueckert, R. R. 1989. Neutralization of picornaviruses: support for the pentamer bridging hypothesis. In Semler, B. L., and Ehrenfeld, E., eds., Molecular Aspects of Picornavirus Infection and Detection, pp. 155–167. American Society for Microbiology, Washington, D.C.
  354. Moxon E. R., Rainey P. B., Nowak M. A., Lenski R. E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Current Biology. 1994;4:24–33. [PubMed: 7922307]
  355. Moya A., Elena S. F., Bracho A., Miralles R., Barrio E. The evolution of RNA viruses: a population genetics view. Proceedings of the National Academy of Sciences USA. 2000;97:6967–6973. [PMC free article: PMC34371] [PubMed: 10860958]
  356. Muñoz-Jordán J. L., Davies K. P., Cross G. A. M. Stable expression of mosaic coats of variant surface glycoproteins in Trypanosoma brucei. Science. 1996;272:1795–1797. [PubMed: 8650579]
  357. Muotiala A., Seppala H., Huovinen P., Vuopio-Varkila J. Molecular comparison of group A streptococci of T1M1 serotype from invasive and noninvasive infections in Finland. Journal of Infectious Diseases. 1997;175:392–399. [PubMed: 9203660]
  358. Murali-Krishna K., Altman J. D., Suresh M., Sourdive D. J. D., Zajac A. J., Miller J. D., Slansky J., Ahmed R. Counting antigen-specific CD8 T cells: a reevaluation of bystander activation during viral infection. Immunity. 1998;8:177–187. [PubMed: 9491999]
  359. Mylin L. M., Bonneau R. H., Lippolis J. D., Tevethia S. S. Hierarchy among multiple H-2b-restricted cytotoxic T-lymphocyte epitopes within simian virus 40 T antigen. Journal of Virology. 1995;69:6665–6677. [PMC free article: PMC189576] [PubMed: 7474076]
  360. Nakagawa T. Y., Rudensky A. Y. The role of lysosomal proteinases in MHC class II–mediated antigen processing and presentation. Immunological Reviews. 1999;172:121–129. [PubMed: 10631942]
  361. Nakajima S., Nobusawa E., Nakajima K. Variation in response among individuals to antigenic sites on the HA protein of human influenza virus may be responsible for the emergence of drift strains in the human population. Virology. 2000;274:220–231. [PubMed: 10936103]
  362. Nakra P., Manivel V., Vishwakarma R. A., Rao K. V. S. B cell responses to a peptide epitope. X. Epitope selection in a primary response is thermodynamically regulated. Journal of Immunology. 2000;164:5615–5625. [PubMed: 10820236]
  363. Nara P. L., Garrity R. Deceptive imprinting: a cosmopolitan strategy for complicating vaccination. Vaccine. 1998;16:1780–1787. [PubMed: 9795381]
  364. Natali A., Oxford J. S., Schild G. C. Frequency of naturally occurring antibody to influenza virus antigenic variants selected in vitro with monoclonal antibody. Journal of Hygiene. 1981;87:185–191. [PMC free article: PMC2134050] [PubMed: 7288173]
  365. Natali A., Pilotti E., Valcavi P. P., Chezzi C., Oxford J. S. Natural and `in vitro' selected antigenic variants of influenza A virus (H2N2). Journal of Infection. 1998;37:19–23. [PubMed: 9733372]
  366. Nayak B. P., Tuteja R., Manivel V., Roy R. P., Vishwakarma R. A., Rao K. V. S. B cell responses to a peptide epitope. V. Kinetic regulation of repertoire discrimination and antibody optimization for epitope. Journal of Immunology. 1998;161:3510–3519. [PubMed: 9759871]
  367. Nee S., Holmes E. C., Rambaut A., Harvey P. H. Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London B. 1995;349:25–31. [PubMed: 8748016]
  368. Neff S., Sa-Carvalho D., Rieder E., Mason P. W., Blystone S. D., Brown E. J., Baxt B. Foot-and-mouth disease virus virulent for cattle utilizes the integrin αvβ3 as its receptor. Journal of Virology. 1998;72:3587–3594. [PMC free article: PMC109579] [PubMed: 9557639]
  369. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
  370. Nei, M., and Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
  371. Neva F. A. Looking back for a view of the future: observations of immunity to induce malaria. American Journal of Tropical Medicine and Hygiene. 1977;26:211–215. [PubMed: 74211]
  372. Newman A. M., Mainhart C. R., Mallet C. P., Lavoie T. B., Smith-Gill S. J. Patterns of antibody specificity during the BALB/c immune response to hen egg white lysozyme. Journal of Immunology. 1992;149:3260–3272. [PubMed: 1431104]
  373. Nguyen-Van-Tam, J. S. 1998. Epidemiology of influenza. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 181–206. Black-well Science, Oxford.
  374. Niedermann G., Butz S., Ihlenfeldt H. G., Grimm R., Lucchiari M., Hoschutzky H., Jung G., Maier B., Eichmann K. Contribution of proteasome-mediated proteolysis to the hierarchy of epitopes presented by major histocompatibility complex class I molecules. Immunity. 1995;2:289–299. [PubMed: 7535183]
  375. Niedermann G., Geier E., Lucchiari-Hartz M., Hitziger N., Ramsperger A., Eichmann K. The specificity of proteasomes: impact on MHC class I processing and presentation of antigens. Journal of Immunology. 1999;158:1507–1515. [PubMed: 10631935]
  376. Niedermann G., King G., Butz S., Birsner U., Grimm R., Shabanowitz J., Hunt D. F., Eichmann K. The proteolytic fragments generated by vertebrate proteasomes: structural relationships to major histocompatibility complex class I binding peptides. Proceedings of the National Academy of Sciences USA. 1996;93:8572–8577. [PMC free article: PMC38714] [PubMed: 8710912]
  377. Nielsen L., Blixenkrone-Møller M., Thylstrup M., Hansen N. J. V., Bolt G. Adaptation of wild-type measles virus to CD46 receptor usage. Archives of Virology. 2001;146:197–208. [PubMed: 11315632]
  378. Niewiesk S., Daenke S., Parker C. E., Taylor G., Weber J., Nightingale S., Bangham C. R. M. Naturally occurring variants of human T-cell leukemia virus type I Tax protein impair its recognition by cytotoxic T lymphocytes and the transactivation function of Tax. Journal of Virology. 1995;69:2649–2653. [PMC free article: PMC188948] [PubMed: 7533860]
  379. Nokes D. J., Anderson R. M., Anderson M. J. Rubella epidemiology in South East England. Journal of Hygiene. 1986;86:291–304. [PMC free article: PMC2129636] [PubMed: 3701043]
  380. Nowak, M. A., and May, R. M. 2000. Virus Dynamics: Mathematical Principles of Immunology and Virology. Oxford University Press, Oxford.
