**8. References**


Using Population Genetics to Guide Malaria Vaccine Design 253

[27] Gardner, M.J., et al., *Genome sequence of the human malaria parasite Plasmodium falciparum.*

[28] Doolan, D.L., et al., *Profiling humoral immune responses to P. falciparum infection with* 

[29] Doolan, D.L., et al., *Utilization of genomic sequence information to develop malaria vaccines.* J

[30] Butler, D., *Mosquito production mooted as fast track to malaria vaccine.* Nature, 2003.

[31] Epstein, J.E., et al., *Live attenuated malaria vaccine designed to protect through hepatic CD8 T* 

[32] van Dijk, M.R., et al., *Genetically attenuated, P36p-deficient malarial sporozoites induce* 

[33] Butler, N.S., et al., *Superior antimalarial immunity after vaccination with late liver stagearresting genetically attenuated parasites.* Cell Host Microbe, 2011. 9(6): p. 451-62. [34] Woodberry, T., et al., *Human T cell recognition of the blood stage antigen Plasmodium* 

[35] Good, M.F., *A whole parasite vaccine to control the blood stages of Plasmodium: the case for* 

[36] Richards, J.S. and J.G. Beeson, *The future for blood-stage vaccines against malaria.* Immunol

[37] Moorthy, V.S., M.F. Good, and A.V. Hill, *Malaria vaccine developments.* Lancet, 2004.

[38] Arevalo-Herrera, M., C. Chitnis, and S. Herrera, *Current status of Plasmodium vivax* 

[39] Galinski, M.R. and J.W. Barnwell, *Plasmodium vivax: who cares?* Malar J, 2008. 7 Suppl 1:

[40] Crabb, B.S. and A.F. Cowman, *Characterization of promoters and stable transfection by* 

[41] Wu, Y., L.A. Kirkman, and T.E. Wellems, *Transformation of Plasmodium falciparum malaria* 

[42] Wu, Y., et al., *Transfection of Plasmodium falciparum within human red blood cells.* Proc Natl

[43] Alonso, P.L., et al., *Duration of protection with RTS,S/AS02A malaria vaccine in prevention* 

[44] Alonso, P.L., et al., *Efficacy of the RTS,S/AS02A vaccine against Plasmodium falciparum* 

[45] Sirima, S.B., S. Cousens, and P. Druilhe, *Protection against malaria by MSP3 candidate* 

[46] Thera, M.A., et al., *A field trial to assess a blood-stage malaria vaccine.* N Engl J Med, 2011.

*of a randomised controlled trial.* Lancet, 2005. 366(9502): p. 2012-8.

*homologous and nonhomologous recombination in Plasmodium falciparum.* Proc Natl

*parasites by homologous integration of plasmids that confer resistance to pyrimethamine.*

*of Plasmodium falciparum disease in Mozambican children: single-blind extended follow-up* 

*infection and disease in young African children: randomised controlled trial.* Lancet, 2004.

*protective immunity and apoptosis of infected liver cells.* Proc Natl Acad Sci U S A, 2005.

*hypoxanthine guanine xanthine phosphoribosyl transferase (HGXPRT) in acute malaria.*

Nature, 2002. 419(6906): p. 498-511.

Exp Biol, 2003. 206(Pt 21): p. 3789-802.

425(6957): p. 437.

102(34): p. 12194-9.

Malar J, 2009. 8: p. 122.

363(9403): p. 150-6.

p. S9.

Cell Biol, 2009. 87(5): p. 377-90.

*vaccine.* Hum Vaccin, 2010. 6(1): p. 124-32.

Acad Sci U S A, 1996. 93(14): p. 7289-94.

Acad Sci U S A, 1995. 92(4): p. 973-7.

364(9443): p. 1411-20.

365(11): p. 1004-13.

Proc Natl Acad Sci U S A, 1996. 93(3): p. 1130-4.

*vaccine.* N Engl J Med, 2011. 365(11): p. 1062-4.

*protein microarrays.* Proteomics, 2008. 8(22): p. 4680-94.

*cell immunity.* Science, 2011. 334(6055): p. 475-80.

*lateral thinking.* Trends Parasitol, 2011. 27(8): p. 335-40.


[6] Genton, B., et al., *A recombinant blood-stage malaria vaccine reduces Plasmodium falciparum* 

[7] Takala, S.L. and C.V. Plowe, *Genetic diversity and malaria vaccine design, testing and efficacy:* 

[8] Barry, A.E., et al., *Contrasting population structures of the genes encoding ten leading vaccine-*

[9] Koch, R., *Dritter Bericht uber die Thatigkeit der Malaria Expedition. .* British Medical Journal,

[10] McGregor, I.A., *The Passive Transfer of Human Malarial Immunity.* Am J Trop Med Hyg,

[11] Nussenzweig, R.S., et al., *Protective immunity produced by the injection of x-irradiated* 

[12] Clyde, D.F., et al., *Immunization of man against sporozite-induced falciparum malaria.* Am J

[13] Clyde, D.F., et al., *Specificity of protection of man immunized against sporozoite-induced* 

[14] Hoffman, S.L., et al., *Protection of humans against malaria by immunization with radiationattenuated Plasmodium falciparum sporozoites.* J Infect Dis, 2002. 185(8): p. 1155-64. [15] Yoshida, N., et al., *Hybridoma produces protective antibodies directed against the sporozoite* 

[16] Vanderberg, J.P., M.M. Weiss, and S.R. Mack, *In vitro cultivation of the sporogonic stages of Plasmodium: a review.* Bull World Health Organ, 1977. 55(2-3): p. 377-92. [17] Robson, K.J., et al., *A highly conserved amino-acid sequence in thrombospondin, properdin and* 

[18] Rogers, W.O., et al., *Characterization of Plasmodium falciparum sporozoite surface protein 2.*

[19] Guerin-Marchand, C., et al., *A liver-stage-specific antigen of Plasmodium falciparum* 

[20] Holder, A.A., et al., *A malaria merozoite surface protein (MSP1)-structure, processing and* 

[21] Smythe, J.A., et al., *Identification of two integral membrane proteins of Plasmodium* 

[22] Coppel, R.L., et al., *Isolate-specific S-antigen of Plasmodium falciparum contains a repeated* 

[23] Deans, J.A., et al., *Vaccination trials in rhesus monkeys with a minor, invariant, Plasmodium knowlesi 66 kD merozoite antigen.* Parasite Immunol, 1988. 10(5): p. 535-52. [24] Hodder, A.N., et al., *The disulfide bond structure of Plasmodium apical membrane antigen-1.* J

[25] Agnandji, S.T., et al., *First results of phase 3 trial of RTS,S/AS01 malaria vaccine in African* 

[26] Florens, L., et al., *A proteomic view of the Plasmodium falciparum life cycle.* Nature, 2002.

*in proteins from sporozoites and blood stages of a human malaria parasite.* Nature, 1988.

