Home LiteratureArticle Details
PMID: 17426010 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Patterns of antigenic diversity and the mechanisms that maintain them.

Journal of the Royal Society, Interface ·Vol. 4 ·No. 16 ·2007-10-22 ·Pages 787-802

Lipsitch M, O'Hagan JJ

Abstract

Many of the remaining challenges in infectious disease control involve pathogens that fail to elicit long-lasting immunity in their hosts. Antigenic variation is a common reason for this failure and a contributor to the complexity of vaccine design. Diversifying selection by the host immune system is commonly, and often correctly, invoked to explain antigenic variability in pathogens. However, there is a wide variety of patterns of antigenic variation across space and time, and within and between hosts, and we do not yet understand the determinants of these different patterns. This review describes five such patterns, taking as examples two bacteria (Streptococcus pneumoniae and Neisseria meningitidis), two viruses (influenza A and HIV-1), as well as the pathogens (taken as a group) for which antigenic variation is negligible. Pathogen-specific explanations for these patterns of diversity are critically evaluated, and the patterns are compared against predictions of theoretical models for antigenic diversity. Major remaining challenges are highlighted, including the identification of key protective antigens in bacteria, the design of vaccines to combat antigenic variability for viruses and the development of more systematic explanations for patterns of antigenic variation.

MeSH Terms
Antigenic Variation/genetics,immunology Antigens, Bacterial/genetics,immunology Antigens, Viral/genetics,immunology
Chemicals
Antigens, Bacterial Antigens, Viral
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lipsitch Marc
Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA. [email protected]
O'Hagan Justin J
References (109)
109 references, click to expand
  1. Global epidemiology of meningococcal disease and vaccine efficacy.
    Pediatr Infect Dis J. 2004 Dec;23(12 Suppl):S274-9 PMID: 15597069
  2. Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution.
    J Virol. 2007 Jan;81(1):193-201 PMID: 17065207
  3. Conquering the meningococcus.
    FEMS Microbiol Rev. 2007 Jan;31(1):3-14 PMID: 17233633
  4. Stochastic processes are key determinants of short-term evolution in influenza a virus.
    PLoS Pathog. 2006 Dec;2(12):e125 PMID: 17140286
  5. Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses.
    J Immunol. 2006 Apr 1;176(7):4094-101 PMID: 16547245
  6. Virulence and transmissibility of pathogens: what is the relationship?
    Trends Microbiol. 1997 Jan;5(1):31-7 PMID: 9025233
  7. Uncloaking the meningococcus: dynamics of carriage and disease.
    Lancet. 1999 Mar 20;353(9157):941-2 PMID: 10459897
  8. Genetic basis for nongroupable Neisseria meningitidis.
    J Infect Dis. 2003 May 15;187(10):1616-28 PMID: 12721942
  9. Identification of a universal Group B streptococcus vaccine by multiple genome screen.
    Science. 2005 Jul 1;309(5731):148-50 PMID: 15994562
  10. Theoretical studies of the effects of heterogeneity in the parasite population on the transmission dynamics of malaria.
    Proc Biol Sci. 1994 Jun 22;256(1347):231-8 PMID: 7914705
  11. Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach.
    Curr Opin Microbiol. 2006 Oct;9(5):532-6 PMID: 16890009
  12. Molecular typing of meningococci: recommendations for target choice and nomenclature.
    FEMS Microbiol Rev. 2007 Jan;31(1):89-96 PMID: 17168996
  13. Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland.
    Infect Immun. 2005 Jan;73(1):431-5 PMID: 15618181
  14. Adaptation of Bordetella pertussis to vaccination: a cause for its reemergence?
    Emerg Infect Dis. 2001;7(3 Suppl):526-8 PMID: 11485646
  15. Exploring the evolution of diversity in pathogen populations.
    Trends Microbiol. 2001 Apr;9(4):181-5 PMID: 11286883
  16. Antibodies to conserved pneumococcal antigens correlate with, but are not required for, protection against pneumococcal colonization induced by prior exposure in a mouse model.
    Infect Immun. 2005 Oct;73(10):7043-6 PMID: 16177389
  17. Epidemiologic studies of Streptococcus pneumoniae in infants. The effects of season and age on pneumococcal acquisition and carriage in the first 24 months of life.
    Am J Epidemiol. 1982 Oct;116(4):692-703 PMID: 7137156
  18. Population dynamics of HIV-1 inferred from gene sequences.
    Genetics. 1999 Feb;151(2):427-38 PMID: 9927440
  19. The contribution of specific pneumococcal serogroups to different disease manifestations: implications for conjugate vaccine formulation and use, part II.