  381. Nowak M. A., May R. M., Phillips R. E., Rowland-Jones S., Lalloo D. G., McAdam S., Klenerman P., Koppe B., Sigmund K., Bangham C. R. M. et al. Antigenic oscillations and shifting immunodominance in HIV-1 infections. Nature. 1995;375:606–611. [PubMed: 7791879]
  382. Núñez J. I., Baranowski E., Molina N., Ruiz-Jarabo C. M., Sánchez C., Domingo E., Sobrino F. A single amino acid substitution in nonstructural protein 3A can mediate adaptation of foot-and-mouth disease virus to the guinea pig. Journal of Virology. 2001;75:3977–3983. [PMC free article: PMC114889] [PubMed: 11264387]
  383. Nyambi P. N., Lewi P., Peeters M., Janssens W., Heyndrickx L., Fransen K., Andries K., Vanden Haesevelde M., Heeney J., Piot P., van der Groen G. Study of the dynamics of neutralization escape mutants in a chimpanzee naturally infected with the simian immunodeficiency virus SIVcpz-ant. Journal of Virology. 1997;71:2320–2330. [PMC free article: PMC191341] [PubMed: 9032368]
  384. Nyambi P. N., Mbah H. A., Burda S., Williams C., Gorny M. K., Nádas A., Zolla-Pazner S. Conserved and exposed epitopes on intact, native, primary human immunodeficiency virus type 1 virions of group M. Journal of Virology. 2000a;74:7096–7107. [PMC free article: PMC112228] [PubMed: 10888650]
  385. Nyambi P. N., Nádas A., Mbah H. A., Burda S., Williams C., Gorny M. K., Zolla-Pazner S. Immunoreactivity of intact virions of human immunodeficiency virus type 1 (HIV-1) reveals the existence of fewer HIV-1 immunotypes than genotypes. Journal of Virology. 2000b;74:10670–10680. [PMC free article: PMC110941] [PubMed: 11044111]
  386. Nyambi P. N., Nkengasong J., Lewi P., Andries K., Janssens W., Fransen K., Heyndrickx L., Piot P., van der Groen G. Multivariate analysis of human immunodeficiency virus type 1 neutralization data. Journal of Virology. 1996;70:6235–6243. [PMC free article: PMC190648] [PubMed: 8709250]
  387. O'Brien S. J., Dean M. In search of AIDS-resistance genes. Scientific American. 1997;277(3):44–51. [PubMed: 9274039]
  388. Ochman H., Lawrence J. G., Groisman E. A. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304. [PubMed: 10830951]
  389. Ochsenbein A. F., Fehr T., Lutz C., Suter M., Brombacher F., Hengartner H., Zinkernagel R. M. Control of early viral and bacterial distribution and disease by natural antibodies. Science. 1999;286:2156–2159. [PubMed: 10591647]
  390. Ochsenbein A. F., Pinschewer D. D., Sierro S., Horvath E., Hengartner H., Zinkernagel R. M. Protective long-term antibody memory by antigen-driven and T help-dependent differentiation of long-lived memory B cells to short-lived plasma cells independent of secondary lymphoid organs. Proceedings of the National Academy of Sciences. 2000;97:13263–13268. [PMC free article: PMC27213] [PubMed: 11069289]
  391. O'hUigin C., Satta Y., Hausmann A., Dawkins R. L., Klein J. The implications of intergenic polymorphism for major histocompatibility complex evolution. Genetics. 2000;156:867–877. [PMC free article: PMC1461294] [PubMed: 11014832]
  392. Oliveira R. P., Broude N. E., Macedo A. M., Cantor C. R., Smith C. L., Pena S. D. J. Probing the genetic population structure of Trypanosoma cruzi with polymorphic microsatellites. Proceedings of the National Academy of Sciences USA. 1998;95:3776–3780. [PMC free article: PMC19913] [PubMed: 9520443]
  393. Oliveira R. P., Melo A. I. R., Macedo A. M., Chiari E., Pena S. D. J. The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites. Memorias do Instituto Oswaldo Cruz. 1999;94(Suppl. 1):65–70. [PubMed: 10677692]
  394. Orive M. E. Senescence in organisms with clonal reproduction and complex life histories. American Naturalists. 1995;145:90–108.
  395. Ossendorp F., Eggers M., Neisig A., Ruppert T., Groettrup M., Sijts A., Mengede E., Kloetzel P.-M., Neefjes J., Koszinowski U., Melief C. A single residue exchange within a viral CTL epitope alters proteasome-mediated degradation resulting in lack of antigen presentation. Immunity. 1996;5:115–124. [PubMed: 8769475]
  396. Otto S. P. Detecting the form of selection from DNA sequence data. Trends in Genetics. 2000;16:526–529. [PubMed: 11102697]
  397. Otto S. P., Hastings I. M. Mutation and selection within the individual. Genetica. 1998;102/103:507–524. [PubMed: 9766963]
  398. Overbaugh J., Bangham C. R. M. Selection forces and constraints on retroviral sequence variation. Science. 2001;292:1106–1109. [PubMed: 11352065]
  399. Oxford J. S. Influenza A pandemics of the 20th century with special reference to 1918: virology, pathology and epidemiology. Reviews in Medical Virology. 2000;10:119–133. [PubMed: 10713598]
  400. Page, R. D. M., and Holmes, E. C. 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Scientific, Oxford.
  401. Palese P., Compans R. W. Inhibition of influenza virus replication in tissue culture by 2-deoxy-2,3-dehydro-N-trifluoro-acetyl-neuraminic acid (FANA): mechanism of action. Journal of General Virology. 1976;33:159–163. [PubMed: 978183]
  402. Parker E. P., Nightingale S., Taylor G. P., Weber J., Bangham C. R. M. Circulating anti-Tax cytotoxic T lymphocytes from human T-cell leukemia virus type I–infected people, with and without tropical spastic paraparesis, recognize multiple epitopes simultaneously. Journal of Virology. 1994;68:2860–2868. [PMC free article: PMC236774] [PubMed: 7512153]
  403. Paul R. E. L., Day K. P. Mating patterns of Plasmodium falciparum. Parasitology Today. 1998;14:197–202. [PubMed: 17040751]
  404. Paul, W. E. 1993. Fundamental Immunology. Raven Press, New York.
  405. Paulson, J. C. 1985. Interactions of animal viruses with cell surface receptors. In Conn, M., ed., The Receptors, pp. 131–219. Academic Press, New York.
  406. Pays E. Gene conversion in trypanosome antigenic variation. Progress in Nucleic Acid Research and Molecular Biology. 1985;32:1–26. [PubMed: 3911274]
  407. Pays E. Pseudogenes, chimeric genes and the timing of antigen variation in African trypanosomes. Trends in Genetics. 1989;5:389–391. [PubMed: 2696181]
  408. Pays E., Lheureux M., Steinert M. The expression-linked copy of the surface antigen gene in Trypanosoma is probably the one transcribed. Nature. 1981;292:265–267. [PubMed: 7254319]
  409. Pays E., Nolan D. Expression and function of surface proteins in Trypanosoma brucei. Molecular and Biochemical Parasitology. 1998;91:3–36. [PubMed: 9574923]
  410. Peng G., Hongo S., Kimura H., Muraki Y., Sugawara K., Kitame F., Numazaki Y., Suzuki H., Nakamura K. Frequent occurrence of genetic re-assortment between influenza C virus strains in nature. Journal of General Virology. 1996;77:1489–1492. [PubMed: 8757991]
  411. Peng G., Hongo S., Muraki Y., Sugawara K., Nishimura H., Kitame F., Nakamura K. Genetic reassortment of influenza C viruses in man. Journal of General Virology. 1994;75:3619–3622. [PubMed: 7996155]
  412. Pinilla C., Martin R., Gran B., Appel J. R., Boggiano C., Wilson D. B., Houghten R. A. Exploring immunological specificity using synthetic peptide combinatorial libraries. Current Opinion in Immunology. 1999;11:193–202. [PubMed: 10322159]
  413. Pircher H., Moskophidis D., Rohrer U., Burki K., Hengartner H., Zinkernagel R. M. Viral escape by selection of cytotoxic T cell–resistant virus variants in vivo. Nature. 1990;346:629–633. [PubMed: 1696684]
  414. Piyasirisilp S., McCutchan F. E., Carr J. K., Sanders-Buell E., Liu W., Chen J., Wagner R., Wolf H., Shao Y., Lai S., Beyrer C., Yu X.-F. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. Journal of Virology. 2000;74:11286–11295. [PMC free article: PMC113233] [PubMed: 11070028]
  415. Plebanski M., Lee E. A. M., Hannan C. M., Flanagan K. L., Gilbert S. C., Gravenor M. B., Hill A. V. S. Altered peptide ligands narrow the repertoire of cellular immune responses by interfering with T-cell priming. Nature Medicine. 1999;5:565–571. [PubMed: 10229235]