*sporozoites of plasmodium berghei.* Nature, 1967. 216(111): p. 160-2.

*falciparum malaria.* Am J Med Sci, 1973. 266(6): p. 398-403.

*stage of malaria parasite.* Science, 1980. 207(4426): p. 71-3.

Proc Natl Acad Sci U S A, 1992. 89(19): p. 9176-80.

Biol Chem, 1996. 271(46): p. 29446-52.

*children.* N Engl J Med, 2011. 365(20): p. 1863-75.

*characterized by gene cloning.* Nature, 1987. 329(6135): p. 164-7.

*function.* Mem Inst Oswaldo Cruz, 1992. 87 Suppl 3: p. 37-42.

*falciparum.* Proc Natl Acad Sci U S A, 1988. 85(14): p. 5195-9.

*sequence of eleven amino acids.* Nature, 1983. 306(5945): p. 751-6.

*New Guinea.* J Infect Dis, 2002. 185(6): p. 820-7.

560-73.

2009. 4(12): p. e8497.

1900: p. 1183-1186.

335(6185): p. 79-82.

419(6906): p. 520-6.

1964. 13: p. SUPPL 237-9.

Med Sci, 1973. 266(3): p. 169-77.

*density and exerts selective pressure on parasite populations in a phase 1-2b trial in Papua* 

*preventing and overcoming 'vaccine resistant malaria'.* Parasite Immunol, 2009. 31(9): p.

*candidate antigens of the human malaria parasite, Plasmodium falciparum.* PLoS One,


Using Population Genetics to Guide Malaria Vaccine Design 255

[67] Gilbert, S.C., et al., *Synergistic DNA-MVA prime-boost vaccination regimes for malaria and* 

[68] McConkey, S.J., et al., *Enhanced T-cell immunogenicity of plasmid DNA vaccines boosted by recombinant modified vaccinia virus Ankara in humans.* Nat Med, 2003. 9(6): p. 729-35. [69] Bejon, P., et al., *Calculation of liver-to-blood inocula, parasite growth rates, and preerythrocytic* 

*challenged with malaria sporozoites.* J Infect Dis, 2005. 191(4): p. 619-26. [70] Bejon, P., et al., *A phase 2b randomised trial of the candidate malaria vaccines FP9 ME-TRAP and MVA ME-TRAP among children in Kenya.* PLoS Clin Trials, 2006. 1(6): p. e29. [71] Bejon, P., et al., *Extended follow-up following a phase 2b randomized trial of the candidate* 

*vaccine efficacy, from serial quantitative polymerase chain reaction studies of volunteers* 

*malaria vaccines FP9 ME-TRAP and MVA ME-TRAP among children in Kenya.* PLoS

*DNA/MVA ME-TRAP against malaria infection in Gambian adults.* PLoS Med, 2004.

*including a 12-month reboosting vaccination, for malaria vaccination in Gambian men.* J

*PF83/AMA-1 an apical membrane antigen of Plasmodium falciparum merozoites.* Mol

[72] Moorthy, V.S., et al., *A randomised, double-blind, controlled vaccine efficacy trial of* 

[73] Moorthy, V.S., et al., *Phase 1 evaluation of 3 highly immunogenic prime-boost regimens,* 

[74] Peterson, M.G., et al., *Integral membrane protein located in the apical complex of Plasmodium* 

[75] Narum, D.L. and A.W. Thomas, *Differential localization of full-length and processed forms of* 

[76] Howell, S.A., et al., *Proteolytic processing and primary structure of Plasmodium falciparum* 

[77] Howell, S.A., et al., *A single malaria merozoite serine protease mediates shedding of multiple surface proteins by juxtamembrane cleavage.* J Biol Chem, 2003. 278(26): p. 23890-8. [78] Collins, C.R., et al., *An inhibitory antibody blocks interactions between components of the* 

[79] Besteiro, S., et al., *Export of a Toxoplasma gondii rhoptry neck protein complex at the host cell* 

[80] Silvie, O., et al., *Malaria sporozoite: migrating for a living.* Trends Mol Med, 2004. 10(3): p.

[81] Johnson, A.H., et al., *Human leukocyte antigen class II alleles influence levels of antibodies to* 

[82] Thomas, A.W., et al., *Aspects of immunity for the AMA-1 family of molecules in humans and non-human primates malarias.* Mem Inst Oswaldo Cruz, 1994. 89 Suppl 2: p. 67-70. [83] Cortes, A., et al., *Allele specificity of naturally acquired antibody responses against* 

[84] Hodder, A.N., P.E. Crewther, and R.F. Anders, *Specificity of the protective antibody response to apical membrane antigen 1.* Infect Immun, 2001. 69(5): p. 3286-94.

*membrane to form the moving junction during invasion.* PLoS Pathog, 2009. 5(2): p.

*the Plasmodium falciparum asexual-stage apical membrane antigen 1 but not to merozoite surface antigen 2 and merozoite surface protein 1.* Infect Immun, 2004. 72(5): p. 2762-71.

*Plasmodium falciparum apical membrane antigen 1.* Infect Immun, 2005. 73(1): p. 422-

*apical membrane antigen-1.* J Biol Chem, 2001. 276(33): p. 31311-20.

*malarial invasion machinery.* PLoS Pathog, 2009. 5(1): p. e1000273.

*tuberculosis.* Vaccine, 2006. 24(21): p. 4554-61.

One, 2007. 2(8): p. e707.

Infect Dis, 2004. 189(12): p. 2213-9.

*falciparum.* Mol Cell Biol, 1989. 9(7): p. 3151-4.

Biochem Parasitol, 1994. 67(1): p. 59-68.

1(2): p. e33.

e1000309.

30.

97-100; discussion 100-1.


[47] Volkman, S.K., et al., *A genome-wide map of diversity in Plasmodium falciparum.* Nat Genet,

[49] Sanders, P.R., et al., *Distinct protein classes including novel merozoite surface antigens in* 

[50] Arumugam, T.U., et al., *Discovery of GAMA, a Plasmodium falciparum merozoite* 

[51] Organisation, W.H. *Malaria Vaccine Rainbow Tables.* . 2010 December 2010; Available from: http://www.who.int/vaccine\_research/links/Rainbow/en/index.html. [52] Snow, R.W., et al., *The global distribution of clinical episodes of Plasmodium falciparum* 

[53] Enea, V., et al., *DNA cloning of Plasmodium falciparum circumsporozoite gene: amino acid* 

[54] Dame, J.B., et al., *Structure of the gene encoding the immunodominant surface antigen on the* 

[55] Good, M.F., et al., *Human T-cell recognition of the circumsporozoite protein of Plasmodium* 

[56] *First Results of Phase 3 Trial of RTS,S/AS01 Malaria Vaccine in African Children.* N Engl J

[57] Cowan, G., et al., *Expression of thrombospondin-related anonymous protein in Plasmodium* 

