Malaria is caused by parasites of the genus Plasmodium. All human-infecting Plasmodium species can establish long-lasting chronic infections1,​2,​3,​4,​5, creating an infectious reservoir to sustain transmission1,6. It is widely accepted that the maintenance of chronic infection involves evasion of adaptive immunity by antigenic variation7. However, genes involved in this process have been identified in only two of five human-infecting species: Plasmodium falciparum and Plasmodium knowlesi. Furthermore, little is understood about the early events in the establishment of chronic infection in these species. Using a rodent model we demonstrate that from the infecting population, only a minority of parasites, expressing one of several clusters of virulence-associated pir genes, establishes a chronic infection. This process occurs in different species of parasites and in different hosts. Establishment of chronicity is independent of adaptive immunity and therefore different from the mechanism proposed for maintenance of chronic P. falciparum infections7,​8,​9. Furthermore, we show that the proportions of parasites expressing different types of pir genes regulate the time taken to establish a chronic infection. Because pir genes are common to most, if not all, species of Plasmodium10, this process may be a common way of regulating the establishment of chronic infections.

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  1. 1.

    & The duration of Plasmodium falciparum infections. Malar. J. 13, 500 (2014).

  2. 2.

    et al. Plasmodium genome in blood donors at risk for malaria after several years of residence in Italy. Transfusion 54, 2419–2424 (2014).

  3. 3.

    & Immunity to malaria: antigenic variation in chronic infections of Plasmodium knowlesi. Nature 208, 1286–1288 (1965).

  4. 4.

    et al. Genetic diversity and dynamics of Plasmodium falciparum and P. vivax populations in multiply infected children with asymptomatic malaria infections in Papua New Guinea. Parasitology 121(3), 257–272 (2000).

  5. 5.

    , , & Plasmodium malariae infection in an asymptomatic 74-year-old Greek woman with splenomegaly. N. Engl. J. Med. 338, 367–371 (1998).

  6. 6.

    , , & Asymptomatic malaria infections: detectability, transmissibility and public health relevance. Nat. Rev. Microbiol. 12, 833–840 (2014).

  7. 7.

    , & Antigenic variation in Plasmodium falciparum. Annu. Rev. Microbiol. 62, 445–470 (2008).

  8. 8.

    , & Antigenic variation at the infected red cell surface in malaria. Annu. Rev. Microbiol. 55, 673–707 (2001).

  9. 9.

    et al. Plasmodium falciparum var gene expression is modified by host immunity. Proc. Natl Acad. Sci. USA 106, 21801–21806 (2009).

  10. 10.

    , , & Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucleic Acids Res. 32, 5712–5720 (2004).

  11. 11.

    , , , & The pir multigene family of Plasmodium: antigenic variation and beyond. Mol. Biochem. Parasitol. 170, 65–73 (2010).

  12. 12.

    et al. Vector transmission regulates immune control of Plasmodium virulence. Nature 498, 228–231 (2013).

  13. 13.

    et al. Functional memory B cells and long-lived plasma cells are generated after a single Plasmodium chabaudi infection in mice. PLoS Pathog. 5, e1000690 (2009).

  14. 14.

    et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol. 12, 86 (2014).

  15. 15.

    et al. Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res. 22, 925–938 (2012).

  16. 16.

    et al. Virulence and competitive ability in genetically diverse malaria infections. Proc. Natl Acad. Sci. USA 102, 7624–7628 (2005).

  17. 17.

    , , & Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success. Evolution 60, 1358–1371 (2006).

  18. 18.

    , , & Rodent malaria parasites suffer from the presence of conspecific clones in three-clone Plasmodium chabaudi infections. Parasitology 127, 411–418 (2003).

  19. 19.

    et al. Virulence, drug sensitivity and transmission success in the rodent malaria, Plasmodium chabaudi. Proc. Biol. Sci. 279, 4677–4685 (2012).

  20. 20.

    , , , & Transmission stage investment of malaria parasites in response to in-host competition. Proc. Biol. Sci. 274, 2629–2638 (2007).

  21. 21.

    et al. RIFINs are adhesins implicated in severe Plasmodium falciparum malaria. Nat. Med. 21, 314–317 (2015).

  22. 22.

    , , , & Evasion of immunity to Plasmodium falciparum: rosettes of blood group A impair recognition of PfEMP1. PLoS ONE 10, e0145120 (2015).

  23. 23.

    et al. Differential spleen remodeling associated with different levels of parasite virulence controls disease outcome in malaria parasite infections. mSphere 1, e00018-15 (2016).

  24. 24.

    , & Relationships between sequestration, antigenic variation and chronic parasitism in Plasmodium chabaudi chabaudi—a rodent malaria model. Parasite Immunol. 12, 45–64 (1990).

  25. 25.

    & Innate immunity to malaria. Nat. Rev. Immunol. 4, 169–180 (2004).

  26. 26.

    et al. On the cytoadhesion of Plasmodium vivax-infected erythrocytes. J. Infect. Dis. 202, 638–647 (2010).

  27. 27.

    et al. A subset of group A-like var genes encodes the malaria parasite ligands for binding to human brain endothelial cells. Proc. Natl Acad. Sci. USA 109, E1772–E1781 (2012).

  28. 28.

    et al. STEVOR is a Plasmodium falciparum erythrocyte binding protein that mediates merozoite invasion and rosetting. Cell Host Microbe. 16, 81–93 (2014).

  29. 29.

    et al. Characterization of the plasmodium interspersed repeats (PIR) proteins of Plasmodium chabaudi indicates functional diversity. Sci. Rep. 6, 23449 (2016).

