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Open Access 01-12-2018 | Research

Genetic polymorphism and natural selection of circumsporozoite surface protein in Plasmodium falciparum field isolates from Myanmar

Authors: Hương Giang Lê, Jung-Mi Kang, Mya Moe, Hojong Jun, Thị Lam Thái, Jinyoung Lee, Moe Kyaw Myint, Khin Lin, Woon-Mok Sohn, Ho-Joon Shin, Tong-Soo Kim, Byoung-Kuk Na

Published in: Malaria Journal | Issue 1/2018

Abstract

Background

Plasmodium falciparum circumsporozoite protein (PfCSP) is one of the most extensively studied malaria vaccine candidates, but the genetic polymorphism of PfCSP within and among the global P. falciparum population raises concerns regarding the efficacy of a PfCSP-based vaccine efficacy. In this study, genetic diversity and natural selection of PfCSP in Myanmar as well as global P. falciparum were comprehensively analysed.

Methods

Blood samples were collected from 51 P. falciparum infected Myanmar patients. Fifty-one full-length PfCSP genes were amplified from the blood samples through a nested polymerase chain reaction, cloned into a TA cloning vector, and then sequenced. Polymorphic characteristics and natural selection of Myanmar PfCSP were analysed using the DNASTAR, MEGA6, and DnaSP programs. Polymorphic diversity and natural selection in publicly available global PfCSP were also analysed.

Results

The N-terminal and C-terminal non-repeat regions of Myanmar PfCSP showed limited genetic variations. A comparative analysis of the two regions in global PfCSP displayed similar patterns of low genetic diversity in global population, but substantial geographic differentiation was also observed. The most notable polymorphisms identified in the N-terminal region of global PfCSP were A98G and 19-amino acid length insertion in global population with different frequencies. Major polymorphic characters in the C-terminal region of Myanmar and global PfCSP were found in the Th2R and Th3R regions, where natural selection and recombination occurred. The central repeat region of Myanmar PfCSP was highly polymorphic, with differing numbers of repetitive repeat sequences NANP and NVDP. The numbers of the NANP repeats varied among global PfCSP, with the highest number of repeats seen in Asian and Oceanian PfCSP. Haplotype network analysis of global PfCSP revealed that global PfCSP clustered into 103 different haplotypes with geographically-separated populations.

Conclusion

Myanmar and global PfCSP displayed genetic diversity. N-terminal and C-terminal non-repeat regions were relatively conserved, but the central repeat region displayed high levels of genetic polymorphism in Myanmar and global PfCSP. The observed geographic pattern of genetic differentiation and the points of evidence for natural selection and recombination suggest that the functional consequences of the polymorphism should be considered for developing a vaccine based on PfCSP.

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World Health Organization. World malaria report 2017. Geneva: World Health Organization; 2017.CrossRef

World Health Organization. Malaria in the Greater Mekong Subregion: Regional and country profiles. Geneva: World Health Organization; 2017.

World Health Organization. Strategy for Malaria Elimination in the Greater Mekong Subregion (2015–2030). Geneva: World Health Organization; 2015.

Kang JM, Cho PY, Moe M, Lee J, Jun H, Lee HW, et al. Comparison of the diagnostic performance of microscopic examination with nested polymerase chain reaction for optimum malaria diagnosis in Upper Myanmar. Malar J. 2017;16:119.CrossRefPubMedPubMedCentral

Agnandji ST, Lell B, Soulanoudjingar SS, Fernandes JF, Abossolo BP, Conzelmann C, et al. First results of phase 3 trial of RTS,S/AS01 malaria vaccine in African children. N Engl J Med. 2011;365:1863–75.CrossRefPubMed

Agnandji ST, Lell B, Fernandes JF, Abossolo BP, Methogo BG, Kabwende AL, et al. A phase 3 trial of RTS,S/AS01 malaria vaccine in African infants. N Engl J Med. 2012;367:2284–95.CrossRefPubMed

Pinzon-Ortiz C, Friedman J, Esko J, Sinnis P. The binding of the circumsporozoite protein to cell surface heparan sulfate proteoglycans is required for Plasmodium sporozoite attachment to target cells. J Biol Chem. 2001;276:26784–91.CrossRefPubMed

Rathore D, Sacci JB, de la Vega P, McCutchan TF. Binding and invasion of liver cells by Plasmodium falciparum sporozoites. Essential involvement of the amino terminus of circumsporozoite protein. J Biol Chem. 2002;277:7092–8.CrossRefPubMed

Coppi A, Natarajan R, Pradel G, Bennett BL, James ER, Roggero MA, et al. The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host. J Exp Med. 2011;208:341–56.CrossRefPubMedPubMedCentral

10.