[58] Ghosh, A.K., et al., *Malaria parasite invasion of the mosquito salivary gland requires* 

[59] Sultan, A.A., et al., *TRAP is necessary for gliding motility and infectivity of plasmodium* 

[60] Kappe, S., et al., *Conservation of a gliding motility and cell invasion machinery in* 

[61] Charoenvit, Y., et al., *Development of two monoclonal antibodies against Plasmodium* 

[62] Wizel, B., et al., *Irradiated sporozoite vaccine induces HLA-B8-restricted cytotoxic T* 

[63] Wizel, B., et al., *HLA-A2-restricted cytotoxic T lymphocyte responses to multiple Plasmodium* 

[64] Aidoo, M., et al., *Identification of conserved antigenic components for a cytotoxic T lymphocyte-inducing vaccine against malaria.* Lancet, 1995. 345(8956): p. 1003-7. [65] Robson, K.J., et al., *Natural polymorphism in the thrombospondin-related adhesive protein of* 

[66] Weedall, G.D., et al., *Differential evidence of natural selection on two leading sporozoite stage malaria vaccine candidate antigens.* Int J Parasitol, 2007. 37(1): p. 77-85.

*sporozoite of the human malaria parasite Plasmodium falciparum.* Science, 1984.

*falciparum: immunodominant T-cell domains map to the polymorphic regions of the* 

*interaction between the Plasmodium TRAP and the Anopheles saglin proteins.* PLoS

*falciparum sporozoite surface protein 2 and mapping of B-cell epitopes.* Infect Immun,

*lymphocyte responses against two overlapping epitopes of the Plasmodium falciparum* 

*falciparum sporozoite surface protein 2 epitopes in sporozoite-immunized volunteers.* J

*sequence of repetitive epitope.* Science, 1984. 225(4662): p. 628-30.

*molecule.* Proc Natl Acad Sci U S A, 1988. 85(4): p. 1199-203.

*falciparum sporozoites.* Lancet, 1992. 339(8806): p. 1412-3.

*Apicomplexan parasites.* J Cell Biol, 1999. 147(5): p. 937-44.

*sporozoite surface protein 2.* J Exp Med, 1995. 182(5): p. 1435-45.

*Plasmodium falciparum.* Am J Trop Med Hyg, 1998. 58(1): p. 81-9.

*Raft-like membranes of Plasmodium falciparum.* J Biol Chem, 2005. 280(48): p. 40169-76.

*micronemal protein, as a novel blood-stage vaccine candidate antigen.* Infect Immun, 2011.

2007. 39(1): p. 113-9.

79(11): p. 4523-32.

225(4662): p. 593-9.

Pathog, 2009. 5(1): p. e1000265.

Immunol, 1995. 155(2): p. 766-75.

1997. 65(8): p. 3430-7.

*sporozoites.* Cell, 1997. 90(3): p. 511-22.

Med, 2011.

[48] Doolan, D.L., *Plasmodium immunomics.* Int J Parasitol, 2010.

*malaria.* Nature, 2005. 434(7030): p. 214-7.


Using Population Genetics to Guide Malaria Vaccine Design 257

[102] Barale, J.C., et al., *Plasmodium falciparum subtilisin-like protease 2, a merozoite candidate for* 

[103] Hackett, F., et al., *PfSUB-2: a second subtilisin-like protein in Plasmodium falciparum* 

[104] Harris, P.K., et al., *Molecular identification of a malaria merozoite surface sheddase.* PLoS

[105] Blackman, M.J., et al., *Antibodies inhibit the protease-mediated processing of a malaria* 

[106] Blackman, M.J., et al., *A single fragment of a malaria merozoite surface protein remains on the* 

[107] Tanabe, K., et al., *Allelic dimorphism in a surface antigen gene of the malaria parasite* 

[108] Miller, L.H., et al., *Analysis of sequence diversity in the Plasmodium falciparum merozoite surface protein-1 (MSP-1).* Mol Biochem Parasitol, 1993. 59(1): p. 1-14. [109] Da Silveira, L.A., et al., *Sequence diversity and linkage disequilibrium within the merozoite* 

[110] Ferreira, M.U., et al., *Sequence diversity and evolution of the malaria vaccine candidate* 

[111] Qari, S.H., et al., *Predicted and observed alleles of Plasmodium falciparum merozoite surface* 

[112] Sakihama, N., et al., *Allelic recombination and linkage disequilibrium within Msp-1 of* 

[113] Takala, S.L., et al., *Dynamics of polymorphism in a malaria vaccine antigen at a vaccine-*

[114] Thera, M.A., et al., *Safety and allele-specific immunogenicity of a malaria vaccine in Malian adults: results of a phase I randomized trial.* PLoS Clin Trials, 2006. 1(7): p. e34. [115] Ogutu, B.R., et al., *Blood stage malaria vaccine eliciting high antigen-specific antibody* 

[116] Goodman, A.L., et al., *New candidate vaccines against blood-stage Plasmodium falciparum* 

[117] Fenton, B., et al., *Structural and antigenic polymorphism of the 35- to 48-kilodalton merozoite* 

[118] Smythe, J.A., et al., *Structural diversity in the Plasmodium falciparum merozoite surface* 

[119] Smythe, J.A., et al., *Structural diversity in the 45-kilodalton merozoite surface antigen of Plasmodium falciparum.* Mol Biochem Parasitol, 1990. 39(2): p. 227-34.

*parasite during red cell invasion and is the target of invasion-inhibiting antibodies.* J Exp

*surface protein-1 (Msp-1) locus of Plasmodium falciparum: a longitudinal study in Brazil.* J

*merozoite surface protein-1 (MSP-1) of Plasmodium falciparum.* Gene, 2003. 304: p. 65-

*protein-1 (MSP-1), a potential malaria vaccine antigen.* Mol Biochem Parasitol, 1998.

*Plasmodium falciparum, the malignant human malaria parasite.* Gene, 1999. 230(1): p. 47-

*concentrations confers no protection to young children in Western Kenya.* PLoS One,

*malaria: prime-boost immunization regimens incorporating human and simian adenoviral vectors and poxviral vectors expressing an optimized antigen based on merozoite surface* 

*surface antigen (MSA-2) of the malaria parasite Plasmodium falciparum.* Mol Cell Biol,

*merozoites.* Mol Biochem Parasitol, 1999. 103(2): p. 183-95.

*merozoite surface protein.* J Exp Med, 1994. 180(1): p. 389-93.

*Plasmodium falciparum.* J Mol Biol, 1987. 195(2): p. 273-87.

6445-50.

75.

54.

92(2): p. 241-52.

2009. 4(3): p. e4708.

1991. 11(2): p. 963-71.

Pathog, 2005. 1(3): p. 241-51.

Med, 1990. 172(1): p. 379-82.

Eukaryot Microbiol, 2001. 48(4): p. 433-9.

*testing site in Mali.* PLoS Med, 2007. 4(3): p. e93.