  416. Plotkin, S. A., and Orenstein, W. A., eds. 1999. Vaccines, 3d ed. W. B. Saunders, Philadelphia.
  417. Porcelli S. A., Modlin R. L. The CD1 system: antigen-presenting molecules for T cell recognition of lipids and glycolipids. Annual Review of Immunology. 1999;17:297–329. [PubMed: 10358761]
  418. Porter P. Immunoglobulins in bovine mammary secretions: quantitative changes in early lactation and absorption by the neonatal calf. Immunology. 1972;23:225–237. [PMC free article: PMC1407913] [PubMed: 4560742]
  419. Potts J. R., Campbell I. D. Fibronectin structure and assembly. Current Opinion in Cell Biology. 1994;6:648–655. [PubMed: 7833045]
  420. Power C. A. Factors that influence T helper cell response to infection. Current Opinion in Infectious Diseases. 2000;13:209–213. [PubMed: 11964788]
  421. Prager E. M. The sequence-immunology correlation revisited: data for cetacean myoglobins and mammalian lysozymes. Journal of Molecular Evolution. 1993;37:408–416. [PubMed: 8308908]
  422. Preiser P. R., Jarra W., Capiod T., Snounou G. A rhoptry-protein-associated mechanism of clonal phenotypic variation in rodent malaria. Nature. 1999;398:618–622. [PubMed: 10217144]
  423. Preston B. D., Dougherty J. P. Mechanisms of retroviral mutation. Trends in Microbiology. 1996;4:16–21. [PubMed: 8824790]
  424. Price D. A., Meier U.-C., Klenerman P., Purbhoo M. A., Phillips R. E., Sewell A. K. The influence of antigenic variation on cytotoxic T lymphocyte responses in HIV-1 infection. Journal of Molecular Medicine. 1998;76:699–708. [PubMed: 9766848]
  425. Price G. E., Ou R., Jiang H., Huang L., Moskophidis D. Viral escape by selection of cytotoxic T cell–resistant variants in influenza A virus pneumonia. Journal of Experimental Medicine. 2000;191:1853–1867. [PMC free article: PMC2213532] [PubMed: 10839802]
  426. Prigozy T. I., Naidenko O., Qasba P., Elewaut D., Brossay L., Khurana A., Natori T., Koezuka Y., Kulkarni A., Kronenberg M. Glycolipid antigen processing for presentation by CD1d molecules. Science. 2001;291:664–667. [PubMed: 11158680]
  427. Puel A., Groot P. C., Lathrop M. G., Demant P., Mouton D. Mapping of genes controlling quantitative antibody production in Biozzi mice. Journal of Immunology. 1995;154:5799–5805. [PubMed: 7751629]
  428. Puglielli M. T., Zajac A. J., van der Most R. G., Dzuris J. L., Sette A., Altman J. D., Ahmed R. In vivo selection of a lymphocytic choriomeningitis virus variant that affects recognition of the GP330043 epitope by H-2Db but not H–2Kb. Journal of Virology. 2001;75:5099–5107. [PMC free article: PMC114915] [PubMed: 11333891]
  429. Racaniello, V. R. 2001. Picornaviridae: the viruses and their replication. In Knipe, D. M., and Howley, P. M., eds., Fields Virology, 4th ed., pp. 685–722. Lippincott-Raven, Philadelphia.
  430. Radman M. Enzymes of evolutionary change. Nature. 1999;401:866–868. [PubMed: 10553899]
  431. Rammensee H. G., Friede T., Stefanovic S. MHC ligand motifs: first listing. Immunogenetics. 1995;41:178–228. [PubMed: 7890324]
  432. Rao K. V. S. Selection in a T-dependent primary humoral response: new insights from polypeptide models. APMIS. 1999;107:807–818. [PubMed: 10519315]
  433. Reeder J. C., Brown G. V. Antigenic variation and immune evasion in Plasmodium falciparum malaria. Immunology and Cell Biology. 1996;74:546–554. [PubMed: 8989593]
  434. Rehermann B., Chang K. M., McHutchison J., Kokka R., Houghton M., Rice C. M., Chisari F. V. Differential cytotoxic T-lymphocyte responsiveness to the hepatitis B and C virus in chronically infected patients. Journal of Virology. 1996;70:7092–7102. [PMC free article: PMC190761] [PubMed: 8794355]
  435. Reichstetter S., Krellner P. H., Meenzen C. M., Kalden J. R., Wassmuth R. Comparative analysis of sequence variability in the upstream regulatory region of the HLA-DQB1 gene. Immunogenetics. 1994;39:207–212. [PubMed: 8276467]
  436. Reider E., Baxt B., Mason P. W. Animal derived antigenic variants of foot-and-mouth disease virus type A12 have low affinity for cells in culture. Journal of Virology. 1994;68:5296–5299. [PMC free article: PMC236478] [PubMed: 8035529]
  437. Reimann J., Schirmbeck R. Alternative pathways for processing exogenous and endogenous antigens that can generate peptides for MHC class I–restricted presentation. Immunological Reviews. 1999;172:131–152. [PubMed: 10631943]
  438. Revollo S., Oury B., Laurent J.-P., Barnabé C., Quesney V., Carriere V., Noël S., Tibayrenc M. Trypanosoma cruzi: impact of clonal evolution of the parasite on its biological and medical properties. Experimental Parasitology. 1998;89:30–39. [PubMed: 9603486]
  439. Reyburn H., Cornélis F., Russell V., Harding R., Moss P., Bell J. Allelic polymorphism of human T-cell receptor V alpha gene segments. Immunogenetics. 1993;38:287–291. [PubMed: 8319979]
  440. Rich S. M., Ferreira M. U., Ayala F. J. The origin of antigenic diversity in Plasmodium falciparum. Parasitology Today. 2000;16:390–396. [PubMed: 10951599]
  441. Rich S. M., Sawyer S. A., Barbour A. G. Antien polymorphism in Borrelia hermsii, a clonal pathogenic bacterium. Proceedings of the National Academy of Sciences USA. 2001;98:15038–15043. [PMC free article: PMC64979] [PubMed: 11742066]
  442. Richards F. F., Konigsberg W. H., Rosenstein R. W., Varga J. M. On the specificity of antibodies: biochemical and biophysical evidence indicates the existence of polyfunctional antibody combining regions. Science. 1975;187:130–137. [PubMed: 46122]
  443. Rickinson A. B., Callan M. F. C., Annels N. E. T-cell memory: lessons from Epstein-Barr virus infection in man. Philosophical Transactions of the Royal Society of London B. 2000;355:391–400. [PMC free article: PMC1692739] [PubMed: 10794060]
  444. Ripley L. S. Predictability of mutant sequences: relationships between mutational mechanisms and mutant specificity. Annals of the New York Academy of Sciences. 1999;870:159–172. [PubMed: 10415481]
  445. Robertson, D. L., Anderson, J. P., Bradac, J. A., Carr, J. K., Foley, B., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L., Kuiken, C., Learn, G. H., Leitner, T., McCutchan, F., Osmanov, S., Peeters, M., Pieniazek, D., Salminen, M., Sharp, P. M., Wolinsky, S., and Korber, B. 1999. HIV-1 nomenclature proposal: a reference guide to HIV-1 classification. In Kuiken, C. L., Foley, B., Hahn, B., Korber, B., McCutchan, F., Marx, P. A., Mellors, J. W., Mullins, J. I., Sodroski, J., and Wolinksy, S., eds., Human Retroviruses and AIDS 1999: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences, pp. 492–505. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
  446. Robertson D. L., Hahn B. H., Sharp P. M. Recombination in AIDS viruses. Journal of Molecular Evolution. 1995;40:249–259. [PubMed: 7723052]
  447. Robertson J. S. Clinical influenza virus and the embryonated hen's egg. Reviews in Medical Virology. 1993;3:97–106.
  448. Robertson, J. S. 1999. An overview of host cell selection. In Brown, F., Robertson, J. S., Schild, G. C., and Wood, J. M., eds., Inactivated Influenza Vaccines Prepared in Cell Culture. Developments in Biological Standards, vol. 98, pp. 7–11. Karger, Basel.