Egan JE, Hoffman SL, Haynes JD, Sadoff JC, Schneider I, Grau GE, et al. Humoral immune responses in volunteers immunized with irradiated Plasmodium falciparum sporozoites. Am J Trop Med Hyg. 1993;49:166–73.CrossRefPubMed

11.

Nardin EH, Nussenzweig RS, McGregor IA, Bryan JH. Antibodies to sporozoites: their frequent occurrence in individuals living in an area of hyperendemic malaria. Science. 1979;206:597–9.CrossRefPubMed

12.

Calvo-Calle JM, de Oliveira GA, Clavijo P, Maracic M, Tam JP, Lu YA, et al. Immunogenicity of multiple antigen peptides containing B and non-repeat T cell epitopes of the circumsporozoite protein of Plasmodium falciparum. J Immunol. 1993;150:1403–12.PubMed

13.

Hughes AL. Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): Evidence for positive selection on immunogenic regions. Genetics. 1991;127:345–53.PubMedPubMedCentral

14.

Waitumbi JN, Anyona SB, Hunja CW, Kifude CM, Polhemus ME, Walsh DS, et al. Impact of RTS,S/AS02(A) and RTS,S/AS01(B) on genotypes of P. falciparum in adults participating in a malaria vaccine clinical trial. PLoS ONE. 2009;4:e7849.CrossRefPubMedPubMedCentral

15.

Bailey JA, Mvalo T, Aragam N, Weiser M, Congdon S, Kamwendo D, et al. Use of massively parallel pyrosequencing to evaluate the diversity of and selection on Plasmodium falciparum csp T-cell epitopes in Lilongwe, Malawi. J Infect Dis. 2012;206:580–7.CrossRefPubMedPubMedCentral

16.

Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA Jr, et al. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol. 2008;9:R171.CrossRefPubMedPubMedCentral

17.

Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012;487:375–9.CrossRefPubMedPubMedCentral

18.

Zeeshan M, Alam MT, Vinayak S, Bora H, Tyagi RK, Alam MS, et al. Genetic variation in the Plasmodium falciparum circumsporozoite protein in India and its relevance to RTS,S malaria vaccine. PLoS One. 2012;7:e43430.CrossRefPubMedPubMedCentral

19.

Snounou G, Singh B. Nested PCR analysis of Plasmodium parasites. Methods Mol Med. 2002;72:189–93.PubMed

20.

Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–2.CrossRefPubMed

21.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary enetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.CrossRefPubMedPubMedCentral

22.

Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3:418–26.PubMed

23.

Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.PubMedPubMedCentral

24.

Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133:693–9.PubMedPubMedCentral

25.

Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecifc phylogenies. Mol Biol Evol. 1999;16:37–48.CrossRefPubMed

26.

Sidjanski SP, Vanderberg JP, Sinnis P. Anopheles stephensi salivary glands bear receptors for region I of the circumsporozoite protein of Plasmodium falciparum. Mol Biochem Parasitol. 1997;90:33–41.CrossRefPubMedPubMedCentral

27.

Escalante AA, Grebert HM, Isea R, Goldman IF, Basco L, Magris M, et al. A study of genetic diversity in the gene encoding the circumsporozoite protein (CSP) of Plasmodium falciparum from different transmission areas-XVI. Asembo Bay Cohort Project. Mol Biochem Parasitol. 2002;125:83–90.CrossRefPubMed

28.

Putaporntip C, Jongwutiwes S, Hughes AL. Natural selection maintains a stable polymorphism at the circumsporozoite protein locus of Plasmodium falciparum in a low endemic area. Infect Genet Evol. 2009;9:567–73.CrossRefPubMedPubMedCentral

29.

Zakeri S, Avazalipoor M, Mehrizi AA, Djadid ND, Snounou G. Restricted T-cell epitope diversity in the circumsporozoite protein from Plasmodium falciparum populations prevalent in Iran. Am J Trop Med Hyg. 2007;76:1046–51.CrossRefPubMed

30.

Plassmeyer ML, Reiter K, Shimp RL Jr, Kotova S, Smith PD, Hurt DE, et al. Structure of the Plasmodium falciparum circumsporozoite protein, a leading malaria vaccine candidate. J Biol Chem. 2009;284:26951–63.CrossRefPubMedPubMedCentral

31.

Rathore D, Nagarkatti R, Jani D, Chattopadhyay R, de la Vega P, Kumar S. An immunologically cryptic epitope of Plasmodium falciparum circumsporozoite protein facilitates liver cell recognition and induces protective antibodies that block liver cell invasion. J Biol Chem. 2005;280:20524–9.CrossRefPubMed

32.