*protein 1.* Infect Immun, 2010. 78(11): p. 4601-12.

*antigen 2.* Proc Natl Acad Sci U S A, 1991. 88(5): p. 1751-5.

*the merozoite surface protein 1-42 maturase.* Proc Natl Acad Sci U S A, 1999. 96(11): p.


[85] Kennedy, M.C., et al., *In vitro studies with recombinant Plasmodium falciparum apical* 

[86] Kocken, C.H., et al., *High-level expression of the malaria blood-stage vaccine candidate* 

[87] Yoshida, S., et al., *Plasmodium berghei circumvents immune responses induced by merozoite* 

[88] Miura, K., et al., *In immunization with Plasmodium falciparum apical membrane antigen 1,* 

[89] Narum, D.L., et al., *Passive immunization with a multicomponent vaccine against conserved* 

[90] Barclay, V.C., et al., *Mixed allele malaria vaccines: host protection and within-host selection.*

[91] Duan, J., et al., *Population structure of the genes encoding the polymorphic Plasmodium* 

[92] Takala, S.L., et al., *Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development.* Sci Transl Med, 2009. 1(2): p. 2ra5. [93] Cortes, A., et al., *Geographical structure of diversity and differences between symptomatic and* 

[94] Kusi, K.A., et al., *Generation of humoral immune responses to multi-allele PfAMA1 vaccines;* 

[95] Kusi, K.A., et al., *Humoral immune response to mixed PfAMA1 alleles; multivalent PfAMA1* 

[96] Dutta, S., et al., *Alanine mutagenesis of the primary antigenic escape residue cluster, c1, of* 

[97] Dutta, S., et al., *Structural basis of antigenic escape of a malaria vaccine candidate.* Proc Natl

[98] Ouattara, A., et al., *Lack of allele-specific efficacy of a bivalent AMA1 malaria vaccine.* Malar

[99] Remarque, E.J., et al., *A diversity-covering approach to immunization with Plasmodium* 

[100] McBride, J.S. and H.G. Heidrich, *Fragments of the polymorphic Mr 185,000 glycoprotein* 

[101] Gerold, P., et al., *Structural analysis of the glycosyl-phosphatidylinositol membrane anchor of* 

*inhibition responses in rabbits.* Infect Immun, 2008. 76(6): p. 2660-70.

*falciparum apical membrane antigen 1 induces broader allelic recognition and growth* 

*from the surface of isolated Plasmodium falciparum merozoites form an antigenic complex.*

*the merozoite surface proteins-1 and -2 of Plasmodium falciparum.* Mol Biochem

*vaccines induce broad specificity.* PLoS One, 2009. 4(12): p. e8110.

*apical membrane antigen 1.* Infect Immun, 2010. 78(2): p. 661-71.

*of a multiallelic response.* Infect Immun, 2002. 70(12): p. 6948-60.

*erythrocyte invasion.* Infect Immun, 2002. 70(8): p. 4471-6.

p. e13727.

5529-36.

75(12): p. 5827-36.

Vaccine, 2008. 26(48): p. 6099-107.

Sci U S A, 2008. 105(22): p. 7857-62.

Immun, 2003. 71(3): p. 1416-26.

Acad Sci U S A, 2007. 104(30): p. 12488-93.

Mol Biochem Parasitol, 1987. 23(1): p. 71-84.

Parasitol, 1996. 75(2): p. 131-43.

2010. 5(11): p. e15391.

J, 2010. 9: p. 175.

*membrane antigen 1 (AMA1): production and activity of an AMA1 vaccine and generation* 

*Plasmodium falciparum apical membrane antigen 1 and induction of antibodies that inhibit* 

*surface protein 1- and apical membrane antigen 1-based vaccines.* PLoS One, 2010. 5(10):

*the specificity of antibodies depends on the species immunized.* Infect Immun, 2007.

*domains of apical membrane antigen 1 and 235-kilodalton rhoptry proteins protects mice against Plasmodium yoelii blood-stage challenge infection.* Infect Immun, 2006. 74(10): p.

*falciparum apical membrane antigen 1: implications for vaccine design.* Proc Natl Acad

*asymptomatic infections for Plasmodium falciparum vaccine candidate AMA1.* Infect

*effect of adjuvant and number of component alleles on the breadth of response.* PLoS One,


Using Population Genetics to Guide Malaria Vaccine Design 259

[136] Huber, W., et al., *Limited sequence polymorphism in the Plasmodium falciparum merozoite* 

[137] Okenu, D.M., A.W. Thomas, and D.J. Conway, *Allelic lineages of the merozoite surface* 

[138] Polley, S.D., et al., *Plasmodium falciparum merozoite surface protein 3 is a target of allele-*

[139] Audran, R., et al., *Phase I malaria vaccine trial with a long synthetic peptide derived from the merozoite surface protein 3 antigen.* Infect Immun, 2005. 73(12): p. 8017-26. [140] Mordmuller, B., et al., *Safety and immunogenicity of the malaria vaccine candidate GMZ2 in* 

[141] Camus, D. and T.J. Hadley, *A Plasmodium falciparum antigen that binds to host* 

[142] Sim, B.K., et al., *Primary structure of the 175K Plasmodium falciparum erythrocyte binding* 

[143] Sim, B.K., et al., *Receptor and ligand domains for invasion of erythrocytes by Plasmodium* 

[144] Tolia, N.H., et al., *Structural basis for the EBA-175 erythrocyte invasion pathway of the* 

[145] Okenu, D.M., et al., *Analysis of human antibodies to erythrocyte binding antigen 175 of* 

[146] Okoyeh, J.N., C.R. Pillai, and C.E. Chitnis, *Plasmodium falciparum field isolates commonly* 

[147] Richards, J.S., et al., *Association between naturally acquired antibodies to erythrocyte-binding* 

[148] Narum, D.L., et al., *Antibodies against the Plasmodium falciparum receptor binding domain* 

[149] Baum, J., A.W. Thomas, and D.J. Conway, *Evidence for diversifying selection on* 

[150] Persson, K.E., et al., *Variation in use of erythrocyte invasion pathways by Plasmodium* 

[151] Jones, T.R., et al., *Protection of Aotus monkeys by Plasmodium falciparum EBA-175 region II DNA prime-protein boost immunization regimen.* J Infect Dis, 2001. 183(2): p. 303-312. [152] El Sahly, H.M., et al., *Safety and immunogenicity of a recombinant nonglycosylated* 

*use erythrocyte invasion pathways that are independent of sialic acid residues of* 

*antigens of Plasmodium falciparum and protection from malaria and high-density* 

*of EBA-175 block invasion pathways that do not involve sialic acids.* Infect Immun, 2000.

*erythrocyte-binding antigens of Plasmodium falciparum and P. vivax.* Genetics, 2003.

*falciparum mediates evasion of human inhibitory antibodies.* J Clin Invest, 2008. 118(1): p.