  449. Robertson J. S., Cook P., Attwell A.-M., Williams S. P. Replicative advantage in tissue culture of egg-adapted influenza virus over tissue-culture derived virus: implications for vaccine manufacture. Vaccine. 1995;13:1583–1588. [PubMed: 8578846]
  450. Robinson J., Malik A., Parham P., Bodmer J. G., Marsh S. G. E. IMGT/HLA database—a sequence database for the human major histocompatibility complex. Tissue Antigens. 2000;55:280–287. [PubMed: 10777106]
  451. Rock K. L., Goldberg A. L. Degradation of cell proteins and the generation of MHC class I–presented peptides. Annual Review of Immunology. 1999;17:739–779. [PubMed: 10358773]
  452. Roden R. B. S., Yutzy W. H., Fallon R., Inglis S., Lowy D. R., Schiller J. T. Minor capsid protein of human genital papillomaviruses contains subdominant, cross-neutralizing epitopes. Virology. 2000;270:254–257. [PubMed: 10792983]
  453. Rodrigo, A. G., and Learn, Jr., G. H., eds. 2000. Computational and Evolutionary Analysis of HIV Molecular Sequences. Kluwer Academic, Boston.
  454. Rogers G. N., Daniels R. S., Skehel J. J., Wiley D. C., Wang X., Higa H. H., Paulson J. C. Host-mediated selection of influenza virus receptor variants. Journal of Biological Chemistry. 1989;260:7362–7367. [PubMed: 3997874]
  455. Rogers G. N., D'Souza G. L. Receptor-binding properties of human and animal H1 influenza virus isolates. Virology. 1989;173:317–322. [PubMed: 2815586]
  456. Rogers G. N., Paulson J. C., Daniels R. S., Skehel J. J., Wilson I. A., Wiley D. C. Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity. Nature. 1983;304:76–78. [PubMed: 6191220]
  457. Rohani P., Earn D. J. D., Grenfell B. T. Opposite patterns of synchrony in sympatric disease metapopulations. Science. 1999;286:968–971. [PubMed: 10542154]
  458. Röhm C., Zhou N., Süss J., MacKenzie J., Webster R. G. Characterization of a novel influenza hemagglutinin, H15: criteria for determination of influenza A subtypes. Virology. 1996;217:508–516. [PubMed: 8610442]
  459. Roost H. P., Backmann M. F., Haag A., Karlinke U., Pliska V., Hengartner H., Zinkernagel R. M. Early high-affinity neutralizing anti-virus IgG responses without further overall improvement of affinity. Proceedings of the National Academy of Sciences USA. 1995;92:1257–1261. [PMC free article: PMC42498] [PubMed: 7877965]
  460. Roost H. P., Charan S., Zinkernagel R. M. Analysis of the kinetics of antiviral memory T help in vivo: characterization of short lived cross-reactive T help. European Journal of Immunology. 1990;20:2547–2554. [PubMed: 2176607]
  461. Rose, M. R. 1991. Evolutionary Biology of Aging. Oxford University Press, Oxford.
  462. Rostand K. S., Esko J. D. Microbial adherence to and invasion through proteoglycans. Infection and Immunity. 1997;65:1–8. [PMC free article: PMC174549] [PubMed: 8975885]
  463. Rottem S., Naot Y. Subversion and exploitation of host cells by mycoplasmas. Trends in Microbiology. 1998;6:436–440. [PubMed: 9846360]
  464. Rouzine I. M., Coffin J. M. Search for the mechanism of genetic variation in the pro gene of human immunodeficiency virus. Journal of Virology. 1999;73:8167–8178. [PMC free article: PMC112834] [PubMed: 10482567]
  465. Rozsa W. F., Marrs C. F. Interesting sequence differences between the pilin gene inversion regions of Moraxella lacunata ATCC 17956 and Moraxella bovis Epp63. Journal of Bacteriology. 1991;173:4000–4006. [PMC free article: PMC208046] [PubMed: 2061282]
  466. Rudensey L. M., Kimata J. T., Long E. M., Chackerian B., Overbaugh J. Changes in the extracellular envelope glycoprotein of variants that evolve during the course of simian immunodeficiency virus SIVMne infection affect neutralizing antibody recognition, syncytium formation, and macrophage tropism but not replication, cytopathicity, or CCR-5 coreceptor recognition. Journal of Virology. 1998;72:209–217. [PMC free article: PMC109366] [PubMed: 9420217]
  467. Rudneva I. A., Sklyanskaya E. I., Barulina O. S., Yamnikova S. S., Kovaleva V. P., Tsvetkova I. V., Kaverin N. V. Phenotypic expression of HA-NA combinations in human-avian influenza A virus reassortants. Archives of Virology. 1996;141:1091–1099. [PubMed: 8712926]
  468. Sa-Carvalho D., Rieder E., Baxt B., Rodarte R., Tanuri A., Mason P. W. Tissue culture adaptation of foot-and-mouth disease virus selects viruses that bind to heparin and are attenuated in cattle. Journal of Virology. 1997;71:5115–5123. [PMC free article: PMC191746] [PubMed: 9188578]
  469. Saha K., Zhang J., Gupta A., Dave R., Yimen M., Zerhouni B. Isolation of primary HIV-1 that target CD8+ T lymphocytes using CD8 as a receptor. Nature Medicine. 2001;7:65–72. [PubMed: 11135618]
  470. Salaun L., Audibert C., Le Lay G., Burucoa C., Fauchere J. L., Picard B. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiology Letters. 1998;161:231–239. [PubMed: 9570115]
  471. Salmivirta M., Lidholt K., Linkahl U. Heparan sulfate: a piece of information. FASEB Journal. 1996;10:1270–1279. [PubMed: 8836040]
  472. Samri A., Haas G., Duntze J., Bouley J.-M., Calvez V., Katlama C., Autran B. Immunogenicity of mutations induced by nucleoside reverse transcriptase inhibitors for human immunodeficiency virus type 1–specific cytotoxic T cells. Journal of Virology. 2000;74:9306–9312. [PMC free article: PMC102130] [PubMed: 10982378]
  473. Sanna P. P., Ramiro-Ibañez F., De Logu A. Synergistic interactions of antibodies in rate of virus neutralization. Virology. 2000;270:386–396. [PubMed: 10792998]
  474. Sasisekharan R., Venkataraman G. Heparin and heparan sulfate: biosynthesis, structure and function. Current Opinion in Chemical Biology. 2000;4:626–631. [PubMed: 11102866]
  475. Scherf A., Hernandez-Rivas R., Buffet P., Bottius E., Benatar C., Pouvelle B., Gysin J., Lanzer M. Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum. EMBO Journal. 1998;17:5418–5426. [PMC free article: PMC1170867] [PubMed: 9736619]
  476. Scherle P., Gerhard W. Functional analysis of influenza-specific helper T cell clones in vivo: T cells specific for internal viral proteins provide cognate help for B cell responses to hemagglutinin. Journal of Experimental Medicine. 1986;164:1114–1128. [PMC free article: PMC2188433] [PubMed: 2944982]
  477. Schneider-Schaulies J. Cellular receptors for viruses: links to tropism and pathogenesis. Journal of General Virology. 2000;81:1413–1429. [PubMed: 10811925]
  478. Schofield D. J., Stephenson J. R., Dimmock N. J. High and low efficiency neutralization epitopes on the haemagglutinin of type A influenza virus. Journal of General Virology. 1997a;78:2441–2446. [PubMed: 9349462]
  479. Schofield D. J., Stephenson J. R., Dimmock N. J. Variations in the neutralizing and haemagglutination-inhibiting activities of five influenza A virus-specific IgGs and their antibody fragments. Journal of General Virology. 1997b;78:2431–2439. [PubMed: 9349461]
  480. Schols D., De Clercq E. Human immunodeficiency virus type 1 gp120 induces anergy in human peripheral blood lymphocytes by inducing interleukin-10 production. Journal of Virology. 1996;70:4953–4960. [PMC free article: PMC190447] [PubMed: 8764000]
  481. Scholtissek, C. 1998. Genetic reassortment of human influenza viruses in nature. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 120–125. Blackwell Science, Oxford.