  30. 30.

    , , & Malaria's deadly grip: cytoadhesion of Plasmodium falciparum-infected erythrocytes. Cell. Microbiol. 15, 1976–1983 (2013).

  31. 31.

    et al. Lymphoid development in mice congenitally lacking T cell receptor alpha beta-expressing cells. Science 256, 1448–1452 (1992).

  32. 32.

    , , & A B cell-deficient mouse by targeted disruption of the membrane exon of the immunoglobulin µ chain gene. Nature 350, 423–426 (1991).

  33. 33.

    et al. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68, 869–877 (1992).

  34. 34.

    et al. Grammomys surdaster, the natural host for Plasmodium berghei parasites, as a model to study whole organism vaccines against malaria. Am. J. Trop. Med. Hyg. (in press).

  35. 35.

    et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13 (2016).

  36. 36.

    , , et al. Variant exported blood-stage proteins encoded by Plasmodium multigene families are expressed in liver stages where they are exported into the parasitophorous vacuole. PLoS Pathog. 12, e1005917 (2016).

  37. 37.

    & Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  38. 38.

    & Streaming fragment assignment for real-time analysis of sequencing experiments. Nat. Methods 10, 71–73 (2013).

  39. 39.

    , & edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

  40. 40.

    et al. GeneDB—an annotation database for pathogens. Nucleic Acids Res. 40, D98–108 (2012).

  41. 41.

    et al. Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat. Biotechnol. 28, 91–98 (2010).

  42. 42.

    et al. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol. Biochem. Parasitol. 143, 67–79 (2005).

  43. 43.

    & Self- and super-organizing maps in R: the kohonen package. J. Stat. Softw. 21, 1–19 (2007).

  44. 44.

    et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).

  45. 45.

    et al. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat. Protoc. 7, 1260–1284 (2012).

  46. 46.

    , , & Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).

  47. 47.

    Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

  48. 48.

    , & A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell 28, 337–350 (2007).

  49. 49.

    MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

  50. 50.

    , , , & Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

  51. 51.

    , & Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

  52. 52.

    et al. Transformation of the rodent malaria parasite Plasmodium chabaudi. Nat. Protoc. 6, 553–561 (2011).

  53. 53.

    et al. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Methods 10, 407–409 (2013).

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This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001101), the UK Medical Research Council (FC001101), and the Wellcome Trust (FC001101); by the Wellcome Trust (grant reference WT101777MA). The Wellcome Trust Sanger Institute is funded by the Wellcome Trust (grant no. WT098051). C.N. is supported by the Wellcome Trust (WT104792) and S.C. and P.E.D. are supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases. The authors acknowledge the Biological Research Facility and Flow Cytometry facility at the Francis Crick Institute for their skilled technical assistance and the staff of the Illumina Bespoke Sequencing team at the Wellcome Trust Sanger Institute for their contribution. The authors thank E. Smith for assistance in making constructs for fluorescence tagging of the parasites, and M. Blackman, C. van Ooij, G. Kassiotis and J. Rayner for critical reading of the manuscript.

Author information

Author notes

    • Philip Spence

    Present address: Institute of Immunology and Infection Research (IIIR), School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL UK

    • Thibaut Brugat
    •  & Adam James Reid

    These authors contributed equally to this work.


  1. The Francis Crick institute, London NW1 1AT, UK

    • Thibaut Brugat
    • , Jing-wen Lin
    • , Deirdre Cunningham
    • , Irene Tumwine
    • , Garikai Kushinga
    • , Sarah McLaughlin
    •  & Jean Langhorne
  2. Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK

    • Adam James Reid
    • , Ulrike Böhme
    • , Mandy Sanders
    • , Ellen Bushell
    • , Tom Metcalf
    • , Oliver Billker
    • , Chris Newbold
    •  & Matthew Berriman
  3. MRC National Institute for Medical Research, London NW7 1AA, UK

    • Philip Spence
  4. Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA

    • Solomon Conteh
    •  & Patrick E. Duffy
  5. Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK

    • Chris Newbold


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T.B., A.J.R., C.N., M.B. and J.La. designed the study. T.B. designed and performed the mouse experiments with the help of I.T., G.K., S.M. and P.S. A.J.R. designed the sequencing experiments and performed the bioinformatic analyses. M.S. coordinated sequencing experiments. U.B. manually annotated the Plasmodium chabaudi AS genome sequence. D.C. and J.Li. created transgenic parasites. P.E.D. and S.C. performed thicket rat experiments, T.M., E.B. and O.B carried out the experiments in the Brown Norway rats. T.B., A.J.R., C.N., M.B. and J.La. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Thibaut Brugat or Adam James Reid or Jean Langhorne.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1-15, Supplementary Tables 2–4 and Supplementary Tables 8–10.

Excel files

  1. 1.

    Supplementary Table 1

    Lists of genes differentially expressed between acute and chronic phases for wild-type and knockout parasites.

  2. 2.

    Supplementary Table 5

    Expression levels of pir genes during chronic and acute stages of infection of wild-type mice, B6 µMT mice, B6.TCRα–/– mice with P. chabaudi AS, wild-type mice with P. chabaudi CB, brown rats with P. berghei and G. surdaster with P. chabaudi AS.

  3. 3.

    Supplementary Table 6

    Expression levels of pir genes in cloned parasite lines.

  4. 4.

    Supplementary Table 7

    Genes where expression level during the acute phase correlated with the time at recrudescence.

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