*erythrocyte binding antigen 175 Region II malaria vaccine in healthy adults living in an area where malaria is not endemic.* Clin Vaccine Immunol, 2010. 17(10): p. 1552-9. [153] Rener, J., et al., *Target antigens of transmission-blocking immunity on gametes of plasmodium* 

*malaria parasite Plasmodium falciparum.* Cell, 2005. 122(2): p. 183-93.

*Plasmodium falciparum.* Infect Immun, 2000. 68(10): p. 5559-66.

*glycophorin A.* Infect Immun, 1999. 67(11): p. 5784-91.

*parasitemia.* Clin Infect Dis, 2010. 51(8): p. e50-60.

*falciparum.* J Exp Med, 1983. 158(3): p. 976-81.

*protein 3 gene in Plasmodium reichenowi and Plasmodium falciparum.* Mol Biochem

*specific immunity and alleles are maintained by natural selection.* J Infect Dis, 2007.

*malaria-exposed, adult individuals from Lambarene, Gabon.* Vaccine, 2010. 28(41): p.

*antigen and identification of a peptide which elicits antibodies that inhibit malaria* 

*surface protein 3.* Mol Biochem Parasitol, 1997. 87(2): p. 231-4.

*erythrocytes and merozoites.* Science, 1985. 230(4725): p. 553-6.

*merozoite invasion.* J Cell Biol, 1990. 111(5 Pt 1): p. 1877-84.

*falciparum.* Science, 1994. 264(5167): p. 1941-4.

Parasitol, 2000. 109(2): p. 185-8.

195(2): p. 279-87.

6698-703.

68(4): p. 1964-6.

163(4): p. 1327-36.

342-51.


[120] Snewin, V.A., et al., *Polymorphism of the alleles of the merozoite surface antigens MSA1 and* 

[121] Falk, N., et al., *Comparison of PCR-RFLP and Genescan-based genotyping for analyzing* 

[122] Schoepflin, S., et al., *Comparison of Plasmodium falciparum allelic frequency distribution in different endemic settings by high-resolution genotyping.* Malar J, 2009. 8: p. 250. [123] Ranford-Cartwright, L.C., et al., *Differential antibody recognition of FC27-like Plasmodium* 

[124] Taylor, R.R., et al., *Human antibody response to Plasmodium falciparum merozoite surface* 

[125] Stanisic, D.I., et al., *Immunoglobulin G subclass-specific responses against Plasmodium* 

[126] Taylor, R.R., et al., *IgG3 antibodies to Plasmodium falciparum merozoite surface protein 2* 

[127] Metzger, W.G., et al., *Serum IgG3 to the Plasmodium falciparum merozoite surface protein 2* 

[128] al-Yaman, F., et al., *Assessment of the role of the humoral response to Plasmodium falciparum* 

[129] Bruce, M.C., et al., *Genetic diversity and dynamics of plasmodium falciparum and P. vivax* 

[130] Franks, S., et al., *Frequent and persistent, asymptomatic Plasmodium falciparum infections in* 

[131] Weisman, S., et al., *Antibody responses to infections with strains of Plasmodium falciparum* 

[132] McCarthy, J.S., et al., *A pilot randomised trial of induced blood-stage Plasmodium falciparum* 

[133] McColl, D.J., et al., *Molecular variation in a novel polymorphic antigen associated with Plasmodium falciparum merozoites.* Mol Biochem Parasitol, 1994. 68(1): p. 53-67. [134] McColl, D.J. and R.F. Anders, *Conservation of structural motifs and antigenic diversity in* 

[135] Oeuvray, C., et al., *Merozoite surface protein-3: a malaria protein inducing antibodies that* 

*from symptomatic illness.* Infect Immun, 2009. 77(3): p. 1165-74.

*clinical malaria.* Parasite Immunol, 1995. 17(9): p. 493-501.

*New Guinea.* Parasitology, 2000. 121 ( Pt 3): p. 257-72.

1991. 49(2): p. 265-75.

25(6): p. 307-12.

804.

959-67.

2011. 6(8): p. e21914.

1997. 90(1): p. 21-31.

84(5): p. 1594-602.

Parasite Immunol, 1996. 18(8): p. 411-20.

Infect Immun, 1995. 63(11): p. 4382-8.

Am J Trop Med Hyg, 1998. 58(4): p. 406-13.

50.

*MSA2 in Plasmodium falciparum wild isolates from Colombia.* Mol Biochem Parasitol,

*infection dynamics of Plasmodium falciparum.* Am J Trop Med Hyg, 2006. 74(6): p. 944-

*falciparum merozoite surface protein MSP2 antigens which lack 12 amino acid repeats.*

*protein 2 is serogroup specific and predominantly of the immunoglobulin G3 subclass.*

*falciparum merozoite antigens are associated with control of parasitemia and protection* 

*(MSP2): increasing prevalence with age and association with clinical immunity to malaria.*

*is strongly associated with a reduced prospective risk of malaria.* Parasite Immunol, 2003.

*MSP2 compared to RESA and SPf66 in protecting Papua New Guinean children from* 

*populations in multiply infected children with asymptomatic malaria infections in Papua* 

*African infants, characterized by multilocus genotyping.* J Infect Dis, 2001. 183(5): p. 796-

*expressing diverse forms of merozoite surface protein 2.* Infect Immun, 2001. 69(2): p.

*infections in healthy volunteers for testing efficacy of new antimalarial drugs.* PLoS One,

*the Plasmodium falciparum merozoite surface protein-3 (MSP-3).* Mol Biochem Parasitol,

*promote Plasmodium falciparum killing by cooperation with blood monocytes.* Blood, 1994.


Using Population Genetics to Guide Malaria Vaccine Design 261

[171] Reiling, L., et al., *Evidence that the erythrocyte invasion ligand PfRh2 is a target of protective* 

[172] Lopaticki, S., et al., *Reticulocyte and erythrocyte binding-like proteins function cooperatively* 

[173] Chen, L., et al., *An EGF-like protein forms a complex with PfRh5 and is required for invasion* 

[174] Palacpac, N.M., et al., *Plasmodium falciparum serine repeat antigen 5 (SE36) as a malaria* 

[175] Demanga, C.G., et al., *Toward the rational design of a malaria vaccine construct using the* 

[176] Pachebat, J.A., et al., *Extensive proteolytic processing of the malaria parasite merozoite surface* 

[177] Barfod, L., et al., *Baculovirus-expressed constructs induce immunoglobulin G that recognizes* 

[178] Salanti, A., et al., *Several domains from VAR2CSA can induce Plasmodium falciparum* 

[179] Srivastava, A., et al., *Full-length extracellular region of the var2CSA variant of PfEMP1 is* 

[180] Snounou, G. and L. Renia, *The vaccine is dead--long live the vaccine.* Trends Parasitol,

[181] Tham, W.H., Healer, J.,Cowman, A.F., *Erythrocyte and reticulocyte binding-like proteins of* 

[182] Mueller, I., et al., *Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria* 

[183] Chitnis, C.E. and A. Sharma, *Targeting the Plasmodium vivax Duffy-binding protein.*

[184] Miller, L.H., et al., *The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-*

[185] Gentil, F., et al., *A recombinant vaccine based on domain II of Plasmodium vivax Apical* 

[186] Castellanos, A., et al., *Plasmodium vivax thrombospondin related adhesion protein:* 

[187] Putaporntip, C., et al., *Mosaic organization and heterogeneity in frequency of allelic* 

[188] Cheng, Q. and A. Saul, *Sequence analysis of the apical membrane antigen I (AMA-1) of* 

*Plasmodium vivax.* Mol Biochem Parasitol, 1994. 65(1): p. 183-7.