  482. Schroer J. A., Bender T., Feldmann T., Kim K. J. Mapping epitopes on the insulin molecule using monoclonal antibodies. European Journal of Immunology. 1983;13:693–700. [PubMed: 6193965]
  483. Schubert U., Antón L. C., Gibbs J., Norbury C. C., Yewdell J. W., Bennink J. R. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature. 2000;404:770–774. [PubMed: 10783891]
  484. Schumacher T. N. M. Immunology: accessory to murder. Nature. 1999;398:26–27. [PubMed: 10078525]
  485. Scott, T. W., Weaver, S. C., and Mallampalli, V. L. 1994. Evolution of mosquito-borne viruses. In Morse, S. S., ed., Evolutionary Biology of Viruses, pp. 293–324. Raven Press, New York.
  486. Seaman M. S., Wang C. R., Forman J. MHC class Ib–restricted CTL provide protection against primary and secondary Listeria monocytogenes infection. Journal of Immunology. 2000;165:5192–5201. [PubMed: 11046052]
  487. Seder R. A., Hill A. V. S. Vaccines against intracellular infections requiring cellular immunity. Nature. 2000;406:793–798. [PubMed: 10963610]
  488. Seed J. R. Competition among serologically different clones of Trypanosoma brucei gambiense in vivo. Journal of Protozoology. 1978;25:526–529. [PubMed: 368326]
  489. Semmes O. J., Jeang K.-T. Mutational analysis of human T-cell leukemia virus type I Tax: regions necessary for function determined with 47 mutant proteins. Journal of Virology. 1992;66:7183–7192. [PMC free article: PMC240413] [PubMed: 1433511]
  490. Seo S. H., Webster R. G. Cross-reactive, cell-mediated immunity and protection of chickens from lethal H5N1 influenza virus infection in Hong Kong poultry markets. Journal of Virology. 2001;75:2516–2525. [PMC free article: PMC115873] [PubMed: 11222674]
  491. Sette A., Alexander J., Ruppert J., Snoke K., Franco A., Ishioka G., Grey H. M. Antigen analog/MHC complexes as specific T cell receptor antagonists. Annual Review of Immunology. 1994;12:413–431. [PubMed: 8011286]
  492. Sharma P. L., Crumpacker C. S. Decreased processivity of human immunodeficiency virus type 1 reverse transcriptase (RT) containing didano-sine-selected mutation Leu75Val: a comparative analysis of RT variants Leu-74Val and lamivudine-selected Met184Val. Journal of Virology. 1999;73:8448–8456. [PMC free article: PMC112864] [PubMed: 10482597]
  493. Shields P. L., Owsianka A., Carman W. F., Boxall E., Hubscher S. G., Shaw J., O'Donnell K., Elias E., Mutimer D. J. Selection of hepatitis B surface `escape' mutants during passive immune prophylaxis following liver transplantion: potential impact of genetic changes on polymerase protein function. Gut. 1999;45:306–309. [PMC free article: PMC1727596] [PubMed: 10403747]
  494. Shin H. D., Winkler C., Stephens J. C., Bream J., Young H., Goedert J. J., O'Brien T. R., Vlahov D., Buchbinder S., Giorgi J., Rinaldo C., Donfield S., Willoughby A., O'Brien S. J., Smith M. W. Genetic restriction of HIV-1 pathogenesis to AIDS by promoter alleles of IL10. Proceedings of the National Academy of Sciences USA. 2000;97:14467–14472. [PMC free article: PMC18942] [PubMed: 11121048]
  495. Shirai M., Arichi T., Chen M., Nishioka M., Ikeda K., Takahashi H., Enomoto N., Saito T., Major M. E., Nakazawa T., Akatsuka T., Feinstone S. M., Berzofsky J. A. T cell recognition of hypervariable region-1 from hepatitis C virus envelope protein with multiple class II MHC molecules in mice and humans: preferential help for induction of antibodies to the hypervari-able region. Journal of Immunology. 1999;162:568–576. [PubMed: 9886434]
  496. Shirai M., Arichi T., Nishioka M., Nomura T., Ikeda K., Kawanishi K., Engelhard V. H., Feinstone S. M., Berzofsky J. A. CTL responses of HLA-A2.1-transgenic mice specific for hepatitis C viral peptides predict epitopes for CTL of humans carrying HLA-A2.1. Journal of Immunology. 1995;154:2733–2742. [PubMed: 7533182]
  497. Sigal L. J., Crotty S., Andino R., Rock K. L. Cytotoxic T-cell immunity to virus-infected non-haematopoietic cells requires presentation of exogenous antigen. Nature. 1999;398:77–80. [PubMed: 10078533]
  498. Silverman M., Zieg J., Hilmen M., Simon M. Phase variation in Salmonella: genetic analysis of a recombinational switch. Proceedings of the National Academy of Sciences USA. 1979;76:391–395. [PMC free article: PMC382945] [PubMed: 370828]
  499. Sim B. C., Aftahi N., Reilly C., Bogen B., Schwartz R. H., Gascoigne N. R., Lo D. Thymic skewing of the CD4/CD8 ratio maps with the T-cell receptor alpha-chain locus. Current Biology. 1998;8:701–704. [PubMed: 9637921]
  500. Skehel J. J., Stevens D. J., Daniels R. S., Douglas A. R., Knossow M., Wilson I. A., Wiley D. C. A carbohydrate side chain on hemagglutinins of Hong Kong influenza viruses inhibits recognition by a monoclonal antibody. Proceedings of the National Academcy of Sciences USA. 1984;81:1779–1783. [PMC free article: PMC345004] [PubMed: 6584912]
  501. Skehel J. J., Wiley D. C. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annual Review of Biochemistry. 2000;69:531–569. [PubMed: 10966468]
  502. Slatkin, M. 1984. Somatic mutations as an evolutionary force. In Greewood, P. J., Harvey, P. H., and Slatkin, M., eds., Essays in Honor of John Maynard Smith, pp. 19–30. Cambridge University Press, Cambridge.
  503. Slifka M. K., Antia R., Whitmire J. K., Ahmed R. Humoral immunity due to long-lived plasma cells. Immunity. 1998;8:363–372. [PubMed: 9529153]
  504. Smith D. J., Forrest S., Ackley D. H., Perelson A. S. Variable efficacy of repeated annual influenza vaccination. Proceedings of the National Academy of Sciences USA. 1999;96:14001–14006. [PMC free article: PMC24180] [PubMed: 10570188]
  505. Smith J. D., Chitnis C. E., Craig A. G., Roberts D. J., Hudson-Taylor D. E., Peter-son D. S., Pinches R., Newbold C. I., Miller L. H. Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes. Cell. 1995;82:101–110. [PMC free article: PMC3730239] [PubMed: 7606775]
  506. Smith M. R., Greene W. C. Identification of HTLV-I tax trans-activator mutants exhibiting novel transcriptional phenotypes. Genes and Development. 1990;4:1875–1885. [PubMed: 2276622]
  507. Smith M. W., Dean M., Carrington M., Winkler C., Huttley G. A., Lomb D. A., Goedert J. J., O'Brien T. R., Jacobson L. P., Kaslow R. et al. Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Science. 1997;277:959–965. [PubMed: 9252328]
  508. Smith V. H., Holt R. D. Resource competition and within-host disease dynamics. Trends in Ecology and Evolution. 1996;11:386–389. [PubMed: 21237891]
  509. Sniegowski P. D., Gerrish P. J., Lenski R. E. Evolution of high mutation rates in experimental populations of E. coli. Nature. 1997;387:703–705. [PubMed: 9192894]
  510. Sobrino F., Sáiz M., Jiménez-Clavero M. A., Núñez J. I., Rosas M. F., Baranowski E., Ley V. Foot-and-mouth disease virus: a long known virus, but a current threat. Veterinary Research. 2001;32:1–30. [PubMed: 11254174]
  511. Solé M., Bantar C., Indest K., Gu Y., Ramamoorthy R., Coughlin R., Philipp M. T. Borrelia burgdorferi escape mutants that survive in the presence of antiserum to the OspA vaccine are killed when complement is also present. Infection and Immunity. 1998;66:2540–2546. [PMC free article: PMC108236] [PubMed: 9596714]