    Clin Infect Dis. 2000 Jan;30(1):122-40 PMID: 10619741
  20. Reverse vaccinology.
    Curr Opin Microbiol. 2000 Oct;3(5):445-50 PMID: 11050440
  21. The causes and consequences of HIV evolution.
    Nat Rev Genet. 2004 Jan;5(1):52-61 PMID: 14708016
  22. Unifying the epidemiological and evolutionary dynamics of pathogens.
    Science. 2004 Jan 16;303(5656):327-32 PMID: 14726583
  23. Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents.
    Science. 1998 May 8;280(5365):912-5 PMID: 9572737
  24. Capsule phase variation in Neisseria meningitidis serogroup B by slipped-strand mispairing in the polysialyltransferase gene (siaD): correlation with bacterial invasion and the outbreak of meningococcal disease.
    Mol Microbiol. 1996 Jun;20(6):1211-20 PMID: 8809773
  25. Invasive pneumococcal infections in Denmark from 1995 to 1999: epidemiology, serotypes, and resistance.
    Clin Diagn Lab Immunol. 2002 Mar;9(2):358-65 PMID: 11874878
  26. Transmissibility of 1918 pandemic influenza.
    Nature. 2004 Dec 16;432(7019):904-6 PMID: 15602562
  27. Meningococcal serogroup W135 in the African meningitis belt: epidemiology, immunity and vaccines.
    Expert Rev Vaccines. 2006 Jun;5(3):319-36 PMID: 16827617
  28. Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design.
    Infect Immun. 2004 Oct;72(10):5955-62 PMID: 15385499
  29. Nasal colonization with Streptococcus pneumoniae includes subpopulations of surface and invasive pneumococci.
    Infect Immun. 2005 Oct;73(10):6945-51 PMID: 16177374
  30. Antibody responses to nasopharyngeal carriage of Streptococcus pneumoniae in adults: a longitudinal household study.
    J Infect Dis. 2005 Aug 1;192(3):387-93 PMID: 15995951
  31. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time.
    Science. 1996 Mar 15;271(5255):1582-6 PMID: 8599114
  32. Epidemiological differences among pneumococcal serotypes.
    Lancet Infect Dis. 2005 Feb;5(2):83-93 PMID: 15680778
  33. Neisseria meningitidis: an overview of the carriage state.
    J Med Microbiol. 2004 Sep;53(Pt 9):821-32 PMID: 15314188
  34. Streptococcus pneumoniae colonisation: the key to pneumococcal disease.
    Lancet Infect Dis. 2004 Mar;4(3):144-54 PMID: 14998500
  35. Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.
    Genetics. 2006 Nov;174(3):1441-53 PMID: 16951087
  36. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes.
    Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):6981-5 PMID: 10860960
  37. Vaccination against colonizing bacteria with multiple serotypes.
    Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6571-6 PMID: 9177259
  38. Consensus and ancestral state HIV vaccines.
    Science. 2003 Mar 7;299(5612):1515-8; author reply 1515-8 PMID: 12624248
  39. The changing epidemiology of meningococcal disease in the United States, 1992-1996.
    J Infect Dis. 1999 Dec;180(6):1894-901 PMID: 10558946
  40. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans.
    Science. 2006 Dec 22;314(5807):1898-903 PMID: 17185596
  41. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum.
    Nature. 2004 Apr 29;428(6986):942-5 PMID: 15118727
  42. Effect of introduction of the pneumococcal conjugate vaccine on drug-resistant Streptococcus pneumoniae.
    N Engl J Med. 2006 Apr 6;354(14):1455-63 PMID: 16598044
  43. Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus.
    Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7152-7 PMID: 12748378
  44. Streptococcus pneumoniae serotype 4 outbreak in a home for the aged: report and review of recent outbreaks.
    Infect Control Hosp Epidemiol. 2000 Nov;21(11):711-7 PMID: 11089655
  45. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.
    PLoS Biol. 2005 Sep;3(9):e300 PMID: 16026181
  46. Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae.
    Emerg Infect Dis. 1999 May-Jun;5(3):336-45 PMID: 10341170
  47. Diversity considerations in HIV-1 vaccine selection.
    Science. 2002 Jun 28;296(5577):2354-60 PMID: 12089434
  48. Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost.