*Membrane Antigen 1 induces high antibody titres in mice.* Vaccine, 2010. 28(38): p. 6183-

*immunogenicity and protective efficacy in rodents and Aotus monkeys.* Mem Inst

*recombination of the Plasmodium vivax merozoite surface protein-1 locus.* Proc Natl Acad

*Plasmodium falciparum.* Trends in Parasitology, 2011. In press.

*group genotype, FyFy.* N Engl J Med, 1976. 295(6): p. 302-4.

*vaccine candidate.* Vaccine, 2011. 29(35): p. 5837-45.

*adhesion-blocking antibodies.* Malar J, 2010. 9: p. 11.

*parasite.* Lancet Infect Dis, 2009. 9(9): p. 555-66.

Trends Parasitol, 2008. 24(1): p. 29-34.

Oswaldo Cruz, 2007. 102(3): p. 411-6.

Sci U S A, 2002. 99(25): p. 16348-53.

Immun, 2010. 78(1): p. 486-94.

Parasitol, 2007. 151(1): p. 59-69.

67.

1107-17.

p. 4357-60.

90.

107(11): p. 4884-9.

2007. 23(4): p. 129-32.

*immunity against Plasmodium falciparum malaria.* J Immunol, 2010. 185(10): p. 6157-

*in invasion of human erythrocytes by malaria parasites.* Infect Immun, 2011. 79(3): p.

*of human erythrocytes by Plasmodium falciparum.* PLoS Pathog, 2011. 7(9): p. e1002199.

*MSP3 family as an example: contribution of antigenicity studies in humans.* Infect

*protein 7 during biosynthesis and parasite release from erythrocytes.* Mol Biochem

*VAR2CSA on Plasmodium falciparum-infected erythrocytes.* Infect Immun, 2006. 74(7):

*required for specific, high-affinity binding to CSA.* Proc Natl Acad Sci U S A, 2010.


[154] Vermeulen, A.N., et al., *Sequential expression of antigens on sexual stages of Plasmodium* 

[155] Quakyi, I.A., et al., *The 230-kDa gamete surface protein of Plasmodium falciparum is also a target for transmission-blocking antibodies.* J Immunol, 1987. 139(12): p. 4213-7. [156] Barr, P.J., et al., *Recombinant Pfs25 protein of Plasmodium falciparum elicits malaria* 

[157] Kocken, C.H., et al., *Cloning and expression of the gene coding for the transmission blocking* 

[158] Kaslow, D.C., et al., *Comparison of the primary structure of the 25 kDa ookinete surface* 

[159] Shi, Y.P., et al., *Single amino acid variation in the ookinete vaccine antigen from field isolates of Plasmodium falciparum.* Mol Biochem Parasitol, 1992. 50(1): p. 179-80. [160] Kaslow, D.C., et al., *A vaccine candidate from the sexual stage of human malaria that contains* 

[161] van Dijk, M.R., et al., *A central role for P48/45 in malaria parasite male gamete fertility.* Cell,

[162] Roeffen, W., et al., *Association between anti-Pfs48/45 reactivity and P. falciparum* 

[163] Duffy, P.E. and D.C. Kaslow, *A novel malaria protein, Pfs28, and Pfs25 are genetically* 

[164] Anthony, T.G., et al., *Evidence of non-neutral polymorphism in Plasmodium falciparum* 

[165] Conway, D.J., et al., *Extreme geographical fixation of variation in the Plasmodium falciparum* 

[166] Wu, Y., et al., *Phase 1 trial of malaria transmission blocking vaccine candidates Pfs25 and Pvs25 formulated with montanide ISA 51.* PLoS One, 2008. 3(7): p. e2636. [167] Kubler-Kielb, J., et al., *Long-lasting and transmission-blocking activity of antibodies to* 

[168] Reyes-Sandoval, A., et al., *Prime-boost immunization with adenoviral and modified vaccinia* 

[169] Hillier, C.J., et al., *Process development and analysis of liver-stage antigen 1, a preerythrocyte-*

[170] Goschnick, M.W., et al., *Merozoite surface protein 4/5 provides protection against lethal* 

*CD8+ T-cell responses.* Infect Immun, 2010. 78(1): p. 145-53.

*transmission-blocking activity in sera from Cameroon.* Parasite Immunol, 1996. 18(2): p.

*linked and synergistic as falciparum malaria transmission-blocking vaccines.* Infect

*gamete surface protein genes Pfs47 and Pfs48/45.* Mol Biochem Parasitol, 2007. 156(2):

*gamete surface protein gene Pfs48/45 compared with microsatellite loci.* Mol Biochem

*Plasmodium falciparum elicited in mice by protein conjugates of Pfs25.* Proc Natl Acad

*virus Ankara vectors enhances the durability and polyfunctionality of protective malaria* 

*stage protein-based vaccine for Plasmodium falciparum.* Infect Immun, 2005. 73(4): p.

*challenge with a heterologous malaria parasite strain.* Infect Immun, 2004. 72(10): p.

*regions.* Mol Biochem Parasitol, 1989. 33(3): p. 283-7.

*EGF-like domains.* Nature, 1988. 333(6168): p. 74-6.

1985. 162(5): p. 1460-76.

2001. 104(1): p. 153-64.

Immun, 1997. 65(3): p. 1109-13.

Parasitol, 2001. 115(2): p. 145-56.

Sci U S A, 2007. 104(1): p. 293-8.

1203-8.

p. 59-68.

103-9.

p. 117-23.

2109-15.

5840-9.

*falciparum accessible to transmission-blocking antibodies in the mosquito.* J Exp Med,

*transmission-blocking immunity in experimental animals.* J Exp Med, 1991. 174(5): p.