Ancsin JB, Kisilevsky R. A binding site for highly sulfated heparan sulfate is identified in the N terminus of the circumsporozoite protein: significance for malarial sporozoite attachment to hepatocytes. J Biol Chem. 2004;279:21824–32.CrossRefPubMed

33.

Conway DJ. Natural selection on polymorphic malaria antigens and the search for a vaccine. Parasitol Today. 1997;13:26–9.CrossRefPubMed

34.

Bongfen SE, Ntsama PM, Offner S, Smith T, Felger I, Tanner M, et al. The N-terminal domain of Plasmodium falciparum circumsporozoite protein represents a target of protective immunity. Vaccine. 2009;27:328–35.CrossRefPubMed

35.

Tan J, Sack BK, Oyen D, Zenklusen I, Piccoli L, Barbieri S, et al. A public antibody lineage that potently inhibits malaria infection through dual binding to the circumsporozoite protein. Nat Med. 2018;24:401–7.CrossRefPubMedPubMedCentral

36.

Ferguson DJ, Balaban AE, Patzewitz EM, Wall RJ, Hopp CS, Poulin B, et al. The repeat region of the circumsporozoite protein is critical for sporozoite formation and maturation in Plasmodium. PLoS ONE. 2014;9:e113923.CrossRefPubMedPubMedCentral

37.

Garçon N, Heppener DG, Cohen J. Development of RTS,S/AS02: a purified subunit-based malaria vaccine candidate formulated with a novel adjuvant. Expert Rev Vaccines. 2003;2:231–8.CrossRefPubMed

38.

Kumkhaek C, Phra-ek K, Renia L, Singhasivanon P, Looareesuwan S, Hirunpetcharat C, et al. Are extensive T cell epitope polymorphisms in the Plasmodium falciparum circumsporozoite antigen, a leading sporozoite vaccine candidate, selected by immune pressure? J Immunol. 2005;175:3935–9.CrossRefPubMed

39.

Bhattacharya PR, Bhatia V, Pillai CR. Genetic diversity of T-helper cell epitopic regions of circumsporozoite protein of Plasmodium falciparum isolates from India. Trans R Soc Trop Med Hyg. 2006;100:395–400.CrossRefPubMed

40.

Udhayakumar V, Ongecha JM, Shi YP, Aidoo M, Orago AS, Oloo AJ, et al. Cytotoxic T cell reactivity and HLA-B35 binding of the variant Plasmodium falciparum circumsporozoite protein CD8+ CTL epitope in naturally exposed Kenyan adults. Eur J Immunol. 1997;27:1952–7.CrossRefPubMed

41.

Hill AV, Elvin J, Willis AC, Aidoo M, Allsopp CE, Gotch FM, et al. Molecular analysis of the association of HLA-B53 and resistance to severe malaria. Nature. 1992;360:434–9.CrossRefPubMed

42.

Gordon DM, McGovern TW, Krzych U, Cohen JC, Schneider I, LaChance R, et al. Safety, immunogenicity, and efficacy of a recombinantly produced Plasmodium falciparum circumsporozoite protein-hepatitis B surface antigen subunit vaccine. J Infect Dis. 1995;171:1576–85.CrossRefPubMed

43.

The RTS,S Clinical Trial Partnership. Efficacy and safety of RTS,S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial. Lancet. 2015;386:31–45.CrossRef

44.

Otieno L, Oneko M, Otieno W, Abuodha J, Owino E, Odero C, et al. Safety and immunogenicity of RTS,S/AS01 malaria vaccine in infants and children with WHO stage 1 or 2 HIV disease: a randomised, double-blind, controlled trial. Lancet Infect Dis. 2016;16:1134–44.CrossRefPubMed

45.

The RTS,S Clinical Trials Partnership. Efficacy and Safety of the RTS,S/AS01 malaria vaccine during 18 months after vaccination: A phase 3 randomized, controlled trial in children and young infants at 11 African sites. PLoS Med. 2014;11:e1001685.CrossRef

46.

Kaslow DC, Biernaux S. RTS,S: toward a first landmark on the malaria vaccine technology roadmap. Vaccine. 2015;33:7425–32.CrossRefPubMed

Title: Genetic polymorphism and natural selection of circumsporozoite surface protein in Plasmodium falciparum field isolates from Myanmar
Authors: Hương Giang Lê
Jung-Mi Kang
Mya Moe
Hojong Jun
Thị Lam Thái
Jinyoung Lee
Moe Kyaw Myint
Khin Lin
Woon-Mok Sohn
Ho-Joon Shin
Tong-Soo Kim
Byoung-Kuk Na
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: Malaria Journal / Issue 1/2018
Electronic ISSN: 1475-2875
DOI: https://doi.org/10.1186/s12936-018-2513-0

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Conclusion

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