  512. Sompayrac, L. M. 1999. How the Immune System Works. Blackwell Science, Malden, Massachusetts.
  513. Sonrier C., Branger C., Michel V., Ruvoen-Clouet N., Ganiere J. P., Andre-Fontaine G. Evidence of cross-protection within Leptospira interrogans in an experimental model. Vaccine. 2000;15:86–94. [PubMed: 10924790]
  514. Soudeyns H., Paolucci S., Chappey C., Daucher M. B., Graziosi C., Vaccarezza M., Cohen O. J., Fauci A. S., Pantaleo G. Selective pressure exerted by immunodominant HIV-1-specific cytotoxic T lymophocyte responses during primary infection drives genetic variation restricted to the cognate epitope. European Journal of Immunology. 1999;29:3629–3635. [PubMed: 10556818]
  515. Sourdive D. J. D., Murali-Krishna K., Altman J. D. Conserved T cell receptor repertoire in primary and memory CD8 T cell responses to an acute viral infection. Journal of Experimental Medicine. 1998;188:71–82. [PMC free article: PMC2525546] [PubMed: 9653085]
  516. Spratt B. G., Bowler L. D., Zhang Q.-Y., Zhou J., Maynard Smith J. Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species. Journal of Molecular Evolution. 1992;34:115–125. [PubMed: 1556747]
  517. Spratt B. G., Maiden M. C. J. Bacterial population genetics, evolution and epidemiology. Philosophical Transactions of the Royal Society of London B. 1999;354:701–710. [PMC free article: PMC1692550] [PubMed: 10365396]
  518. Spriggs M. K. One step ahead of the game: viral immunomodulatory molecules. Annual Review of Immunology. 1996;14:101–130. [PubMed: 8717509]
  519. Springer T. A. Adhesion receptors of the immune system. Nature. 1990;346:425–434. [PubMed: 1974032]
  520. Stalhammar-Carlemalm M., Areschoug T., Larsson C., Lindahl G. Cross-protection between group A and group B streptococci due to cross-reacting surface proteins. Journal of Infectious Disease. 2000;182:142–149. [PubMed: 10882591]
  521. Staudt L. M., Gerhard W. Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutinin. I. Significant variation in repertoire expression between individual mice. Journal of Experimental Medicine. 1983;157:687–704. [PMC free article: PMC2186921] [PubMed: 6600489]
  522. Stearns S. C., Ackermann M., Doebeli M., Kaiser M. Experimental evolution of aging, growth, and reproduction in fruitflies. Proceedings of the National Academy of Sciences USA. 2000;97:3309–3313. [PMC free article: PMC16235] [PubMed: 10716732]
  523. Steinhauer, D. A., and Wharton, S. A. 1998. Structure and function of the haemagglutinin. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 54–64. Blackwell Science, Oxford.
  524. Stern A., Brown M., Nickel P., Meyer T. F. Opacity genes in Neisseria gonorrhoeae: control of phase and antigenic variation. Cell. 1986;47:61–71. [PubMed: 3093085]
  525. Stern A., Meyer T. F. Common mechanism controlling phase and antigenic variation in pathogenic neisseriae. Molecular Microbiology. 1987;1:5–12. [PubMed: 2455211]
  526. Stevenson, P. G., and Doherty, P. C. 1998. Cell-mediated imune response to influenza virus. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 278–287. Blackwell Science, Oxford.
  527. Stoenner H. G., Dodd T., Larsen C. Antigenic variation of Borrelia hermsii. Journal of Experimental Medicine. 1982;156:1297–1311. [PMC free article: PMC2186838] [PubMed: 7130900]
  528. Strauss, E. G., Straus, J. H., and Levine, A. J. 1996. Virus evolution. In Fields, B. N., Knipe, D. M., and Howley, P. M., eds., Fundamental Virology, 3d ed., pp. 141–159. Lippincott-Raven, Philadelphia.
  529. Su C., Jakobsen I., Gu X., Nei M. Diversity and evolution of T-cell recpetor variable region genes in mammals and birds. Immunogenetics. 1999;50:301–308. [PubMed: 10630294]
  530. Su C., Nei M. Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage. Proceedings of the National Academy of Sciences USA. 1999;96:9710–9715. [PMC free article: PMC22275] [PubMed: 10449759]
  531. Su X., Heatwole V. M., Wertheimer S. P., Guinet F., Herrfeldt J. V., Peterson D. S., Ravetch J. V. W. A large and diverse gene family (var ) encodes 200–350 kD proteins implicated in the antigenic variation and cytoadherence of Plasmodium falciparum–infected erythrocytes. Cell. 1995;82:89–100. [PubMed: 7606788]
  532. Suerbaum S., Maynard Smith J., Bapumia K., Morelli G., Smith N. H., Kunstmann E., Dyrek I., Achtman M. Free recombination within Helicobacter pylori. Proceedings of the National Academy of Sciences USA. 1998;95:12619–12624. [PMC free article: PMC22880] [PubMed: 9770535]
  533. Suzuki Y., Gojobori T. A method for detecting positive selection at single amino acid sites. Molecular Biology and Evolution. 1999;16:1315–1328. [PubMed: 10563013]
  534. Swain S. L. Generation and in vivo persistence of polarized Th1 and Th2 memory cells. Immunity. 1994;1:543–552. [PubMed: 7600283]
  535. Tada Y., Hongo S., Muraki Y., Sugawara K., Kitame F., Nakamura K. Evolutionary analysis of influenza C virus M genes. Virus Genes. 1997;15:53–59. [PubMed: 9354270]
  536. Taddei F., Radman M., Maynard Smith J., Toupance B., Gouyon P. H., Godelle B. Role of mutator alleles in adaptive evolution. Nature. 1997;387:700–702. [PubMed: 9192893]
  537. Taylor H. P., Armstrong S. J., Dimmock N. J. Quantitative relationships between an influenza virus and neutralizing antibody. Virology. 1987;159:288–298. [PubMed: 3617501]
  538. Terry C. F., Loukaci V., Green F. R. Cooperative influence of genetic polymorphisms on interleukin 6 transcriptional regulation. Journal of Biological Chemistry. 2000;275:18138–18144. [PubMed: 10747905]
  539. Thomas, D. B., Patera, A. C., Graham, C. M., and Smith, C. A. 1998. Antibody-mediated immunity. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 267–277. Blackwell Science, Oxford.