*target antigen Pfs48/45 of Plasmodium falciparum.* Mol Biochem Parasitol, 1993. 61(1):

*antigens of Plasmodium falciparum and Plasmodium gallinaceum reveal six conserved* 


Using Population Genetics to Guide Malaria Vaccine Design 263

[207] Smith, J.D., et al., *Switches in expression of Plasmodium falciparum var genes correlate with* 

[208] Baruch, D.I., et al., *Immunization of Aotus monkeys with a functional domain of the* 

[209] Salanti, A., et al., *Evidence for the involvement of VAR2CSA in pregnancy-associated* 

[210] Trimnell, A.R., et al., *Global genetic diversity and evolution of var genes associated with* 

[211] Hommel, M., et al., *Evaluation of the antigenic diversity of placenta-binding Plasmodium* 

[212] Bockhorst, J., et al., *Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA.* Mol Biochem Parasitol, 2007. 155(2): p. 103-12. [213] Avril, M., et al., *Antibodies to a full-length VAR2CSA immunogen are broadly strain-*

[214] Bigey, P., et al., *The NTS-DBL2X region of VAR2CSA induces cross-reactive antibodies that* 

[215] Beeson, J.G., et al., *Antigenic differences and conservation among placental Plasmodium* 

[216] Hartl, D.L., Clark, A.G. , *Principles of Population Genetics*. 3 ed. 1997, Sunderland,

[217] Conway, D.J., *Natural selection on polymorphic malaria antigens and the search for a vaccine.*

[218] Tetteh, K.K., et al., *Prospective identification of malaria parasite genes under balancing* 

[219] Ochola, L.I., et al., *Allele frequency-based and polymorphism-versus-divergence indices of* 

[220] Guerra, C.A., et al., *The international limits and population at risk of Plasmodium vivax* 

[221] Zakeri, S., et al., *Circumsporozoite protein gene diversity among temperate and tropical Plasmodium vivax isolates from Iran.* Trop Med Int Health, 2006. 11(5): p. 729-37. [222] Putaporntip, C., et al., *Diversity in the thrombospondin-related adhesive protein gene* 

[223] Ord, R.L., A. Tami, and C.J. Sutherland, *ama1 genes of sympatric Plasmodium vivax and P.* 

[224] Gunasekera, A.M., et al., *Genetic diversity and selection at the Plasmodium vivax apical* 

[225] Moon, S.U., et al., *High frequency of genetic diversity of Plasmodium vivax field isolates in* 

*falciparum from Venezuela differ significantly in genetic diversity and recombination* 

*membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population.* Mol Biol Evol, 2007.

*transmission in 2009.* PLoS Negl Trop Dis, 2010. 4(8): p. e774.

*(TRAP) of Plasmodium vivax.* Gene, 2001. 268(1-2): p. 97-104.

*balancing selection in a new filtered set of polymorphic genes in Plasmodium falciparum.*

*placental and severe childhood malaria.* Mol Biochem Parasitol, 2006.

Proc Natl Acad Sci U S A, 2002. 99(6): p. 3860-5.

*malaria.* J Exp Med, 2004. 200(9): p. 1197-203.

*antibodies.* J Infect Dis, 2006. 193(5): p. 721-30.

82(1): p. 101-10.

2010. 78(5): p. 1963-78.

2011. 6(2): p. e16622.

Dis, 2011. 204(7): p. 1125-33.

Maryland: Sinauer Associates.

Parasitol Today, 1997. 13(1): p. 26-9.

*selection.* PLoS One, 2009. 4(5): p. e5568.

Mol Biol Evol, 2010. 27(10): p. 2344-51.

*frequency.* PLoS One, 2008. 3(10): p. e3366.

*Myanmar.* Acta Trop, 2009. 109(1): p. 30-6.

24(4): p. 939-47.

*changes in antigenic and cytoadherent phenotypes of infected erythrocytes.* Cell, 1995.

*Plasmodium falciparum variant antigen induces protection against a lethal parasite line.*

*falciparum variants and the antibody repertoire among pregnant women.* Infect Immun,

*transcendent but do not cross-inhibit different placental-type parasite isolates.* PLoS One,

*inhibit adhesion of several plasmodium falciparum isolates to chondroitin sulfate A.* J Infect

*falciparum-infected erythrocytes and acquisition of variant-specific and cross-reactive* 


[189] Lima-Junior, J.C., et al., *Promiscuous T-cell epitopes of Plasmodium merozoite surface protein* 

[190] Marsh, K. and S. Kinyanjui, *Immune effector mechanisms in malaria.* Parasite Immunol,

[191] Gupta, S., et al., *Immunity to non-cerebral severe malaria is acquired after one or two* 

[192] Fowkes, F.J., et al., *The relationship between anti-merozoite antibodies and incidence of* 

[193] Scopel, K.K., et al., *Variant-specific antibodies to merozoite surface protein 2 and clinical* 

[194] Osier, F.H., et al., *Allele-specific antibodies to Plasmodium falciparum merozoite surface* 

[195] Kusi, K.A., et al., *Safety and immunogenicity of multi-antigen AMA1-based vaccines* 

[196] Druilhe, P., et al., *A malaria vaccine that elicits in humans antibodies able to kill Plasmodium* 

[197] Waitumbi, J.N., et al., *Impact of RTS,S/AS02(A) and RTS,S/AS01(B) on genotypes of P.* 

[198] Enosse, S., et al., *RTS,S/AS02A malaria vaccine does not induce parasite CSP T cell epitope selection and reduces multiplicity of infection.* PLoS Clin Trials, 2006. 1(1): p. e5. [199] Beeson, J.G. and B.S. Crabb, *Towards a vaccine against Plasmodium vivax malaria.* PLoS

[200] VanBuskirk, K.M., et al., *Antigenic drift in the ligand domain of Plasmodium vivax duffy* 

[201] Cole-Tobian, J.L., et al., *Strain-specific duffy binding protein antibodies correlate with* 

*strains in Papua New Guinean children.* Infect Immun, 2009. 77(9): p. 4009-17. [202] Verra, F., et al., *Contrasting signatures of selection on the Plasmodium falciparum erythrocyte binding antigen gene family.* Mol Biochem Parasitol, 2006. 149(2): p. 182-90. [203] Mamillapalli, A., et al., *Polymorphism and epitope sharing between the alleles of merozoite* 

[204] Jiang, L., et al., *Evidence for erythrocyte-binding antigen 175 as a component of a ligand-*

[205] Barry, A.E., et al., *Population genomics of the immune evasion (var) genes of Plasmodium* 

[206] Chen, D.S., et al., *A molecular epidemiological study of var gene diversity to characterize the* 

*malaria in the Brazilian Amazon.* Vaccine, 2010. 28(18): p. 3185-91.

2006. 28(1-2): p. 51-60.

7(1): p. e1000218.

201.

10: p. 182.

4(11): p. e7849.

1556-62.

8.

e16629.

Med, 2007. 4(12): p. e350.

2007. 76(6): p. 1084-91.

*infections.* Nat Med, 1999. 5(3): p. 340-3.

*falciparum.* PLoS Med, 2005. 2(11): p. e344.

*falciparum.* PLoS Pathog, 2007. 3(3): p. e34.

*9 (PvMSP9) induces IFN-gamma and IL-4 responses in individuals naturally exposed to* 

*Plasmodium falciparum malaria: A systematic review and meta-analysis.* PLoS Med, 2010.

