Trends in Parasitology
ReviewMalaria Epidemiology at the Clone Level
Section snippets
Genotyping Malaria Parasites: Lessons Learned and the Way Forward
Genotyping of malaria parasites, that is, distinguishing between clones (see Glossary) and assessing the relationship among them by typing polymorphic genetic markers such as microsatellites, antigens, or SNPs, has become a standard tool in epidemiological research in the last two decades. A widely used panel of Plasmodium falciparum microsatellite markers was published in 2000 [1], and genome-wide SNP panels have been used in numerous studies 2, 3, 4. Whole-genome sequencing of P. falciparum
The Molecular Force of Blood-Stage Infection to Assess Exposure at the Individual Level
Individuals in malaria endemic regions are often coinfected with overlapping infections of different clones. Thus, while these individuals test positive by PCR during many months, the underlying infections dynamics – that is, the number and timing of the acquisition of new infections – remains unknown. Genotyping allows us to assess the molecular force of blood-stage infection (molFOB), that is, the incidence of genetically distinct parasite clones acquired over time. molFOB has proven to be a
Assessing Population Structure to Inform and Guide Malaria Control
Population genetic structure in relation to malaria control is being studied on the basis of different concepts, and at different spatial scales. A first concept aims to identify genetically isolated parasite populations, suggesting limited gene flow among them (Figure 1A). These populations could be preferentially targeted for elimination, as the risk for parasite reintroduction is considered to be small. Such studies are usually conducted at countrywide spatial scales, aiming to identify
Genetic Diversity and Population Structure as Surrogate Markers for Transmission Intensity
Given the need for reliable estimates of malaria transmission levels to design and evaluate control strategies, parasite genetic diversity and population structure have been assessed as surrogate markers for transmission intensity – with lower diversity, less gene flow, and more substructure expected once transmission is low. While, overall, a trend towards lower diversity was observed in regions of low and focal transmission, often differences in diversity were minimal despite substantial
Genotyping to Elucidate P. vivax Relapse Patterns
Unlike P. falciparum, P. vivax (and P. ovale) can remain latent in the liver as hypnozoites for months to years before relapsing to develop new blood-stage infections. The epidemiology of relapses is little understood – for example, the timing and triggers of relapses 60, 61, 62, the spectrum of clinical symptoms caused by relapses, or gametocyte carriage and thus the transmission potential of relapses. Studying these questions is hampered by a lack of methods to distinguish between primary
Assessing Drug Efficacy and Understanding the Spread of Drug Resistance
One of the best examples of how genotyping and studies on population structure have had direct impact on malaria control is their role in our understanding of drug resistance – both to estimate the level of treatment failure in drug trials, and to identify new markers of resistance. Drug resistance has been a major concern for malaria control since chloroquine-resistant P. falciparum emerged in Southeast Asia and Africa in the 1950s and 1960s [73]. P. falciparum resistance against nearly every
Towards SNPs and Whole-Genome Sequencing – or the Right Marker for the Right Question
With the rapid development of novel protocols for SNP typing, amplicon sequencing, and whole-genome sequencing (Table 1), it will be important to select the typing methodology and SNP subsets best suited for specific research questions.
If the molecular force of infection is of interest, or to genotype in drug trials, a single polymorphic marker, or polymorphic markers of a few sizes will, in most cases, offer sufficient discriminatory power. While diversity of P. falciparum microsatellites
Concluding Remarks and Future Perspectives
Parasite genotyping has become a standard in drug trials and in many epidemiological studies. The development of novel assays to type genome-wide SNPs and whole-genome sequencing extends studies beyond the simple discrimination of clones. They allow detailed insights on longitudinal clone dynamics, and assessing different degrees of relationship among parasites, for example to understand small-scale parasite gene flow in elimination settings. In combination with data on human migration, vector
Acknowledgments
The authors thank Manuel W. Hetzel for critical comments on the manuscript. This work was supported by the NIH International Centers of Excellence in Malaria Research grants U19AI129392 and U19AI129326.
Glossary
- Amplicon
- amplification product of a PCR. Amplicon sequencing is a genotyping method where a polymorphic region is PCR-amplified followed by deep-sequencing.
- Antigen
- a protein that induces an immune reaction. Antigens are often highly diverse; thus, when clones infect a host consecutively, later infections are not recognized by the antibodies induced by the antigen of the first clone.
- Clonal population structure
- a population of parasites that are genetically identical.
- Clone
- cells (e.g., parasites)
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