  540. Thursz M., Kwiatkowski D., Allsopp C. E. M., Greenwood B. M., Thomas H. C., Hill A. V. S. Association of an HLA class II allele with clearance of hepatitis B virus infection in The Gambia. New England Journal of Medicine. 1995;332:1065–1069. [PubMed: 7898524]
  541. Tibayrenc M. Toward an integrated genetic epidemiology of parasitic protozoa and other pathogens. Annual Review of Genetics. 1999;33:171–191. [PubMed: 10690415]
  542. Tibayrenc M., Ayala F. J. Isozyme variability in Trypanosoma cruzi, the agent of Chagas' disease: genetical, taxonomical, and epidemiological significance. Evolution. 1988;42:277–292. [PubMed: 28567853]
  543. Tibayrenc M., Kjellberg F., Arnaud J., Oury B., Brenière S., Dardé M.-L., Ayala F. J. Are eukaryotic microorganisms clonal or sexual? A population genetics vantage. Proceedings of the National Academy of Sciences USA. 1991;88:5129–5133. [PMC free article: PMC51825] [PubMed: 1675793]
  544. Tibayrenc M., Kjellberg F., Ayala F. J. A clonal theory of parasitic protozoa: the population genetic structure of Entamoeba, Giardia, Leishmania and Trypanosomes, and its medical and taxonomic consequences. Proceedings of the National Academy of Sciences USA. 1990;87:2414–2418. [PMC free article: PMC53699] [PubMed: 2320563]
  545. Tibayrenc M., Ward P., Moya A., Ayala F. J. Natural populations of Trypanosoma cruzi, the agent of Chagas' disease, have a complex multiclonal structure. Proceedings of the National Academy of Sciences USA. 1986;83:115–119. [PMC free article: PMC322802] [PubMed: 3510428]
  546. Tissot A. C., Ciatto C., Mitti P. R. E., Grütter M. G., Plückthun A. Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex. Journal of Molecular Biology. 2000;302:873–885. [PubMed: 10993729]
  547. Tortorella D., Gewurz B. E., Furman M. H., Schust D. J., Ploegh H. L. Viral subversion of the immune system. Annual Review of Immunology. 2000;18:861–926. [PubMed: 10837078]
  548. Turner C. M. R. The rate of antigenic variation in fly-transmitted and syringe-passaged infections of Trypanosoma brucei. FEMS Microbiology Letters. 1997;153:227–231. [PubMed: 9252591]
  549. Turner C. M. R. Antigenic variation in Trypanosoma brucei infections: an holistic view. Journal of Cell Science. 1999;112:3187–3192. [PubMed: 10504324]
  550. Turner C. M. R., Aslam N., Angus S. D. Inhibition of growth of Trypanosoma brucei parasites in chronic infections. Parasitology Research. 1996;82:61–66. [PubMed: 8825447]
  551. Turner C. M. R., Barry J. D. High frequency of antigenic variation in Trypanosoma brucei rhodesiense infections. Parasitology. 1989;99:67–75. [PubMed: 2797873]
  552. Underwood P. A. Mapping of antigenic changes in the haemagglutinin of Hong Kong influenza (H3N2) strains using a large panel of monoclonal antibodies. Journal of General Virology. 1982;62:153–169. [PubMed: 6182265]
  553. Underwood P. A. An antigenic map of the haemagglutinin of the influenza Hong Kong subtype (H3N2), constructed using mouse monoclonal antibodies. Molecular Immunology. 1984;21:663–671. [PubMed: 6205255]
  554. van de Putte P., Plasterk R., Kuijpers A. A Mu gin complementing function and an invertible DNA region in Escherichia coli K-12 are situated on the genetic element e14. Journal of Bacteriology. 1984;158:517–522. [PMC free article: PMC215459] [PubMed: 6233259]
  555. van Hattum J., Schreuder G. M., Schalm S. W. HLA antigens in patients with various courses after hepatitis B virus infection. Hepatology. 1987;7:11–14. [PubMed: 2433202]
  556. van Regenmortel M. H. V. From absolute to exquisite specificity: reflections on the fuzzy nature of species, specificity and antigenic sites. Journal of Immunological Methods. 1998;216:37–48. [PubMed: 9760214]
  557. van Regenmortel M. H. V., Altschuh D., Chatellier J., Christensen L., Rauffer-Bruyère N., Richalet S., Witz J., Zeder-Lutz G. Measurement of antigen-antibody interactions with biosensors. Journal of Molecular Recognition. 1998;11:163–167. [PubMed: 10076831]
  558. Vickerman K. Trypanosome sociology and antigenic variation. Parasitology. 1989;99:S37–S47. [PubMed: 2682484]
  559. Vidal N., Peeters M., Mulanga-Kabeya C., Nzilambi N., Robertson D., Ilunga W., Sema H., Tshimanga K., Bongo B., Delaporte E. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in central Africa. Journal of Virology. 2000;74:10498–10507. [PMC free article: PMC110924] [PubMed: 11044094]
  560. Vijayakrishnan L., Kumar V., Agrewala A., Mishra G. C., Rao K. V. S. Antigen-specific early primary humoral responses modulate immunodominance of B cell epitopes. Journal of Immunology. 1994;153:1613–1625. [PubMed: 7519207]
  561. Villadangos J. A., Bryant R. A. R., Deussing J., Driessen C., Lennon-Dumenil A.-M., Riese R. J., Roth W., Saftig P., Shi G.-P., Chapman H. A., Peters C., Ploegh H. L. Proteases involved in MHC class II antigen presentation. Immunological Reviews. 1999;172:109–120. [PubMed: 10631941]
  562. Vincent R., Louis-Plence P., Gaillard F., Clot J., Eliaou J.-F. Qualitative and quantitative analysis of HLA-DRB gene expression. Journal of Rheumatology. 1997;24:225–226. [PubMed: 9002047]
  563. Virji M., Evans D., Hadfield A., Grunert F., Telxeira A. M., Watt S. M. Critical determinants of host receptor targeting by Neisseria meningitidis and Neisseria gonorrhoeae: identification of Opa adhesiotopes on the N-domain of CD66 molecules. Molecular Microbiology. 1999;34:538–551. [PubMed: 10564495]
  564. Vogel T., Kurth R., Norley S. The majority of neutralizing Abs in HIV-1 infected patients recognize linear V3 loop sequences. Journal of Immunology. 1994;153:1895–1904. [PubMed: 7519220]
  565. Volkman S. K., Barry A. E., Lyons E. J., Nielsen K. M., Thomas S. M., Choi M., Thakore S. S., Day K. P., Wirth D. F., Hartl D. L. Recent origin of Plasmodium falciparum from a single progenitor. Science. 2001;293:482–484. [PubMed: 11463913]
  566. Wakely J. Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA. Journal of Molecular Evolution. 1993;37:613–623. [PubMed: 8114114]
  567. Walker G. C. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiological Reviews. 1984;48:60–93. [PMC free article: PMC373003] [PubMed: 6371470]
  568. Wang M.-L., Skehel J. J., Wiley D. C. Comparative analyses of the specificities of anti-influenza hemagglutinin antibodies in human sera. Journal of Virology. 1986;57:124–128. [PMC free article: PMC252706] [PubMed: 3941436]
  569. Watts C., Amigorena S. Antigen traffic pathways in dendritic cells. Traffic. 2000;1:312–317. [PubMed: 11208116]
  570. Weaver S. C., Brault A. C., Kang W., Holland J. J. Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cells. Journal of Virology. 1999;73:4316–4326. [PMC free article: PMC104213] [PubMed: 10196330]
  571. Weber J., Fenyo E.-M., Beddows S., Kaleebu P., Bjorndal A. Neutralization serotypes of HIV-1 field isolates are not predicted by genetic subtype. Journal of Virology. 1996;70:7827–7832. [PMC free article: PMC190853] [PubMed: 8892904]
  572. Webster R. G., Air G. M., Metzger D. W., Colman P. M., Varghese J. N., Baker A. T., Laver W. G. Antigenic structure and variation in an influenza virus N9 neuraminidase. Journal of Virology. 1987;61:2910–2916. [PMC free article: PMC255818] [PubMed: 3612957]
  573. Webster, R. G., and Bean, W. J. 1998. Evolution and ecology of influenza viruses: interspecies transmission. In Nicholson, K. G., Webster, R. G., and Hay, A. J., eds., Textbook of Influenza, pp. 109–119. Blackwell Science, Oxford.
