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Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection


Malaria is caused by parasites of the genus Plasmodium. All human-infecting Plasmodium species can establish long-lasting chronic infections15, 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 infections79. 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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Figure 1: Chronic infections modify the transcriptome of P. chabaudi independently of the adaptive immune response.
Figure 2: Chronic infections are characterized by the expression of distinctive clusters of pir genes in P. chabaudi.
Figure 3: Chronic infections select for virulent P. chabaudi parasites expressing distinctive clusters of pir genes.
Figure 4: Chronicity and virulence of infection are dictated by the initial composition of P. chabaudi population.


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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




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.

Corresponding authors

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

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1-15, Supplementary Tables 2–4 and Supplementary Tables 8–10. (PDF 12515 kb)

Supplementary Table 1

Lists of genes differentially expressed between acute and chronic phases for wild-type and knockout parasites. (XLSX 270 kb)

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. (XLSX 220 kb)

Supplementary Table 6

Expression levels of pir genes in cloned parasite lines. (XLSX 51 kb)

Supplementary Table 7

Genes where expression level during the acute phase correlated with the time at recrudescence. (XLSX 57 kb)

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Brugat, T., Reid, A., Lin, Jw. et al. Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection. Nat Microbiol 2, 16276 (2017).

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