*expression of Plasmodium falciparum malaria in rural Amazonians.* Am J Trop Med Hyg,

*protein-2 and protection against clinical malaria.* Parasite Immunol, 2010. 32(3): p. 193-

*formulated with CoVaccine HT and Montanide ISA 51 in rhesus macaques.* Malar J, 2011.

*falciparum in adults participating in a malaria vaccine clinical trial.* PLoS One, 2009.

*binding protein confers resistance to inhibitory antibodies.* J Infect Dis, 2004. 190(9): p.

*protection against infection with homologous compared to heterologous plasmodium vivax* 

*surface protein-1 of Plasmodium falciparum among Indian isolates.* Malar J, 2007. 6: p. 95.

*blocking blood-stage malaria vaccine.* Proc Natl Acad Sci U S A, 2011. 108(18): p. 7553-

*reservoir of Plasmodium falciparum in humans in Africa.* PLoS One, 2011. 6(2): p.


**Part 6** 

**Genomics of Malaria** 


**Part 6** 

**Genomics of Malaria** 

264 Malaria Parasites

[226] Nobrega de Sousa, T., L.H. Carvalho, and C.F. Alves de Brito, *Worldwide genetic* 

[227] Zakeri, S., S. Razavi, and N.D. Djadid, *Genetic diversity of transmission blocking vaccine* 

[228] Hurlbert, S.H., *The non-concept of species diversity: a critique and alternative parameters. .*

[229] Excoffier, L. and G. Heckel, *Computer programs for population genetics data analysis: a* 

[230] Jalloh, A., et al., *Sequence variation in the T-cell epitopes of the Plasmodium falciparum* 

[231] Tanabe, K., N. Sakihama, and A. Kaneko, *Stable SNPs in malaria antigen genes in isolated* 

[232] Mu, J., et al., *Recombination Hotspots and Population Structure in Plasmodium falciparum.*

[233] Pritchard, J.K., M. Stephens, and P. Donnelly, *Inference of population structure using* 

[234] Friedman, S.R. and S. Aral, *Social networks, risk-potential networks, health, and disease.* J

[235] Bull, P.C., et al., *Plasmodium falciparum antigenic variation. Mapping mosaic var gene* 

[236] Conway, D.J., et al., *A principal target of human immunity to malaria identified by molecular population genetic and immunological analyses.* Nat Med, 2000. 6(6): p. 689-92. [237] Weedall, G.D. and D.J. Conway, *Detecting signatures of balancing selection to identify targets of anti-parasite immunity.* Trends Parasitol, 2010. 26(7): p. 363-9. [238] Cui, L., et al., *The genetic diversity of Plasmodium vivax populations.* Trends Parasitol,

[239] Innan, H., *Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of* 

[240] Prugnolle, F., et al., *African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum.* Proc Natl Acad Sci U S A, 2010. 107(4): p. 1458-63. [241] Tajima, F., *Statistical method for testing the neutral mutation hypothesis by DNA* 

[242] Polley, S.D., W. Chokejindachai, and D.J. Conway, *Allele frequency-based analyses* 

*robustly map sequence sites under balancing selection in a malaria vaccine candidate* 

*sequences onto a network of shared, highly polymorphic sequence blocks.* Mol Microbiol,

*study in southern Vietnam.* J Clin Microbiol, 2006. 44(4): p. 1229-35.

*development.* PLoS One, 2011. 6(8): p. e22944.

*survival guide.* Nat Rev Genet, 2006. 7(10): p. 745-58.

*populations.* Science, 2004. 303(5657): p. 493.

*multilocus genotype data.* 2000. 155(2): p. 945.

*neutrality tests.* Genetics, 2006. 173(3): p. 1725-33.

*polymorphism.* Genetics, 1989. 123(3): p. 585-95.

*antigen.* Genetics, 2003. 165(2): p. 555-61.

Trop, 2009. 109(3): p. 176-80.

Ecology, 1971. 52(577-586).

PLoS Biol, 2005. 3(10): p. e335.

2008. 68(6): p. 1519-34.

2003. 19(5): p. 220-6.

Urban Health, 2001. 78(3): p. 411-8.

*variability of the Duffy binding protein: insights into Plasmodium vivax vaccine* 

*candidate (Pvs25 and Pvs28) antigen in Plasmodium vivax clinical isolates from Iran.* Acta

*circumsporozoite protein among field isolates is temporally stable: a 5-year longitudinal* 

**13** 

*Institut Pasteur* 

*France* 

**Human Genetic Contribution to the Outcome** 

The study of the contribution of human genetics to the risk of severe malaria has a long history, with Haldane in the 1950s reporting a major role of the sickle cell mutation (HbS), in the protection against severe disease (Haldane, 1949). Since then, genetic variants of βglobin (HbE: Hutagalung et al., 1999; HbC: Agarwal et al., 2000; HbS: Aidoo et al., 2002), α-globin (Mockenhaupt et al., 2004), Band 3 protein (Foo et al., 1992), HLA (Hill et al., 1991) and several cytokine loci (Tumor Necrosis Factor-alpha: Knight et al., 1999; Interleukin-12: Morahan et al., 2002a; Interferon-alpha receptor-1: Aucan et al., 2003; Interleukin-4: Gyan et al., 2004) have been demonstrated to confer protection to severe malaria. To date, the majority of studies have been case/control association studies, comparing severe malaria to uncomplicated cases. Due to the fact that *Plasmodium falciparum* is the etiological agent of severe malaria, all studies have consequently focussed on this parasite. The other congeneric species and notably *Plasmodium vivax*, can, however, cause severe disease, albeit at a much lower incidence, and warrant an increased research

Here we argue that for infectious diseases in general and for malaria parasites in particular, more attention should be paid to the "biological" course and outcome of infection in addition to severe disease. This is for several reasons: (i) the majority of infections in endemic settings do not cause severe disease. Indeed, severe disease is a collective term that englobes multiple pathologies (including cerebral malaria, severe malaria anaemia, metabolic acidosis, multiple organ failure) that likely involve very different biological pathways and thus should not be analysed as a single phenotype; (ii) the progression from clinical malaria to asymptomatic infection defines the acquisition of clinical immunity and identifying the mechanisms underlying this tipping point is central to the development of disease control methods; (iii) *P. falciparum* is remarkable in that sterilising anti-parasite immunity is never achieved. Although the parasite has a variety of mechanisms enabling this, the human also plays a part. Identifying pathways that "enable" the parasite to persist without elimination will provide insight into this apparent immune defence dysfunction; (iv) the biology of the parasite within the host will be informative as to how the parasite

**1. Introduction** 

effort (Price et al., 2007).

**of Infection with Malaria Parasites** 

Alison Machado, Cheikh Loucoubar, Laura Grange,

*Unité de Génétique Fonctionnelle des Maladies Infectieuses,* 

Jean-François Bureau, Anavaj Sakuntabhai and Richard Paul