    J Virol. 2005 May;79(9):5721-31 PMID: 15827187
  49. Reversion of CTL escape-variant immunodeficiency viruses in vivo.
    Nat Med. 2004 Mar;10(3):275-81 PMID: 14966520
  50. Ecological and immunological determinants of influenza evolution.
    Nature. 2003 Mar 27;422(6930):428-33 PMID: 12660783
  51. Association between carriage of Streptococcus pneumoniae and Staphylococcus aureus in Children.
    JAMA. 2004 Aug 11;292(6):716-20 PMID: 15304469
  52. Epidemiologic interference of virus populations.
    J Math Biol. 1979 Oct;8(3):291-300 PMID: 501225
  53. Immune control of HIV: the obstacles of HLA and viral diversity.
    Nat Immunol. 2001 Jun;2(6):473-5 PMID: 11376327
  54. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo.
    PLoS Biol. 2006 Apr;4(4):e90 PMID: 16515366
  55. CD4+ T cells mediate antibody-independent acquired immunity to pneumococcal colonization.
    Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4848-53 PMID: 15781870
  56. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing.
    Science. 2000 Mar 10;287(5459):1816-20 PMID: 10710308
  57. HIV evolution: CTL escape mutation and reversion after transmission.
    Nat Med. 2004 Mar;10(3):282-9 PMID: 14770175
  58. Epidemiology and pathogenesis of influenza.
    J Antimicrob Chemother. 1999 Nov;44 Suppl B:3-9 PMID: 10877456
  59. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes.
    Nature. 1999 Feb 4;397(6718):436-41 PMID: 9989410
  60. Mapping the antigenic and genetic evolution of influenza virus.
    Science. 2004 Jul 16;305(5682):371-6 PMID: 15218094
  61. Reversion of immune escape HIV variants upon transmission: insights into effective viral immunity.
    Trends Microbiol. 2005 Jun;13(6):243-6 PMID: 15936652
  62. Age- and serogroup-related differences in observed durations of nasopharyngeal carriage of penicillin-resistant pneumococci.
    J Clin Microbiol. 2007 Mar;45(3):948-52 PMID: 17202280
  63. The maintenance of strain structure in populations of recombining infectious agents.
    Nat Med. 1996 Apr;2(4):437-42 PMID: 8597954
  64. The effects of host heterogeneity on pathogen population structure.
    Philos Trans R Soc Lond B Biol Sci. 1999 Apr 29;354(1384):711-9 PMID: 10365397
  65. Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution.
    J Virol. 2005 Nov;79(21):13239-49 PMID: 16227247
  66. Geographic diversity and temporal trends of antimicrobial resistance in Streptococcus pneumoniae in the United States.
    Nat Med. 2003 Apr;9(4):424-30 PMID: 12627227
  67. Host and bacterial factors contributing to the clearance of colonization by Streptococcus pneumoniae in a murine model.
    Infect Immun. 2005 Nov;73(11):7718-26 PMID: 16239576
  68. Immunology of hepatitis B virus and hepatitis C virus infection.
    Nat Rev Immunol. 2005 Mar;5(3):215-29 PMID: 15738952
  69. The impact of cross-immunity, mutation and stochastic extinction on pathogen diversity.
    Proc Biol Sci. 2004 Dec 7;271(1556):2431-8 PMID: 15590592
  70. The frequency and rate of pilin antigenic variation in Neisseria gonorrhoeae.
    Mol Microbiol. 2005 Oct;58(2):510-9 PMID: 16194236
  71. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus.
    Biol Direct. 2006 Oct 26;1:34 PMID: 17067369
  72. Dynamics and selection of many-strain pathogens.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17209-14 PMID: 12481034
  73. Positive Darwinian evolution in human influenza A viruses.
    Proc Natl Acad Sci U S A. 1991 May 15;88(10):4270-4 PMID: 1840695
  74. Human immunity to the meningococcus. II. Development of natural immunity.
    J Exp Med. 1969 Jun 1;129(6):1327-48 PMID: 4977281
  75. Are anticapsular antibodies the primary mechanism of protection against invasive pneumococcal disease?
    PLoS Med. 2005 Jan;2(1):e15 PMID: 15696204
  76. Association of influenza epidemics with global climate variability.
    Eur J Epidemiol. 2004;19(11):1055-9 PMID: 15648600
  77. Constancy of distribution of serogroups of invasive pneumococcal isolates among children: experience during 4 decades.
    Clin Infect Dis. 2001 Apr 15;32(8):1155-61 PMID: 11283804
  78. Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children.
    Lancet. 2004 Jun 5;363(9424):1871-2 PMID: 15183627
  79. Distribution of serogroups and genotypes among disease-associated and carried isolates of Neisseria meningitidis from the Czech Republic, Greece, and Norway.