  574. Webster R. G., Bean W. J., Gorman O. T., Chambers T. M., Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiological Review. 1992;56:152–179. [PMC free article: PMC372859] [PubMed: 1579108]
  575. Webster R. G., Brown L. E., Laver W. G. Antigenic and biological characterization of influenza virus neuraminidase (N2) with monoclonal antibodies. Virology. 1984;135:30–42. [PubMed: 6203218]
  576. Webster R. G., Shortridge K. F., Kawaoka Y. Influenza: interspecies transmission and emergence of new pandemics. FEMS Immunology and Medical Microbiology. 1997;18:275–279. [PMC free article: PMC7314015] [PubMed: 9348163]
  577. Wedemayer G. J., Patten P. A., Wang L. H., Schultz P. G., Stevens R. C. Structural insights into the evolution of an antibody combining site. Science. 1997;276:1665–1669. [PubMed: 9180069]
  578. Weidt G., Deppert W., Utermöhlen O., Heukeshoven J., Lehmann-Grube F. Emergence of virus escape mutants after immunization with epitope vaccine. Journal of Virology. 1995;69:7147–7151. [PMC free article: PMC189635] [PubMed: 7474135]
  579. Weidt G., Utermöhlen O., Heukeshoven J., Lehmann-Grube F., Deppert W. Relationship among immunodominance of single CD8+ T cell epitopes, virus load, and kinetics of primary antiviral CTL response. Journal of Immunology. 1998;160:2923–2931. [PubMed: 9510196]
  580. Wettstein P. J. Immunodominance in the T-cell response to multiple non-H-2 histocompatibility antigens. II. Observation of a hierarchy among dominant antigens. Immunogenetics. 1986;24:24–31. [PubMed: 2426194]
  581. Wetz K., Willingmann P., Zeichhardt H., Habermehl K.-O. Neutralization of poliovirus by polyclonal antibodies requires binding of a single molecule per virion. Archives of Virology. 1986;91:207–220. [PubMed: 3022677]
  582. Whitmire J. K., Murali-Krishna K., Altman J., Ahmed R. Antiviral CD4 and CD8 T-cell memory: differences in the size of the response and activation requirements. Philosophical Transactions of the Royal Society of London B. 2000;355:373–379. [PMC free article: PMC1692741] [PubMed: 10794058]
  583. Wiley D. C., Wilson I. A., Skehel J. J. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature. 1981;289:373–378. [PubMed: 6162101]
  584. Willems R., Paul A., van der Heide H. G. J., ter Avest A. R., Mooi F. R. Fimbrial phase variation in Bordetella pertussis: a novel mechanism for transcriptional regulation. EMBO Journal. 1990;9:2803–2809. [PMC free article: PMC551991] [PubMed: 1975238]
  585. Wilson I. A., Cox N. J. Structural basis of immune recognition of influenza virus hemagglutinin. Annual Review of Immunology. 1990;8:737–771. [PubMed: 2188678]
  586. Wilson I. A., Skehel J. J., Wiley D. C. Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature. 1981;289:366–373. [PubMed: 7464906]
  587. Wodarz D., Nowak M. A. CD8 memory, immunodominance, and antigenic escape. European Journal of Immunology. 2000;30:2704–2712. [PubMed: 11009106]
  588. Wodarz D., Nowak M. A., Bangham C. R. M. The dynamics of HTLV-I and the CTL response. Immunology Today. 1999;20:220–227. [PubMed: 10322301]
  589. Wohlfart C. Neutralization of adenoviruses: kinetics, stoichiometry and mechanisms. Journal of Virology. 1988;62:2321–2328. [PMC free article: PMC253388] [PubMed: 3373570]
  590. Worobey M. Extensive homologous recombination among widely divergent TT viruses. Journal of Virology. 2000;74:7666–7670. [PMC free article: PMC112290] [PubMed: 10906223]
  591. Worobey M., Holmes E. C. Evolutionary aspects of recombination in RNA viruses. Journal of General Virology. 1999;80:2535–2543. [PubMed: 10573145]
  592. Worobey M., Rambaut A., Holmes E. C. Widespread intra-serotype recombination in natural populations of dengue virus. Proceedings of the National Academy of Sciences USA. 1999;96:7352–7357. [PMC free article: PMC22089] [PubMed: 10377418]
  593. Wren B. W. A family of clostridial and streptococcal ligand-binding proteins with conserved C-terminal repeat sequences. Molecular Microbiology. 1991;5:797–803. [PubMed: 1830357]
  594. Wright, P. F., and Webster, R. G. 2001. Orthomyxoviruses. In Knipe, D. M., and Howley, P. M., eds., Fields Virology, 4th ed., pp. 1533–1579. Lippincott-Raven, Philadelphia.
  595. Wright, S. 1969. Evolution and the Genetics of Populations. Vol. 2, The Theory of Gene Frequencies. University of Chicago Press, Chicago.
  596. Wright, S. 1978. Evolution and the Genetics of Populations. Vol. 4, Variability within and between Natural Populations. University of Chicago Press, Chicago.
  597. Wu J., Longmate J. A., Adamus G., Hargrave P. A., Wakeland E. K. Interval mapping of quantitative trait loci controlling humoral immunity to exogenous antigens. Journal of Immunology. 1996;157:2498–2505. [PubMed: 8805650]
  598. Xu J., Mitchell T. G., Vilgalys R. PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans. Molecular Ecology. 1999;8:59–73. [PubMed: 9919698]
  599. Yamaguchi-Kabata Y., Gojobori T. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. Journal of Virology. 2000;74:4335–4350. [PMC free article: PMC111951] [PubMed: 10756049]
  600. Yang Z. H., Bielawski J. P. Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution. 2000;15:496–503. [PMC free article: PMC7134603] [PubMed: 11114436]
  601. Yewdell J. W., Bennink J. R. Immunodominance in major histocompatibility complex class I–restricted T lymphocyte responses. Annual Review of Immunology. 1999;17:51–88. [PubMed: 10358753]
  602. Yewdell J. W., Caton A. J., Gerhard W. Selection of influenza A adsorptive mutants by growth in the presence of a mixture of monoclonal anti-haemagglutinin antibodies. Journal of Virology. 1986;57:623–628. [PMC free article: PMC252777] [PubMed: 2418215]
  603. Yewdell J. W., Webster R. G., Gerhard W. U. Antigenic variation in three distinct determinants of an influenza type A haemagglutinin molecule. Nature. 1979;279:246–248. [PubMed: 86955]
  604. York I. A., Goldberg A. L., Mo X. Y., Rock K. L. Proteolysis and class I major histocompatibility complex antigen presentation. Immunological Reviews. 1999;172:49–66. [PubMed: 10631936]
  605. Yoshida M. Multiple viral strategies of HTLV-1 for dysregulation of cell growth control. Annual Review of Immunology. 2001;19:475–496. [PubMed: 11244044]
  606. Young A. C., Zhang W., Sacchettini J. C., Nathenson S. G. The three-dimensional structure of H-2Db at 2.4 Å resolution: implications for antigen-determinant selection. Cell. 1994;76:39–50. [PubMed: 7506996]
  607. Yusim K., Peeters M., Pybus O. G., Bhattacharya T., Delaporte E., Mulanga C., Muldoon M., Theiler J., Korber B. Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution. Philosophical Transactions of the Royal Society of London B. 2001;356:855–866. [PMC free article: PMC1088479] [PubMed: 11405933]
  608. Zhang J., Tang L.-Y., Li T., Ma Y., Sapp C. M. Most retroviral recombinations occur during minus-strand DNA synthesis. Journal of Virology. 2000;74:2313–2322. [PMC free article: PMC111713] [PubMed: 10666262]
  609. Zhou J., Spratt B. G. Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis—interspecies recombination within the argF gene. Molecular Microbiology. 1992;6:2135–2146. [PubMed: 1406254]
  610. Zinkernagel R. M., Althage A., Cooper S., Kreeb G., Klein P. A., Sefton B., Flaherty L., Stimpfling J., Shreffler D., Klein J. Ir-genes in H-2 regulate generation of anti-viral cytotoxic T cells. Mapping to K or D and dominance or unresponsiveness. Journal of Experimental Medicine. 1978;148:592–606. [PMC free article: PMC2184956] [PubMed: 212503]
  611. Zinkernagel R. M., Bachmann M. F., Kündig T. M., Oehen S., Pirchet H., Hengartner H. On immunological memory. Annual Review of Immunology. 1996;14:333–367. [PubMed: 8717518]
  612. Zolla-Pazner S., Gorny M. K., Nyambi P. N., VanCott T. C., Nádas A. Immunotyping of HIV-1: an approach to immunologic classification of HIV. Journal of Virology. 1999;73:4042–4051. [PMC free article: PMC104183] [PubMed: 10196300]
Copyright © 2002, Steven A Frank.
Bookshelf ID: NBK2392


Related information

  • PMC
    PubMed Central citations
  • PubMed
    Links to PubMed

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...