Immune Characterization of Plasmodium falciparum Parasites with a Shared Genetic Signature in a Region of Decreasing Transmission

Abstract

Malaria is a devastating tropical disease caused by the protozoan parasite Plasmodium. The most severe form of malaria is caused by Plasmodium falciparum and results in 200 million to 300 million people developing clinical disease annually and at least 655,000 deaths worldwide (1, 2). Malaria remains one of the leading causes of death in children under the age of 5 years in subSaharan Africa (3). The clinical manifestations of the disease are caused by the erythrocytic stage of the parasite's life cycle, and the majority of the immune response that develops is directed against this stage (4-6), both against parasite proteins involved in invasion and against proteins exported to the surface of the infected erythrocyte.With the implementation of successful malaria control measures, transmission has declined in some regions, including Senegal. With the drop in transmission intensity, the complexity of exposure, multiplicity of infection, and population-level parasite diversity have decreased; as a result, different individuals-from different households and over different temporal periods of the transmission season-are infected with the same parasite genotype (7). Such observations have been facilitated by recently developed molecular genetic tools enabling rapid tracking of individual parasite genotypes within the population and over time (7,8). In this study, we focus on a cluster of genetically identical parasites, termed common-genetic-signature (CGS) parasites, which was the first and one of the largest to be observed; these parasites both emerged and declined rapidly, reaching 24% of clinical isolates in 2008, declining to 3.4% in 2009, and then disappearing from all subsequently monitored populations.Here we begin to address whether the rapid expansion and contraction of this particular parasite genotype can be partially explained by the specific humoral immune responses of infected individuals to these parasites. To do this, we have utilized two different standardized in vitro assays that measure antibodies to erythrocytic parasites, viz., in vitro parasite growth inhibition as-

Estimating the overlap between two malaria parasites’ var repertoires

“…For instance, when two parasites are completely different, n ab = 0, so PTS = 0; when two parasites are identical, and both repertoires have been fully sampled, n ab = n a = n b , so PTS = 1. However, when n a or n b is smaller (as is overwhelmingly the case in existing studies [7][8][9][10][11][12][13]) PTS is conservative and systematically underestimates the true overlap between repertoires [20]. For example, if we were able to fully sample two parasites that share 30 of their 60 var tags, their PTS would be 0.5.…”

“…Recent studies of P. falciparum epidemiology and evolution have begun to learn from comparisons of the sets of genomic var repertoires between parasites [7][8][9][10][11][12][13]. Since var repertoires are, themselves, under selection, theory suggests that if a human population has been exposed to particular var genes, then repertoires that contain those var genes will have a lower fitness than repertoires that are entirely unrecognized by local hosts, shaping the var population structure [14,15].…”

“…Since var repertoires are, themselves, under selection, theory suggests that if a human population has been exposed to particular var genes, then repertoires that contain those var genes will have a lower fitness than repertoires that are entirely unrecognized by local hosts, shaping the var population structure [14,15]. In fact, preliminary studies have found evidence to support the idea that population immunity is shaping the content of var repertoires [10,11], paving the way for these hypervariable gene repertoires to be used in high-sensitivity genetic epidemiological studies. A followup study to Ref.…”

“…A followup study to Ref. [10] found that var repertoires in a region of decreasing transmission have coalesced into highly related clusters that appear to be non-overlapping with each other, driven by local immune * daniel.larremore@colorado.edu adaptation [13], although at the time of writing this study remains under peer review (June, 2018). Methods by which we estimate the extent to which var repertoires overlap are therefore important, particularly as studies of the population genetics and genetic epidemiology of malaria's antigens become more sophisticated and data rich.…”

“…Instead, experimentalists use degenerate PCR primers targeting a small "tag" sequence within a particular domain called DBLα [16] which is found in almost all var genes. Due to their experimental accessibility, DBLα tags have been widely used to study the structure and function of var genes [1,6,7,10,13,[16][17][18][19]. Still, these PCR techniques generate a random sample of 60 or fewer unique tag sequences from each parasite.…”