A High Resolution Case Study of a Patient with Recurrent Plasmodium vivax Infections Shows That Relapses Were Caused by Meiotic Siblings

Abstract

Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria.

Uncovering the transmission dynamics ofPlasmodium vivaxusing population genetics

“…Despite microsatellite genotyping suggesting that all infections were clonal, the deep sequencing approach found that relapses shared large fragments of identical sequence consistent with the primary infection and relapses being the products of the same meiotic recombination. 75 New molecular approaches such as high-resolution SNP genotyping and genome wide sequencing will bring a higher level of resolution to study relapses.…”

Do hypnozoites cause relapse in malaria?

“…If the hypnozoite hypothesis is correct, it is necessary for genotypically homologous sporozoites injected by the mosquito to behave in two different ways, with some sporozoites initiating early hepatic schizogony but others becoming latent as hypnozoites. For example, a sophisticated molecular genetic study ascribed homologous P. vivax recurrences in a patient to activation of hypnozoites; and it was concluded that these probably originated from meiotic siblings in the mosquito host [17]. This is a valid deduction in terms of the hypnozoite theory of relapse.…”

“…Parasites present in the bloodstream during recurrent malaria are in broad terms either genetically 'heterologous' or 'homologous' as compared with those of the initial clinical infection. Considering genetic variation within a given parasite clone, recrudescent parasites from the human host (bloodstream parasites) might sometimes become designated in the laboratory as heterologous instead of homologous, or vice versa, because of the markers selected and/or there being too few markers [17,89]. This would occasionally result in inaccurate conclusions being drawn in some epidemiological and other P. vivax studies.…”

The utility of genomic data forPlasmodium vivaxpopulation surveillance

“…Full genome sequencing indicated that the circulating genotypes in three relapses of a Sudanese patient who had travelled to a non-endemic country after primary infection likely originated from a single meiosis event. 53 While the three possible processes have all found support, confidently classifying recurrent infections as a relapse remains challenging. Major limitations are that accurately capturing the diversity of primary infections and an understanding of the distribution of genetic diversity in the P. vivax population are required to rule out reinfection.…”