    J Clin Microbiol. 2004 Nov;42(11):5146-53 PMID: 15528708
  80. The Stonehouse survey: nasopharyngeal carriage of meningococci and Neisseria lactamica.
    Epidemiol Infect. 1987 Dec;99(3):591-601 PMID: 3123263
  81. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
    Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5 PMID: 16172379
  82. On the determinants of population structure in antigenically diverse pathogens.
    Proc Biol Sci. 2002 Feb 7;269(1488):227-33 PMID: 11839191
  83. Antigenic variants of measles virus.
    Nature. 1981 Sep 3;293(5827):67-9 PMID: 6167866
  84. Influenza and the challenge for immunology.
    Nat Immunol. 2006 May;7(5):449-55 PMID: 16622432
  85. Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation.
    Annu Rev Genet. 2006;40:307-33 PMID: 17094739
  86. Opportunities for control of meningococcal disease in the United States.
    Annu Rev Med. 2004;55:333-53 PMID: 14746525
  87. Acquisition and invasiveness of different serotypes of Streptococcus pneumoniae in young children.
    Epidemiol Infect. 1993 Aug;111(1):27-39 PMID: 8348930
  88. Carried meningococci in the Czech Republic: a diverse recombining population.
    J Clin Microbiol. 2000 Dec;38(12):4492-8 PMID: 11101585
  89. Lessons from meningococcal carriage studies.
    FEMS Microbiol Rev. 2007 Jan;31(1):52-63 PMID: 17233635
  90. Clonal diversity of Neisseria meningitidis from a population of asymptomatic carriers.
    Infect Immun. 1988 Aug;56(8):2060-8 PMID: 3135270
  91. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004.
    AIDS. 2006 Oct 24;20(16):W13-23 PMID: 17053344
  92. Capsular serotype-specific attack rates and duration of carriage of Streptococcus pneumoniae in a population of children.
    J Infect Dis. 2006 Sep 1;194(5):682-8 PMID: 16897668
  93. The immune response to pneumococcal proteins during experimental human carriage.
    J Exp Med. 2002 Feb 4;195(3):359-65 PMID: 11828011
  94. A status-based approach to multiple strain dynamics.
    J Math Biol. 2002 Feb;44(2):169-84 PMID: 11942531
  95. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.
    Nat Rev Microbiol. 2006 Nov;4(11):826-36 PMID: 17041630
  96. Switching trypanosome coats: what's in the wardrobe?
    Trends Genet. 2006 Nov;22(11):614-20 PMID: 16908087
  97. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS.
    Nat Med. 1997 Feb;3(2):212-7 PMID: 9018241
  98. Rapid evolution of the neutralizing antibody response to HIV type 1 infection.
    Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4144-9 PMID: 12644702
  99. Variant antigen gene expression in malaria.
    Cell Microbiol. 2006 Sep;8(9):1371-81 PMID: 16848786
  100. Cross-species transmission and recombination of 'AIDS' viruses.
    Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29;349(1327):41-7 PMID: 8748018
  101. The phylogeography of human viruses.
    Mol Ecol. 2004 Apr;13(4):745-56 PMID: 15012753
  102. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17020-4 PMID: 12471157
  103. Recent developments in pertussis.
    Lancet. 2006 Jun 10;367(9526):1926-36 PMID: 16765762
  104. Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA.
    Science. 1998 Mar 27;279(5359):2103-6 PMID: 9516110
  105. A genome-wide map of diversity in Plasmodium falciparum.
    Nat Genet. 2007 Jan;39(1):113-9 PMID: 17159979
  106. Self-generated diversity produces "insurance effects" in biofilm communities.
    Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16630-5 PMID: 15546998
  107. Neutral microepidemic evolution of bacterial pathogens.
    Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1968-73 PMID: 15684071
  108. Efficacy, safety and immunogenicity of heptavalent pneumococcal conjugate vaccine in children. Northern California Kaiser Permanente Vaccine Study Center Group.
    Pediatr Infect Dis J. 2000 Mar;19(3):187-95 PMID: 10749457
  109. Capsule switching of Neisseria meningitidis.
    Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):271-6 PMID: 8990198
Article Info
Journal
Journal of the Royal Society, Interface
Abbr.
J R Soc Interface
ISSN
1742-5689
Published
2007-10-22
Pages
787-802
Language
English
Region
England
NLM ID
101217269
PMCID
PMC2394542
Subset
IM
Grants
NIAID NIH HHS · R01 AI048935 · United States
NIGMS NIH HHS · U01 GM076497 · United States
NIAID NIH HHS · 1R01 AI48935 · United States
NIGMS NIH HHS · 5U01GM076497 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]