Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa

Var genes, strain hyperdiversity, and malaria transmission dynamics

The microbiological paradigm for surveillance of diverse pathogens requires knowledge of the variation of the major surface antigen under the most intense immune selection as immune responses to these antigens drive transmission dynamics. This creates a pathway for population genetics/genomics to be combined with mathematical modelling to describe transmission dynamics to inform public health policy. Here we consider how we can bring population genetics and population dynamics together for a highly recombining pathogen like Plasmodium falciparum. We do this through the lens of what has been recently learnt about the population genetics of the var multigene family encoding the major surface antigen of the blood stages of Plasmodium falciparum, known as PfEMP1.

From multiplicity of infection to force of infection for sparsely sampled Plasmodium falciparum populations at high transmission

High multiplicity of infection or MOI, the number of genetically distinct parasite strains co-infecting a single human host, characterizes infectious diseases including falciparum malaria at high transmission. This high MOI accompanies high asymptomatic Plasmodium falciparum prevalence despite high exposure, creating a large transmission reservoir challenging intervention. High MOI and asymptomatic prevalence are enabled by immune evasion of the parasite achieved via vast antigenic diversity. Force of infection or FOI, the number of new infections acquired by an individual host over a given time interval, is the dynamic sister quantity of MOI, and a key epidemiological parameter for monitoring antimalarial interventions and assessing vaccine or drug efficacy in clinical trials. FOI remains difficult, expensive, and labor-intensive to accurately measure, especially in high-transmission regions, whether directly via cohort studies or indirectly via the fitting of epidemiological models to repeated cross-sectional surveys. We propose here the application of queuing theory to obtain FOI from MOI, in the form of either a two-moment approximation method or Little's Law. We illustrate these two methods with MOI estimates obtained under sparse sampling schemes with the " var coding" approach. The two methods use infection duration data from naive malaria therapy patients with neurosyphilis. Consequently, they are suitable for FOI inference in subpopulations with a similar immune profile and the highest vulnerability, for example, infants or toddlers. Both methods are evaluated with simulation output from a stochastic agent-based model, and are applied to an interrupted time-series study from Bongo District in northern Ghana before and immediately after a three-round transient indoor residual spraying (IRS) intervention. The sampling of the simulation output incorporates limitations representative of those encountered in the collection of field data, including under-sampling of var genes, missing data, and antimalarial drug treatment. We address these limitations in MOI estimates with a Bayesian framework and an imputation bootstrap approach. Both methods yield good and replicable FOI estimates across various simulated scenarios. Applying these methods to the subpopulation of children aged 1-5 years in Ghana field surveys shows over a 70% reduction in annual FOI immediately post-intervention. The proposed methods should be applicable to geographical locations lacking cohort or cross-sectional studies with regular and frequent sampling but having single-time-point surveys under sparse sampling schemes, and for MOI estimates obtained in different ways. They should also be relevant to other pathogens whose immune evasion strategies are based on large antigenic variation resulting in high MOI.

Low nucleotide diversity of the Plasmodium falciparum AP2-EXP2 gene among clinical samples from Ghana

BACKGROUND

PfAP2-EXP2 is located within chromosome 6 of Plasmodium falciparum recently identified to be undergoing an extensive selective sweep in West African isolates. The gene encoding this transcription factor, PfAP2-EXP2, is essential and thus likely subject to purifying selection that limits variants in the parasite population despite its genomic location.

METHODS

72 Plasmodium falciparum field samples and 801 clinical sequences from the Pf6 MalariaGEN dataset of Ghanaian origin, were integrated and analysed.

RESULTS

A total of 14 single nucleotide variants of which 5 were missense variants, were identified after quality checks and filtering. Except for one, all identified variants were rare among the clinical samples obtained in this study (Minor allelic frequency < 0.01). Further results revealed a considerably low dN/dS value (0.208) suggesting the presence of purifying selection. Further, all the mutant amino acids were wildtype residues in AP2-EXP2 orthologous proteins-tentatively suggesting a genus-level conservation of amino acid residues. Computational analysis and predictions corroborated these findings.

CONCLUSIONS

Despite the recent extensive selective sweep within chromosome 6 of West African isolates, PfAP2-EXP2 of Ghanaian origin exhibits low nucleotide diversity and very low dN/dS consistent with purifying selection acting to maintain the function of an essential gene. The conservation of AP2-EXP2 is an important factor that makes it a potential drug target.

Molecular markers for malaria genetic epidemiology: progress and pitfalls

Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.

Artemisinin resistance-associated gene mutations in Plasmodium falciparum: A case study of severe malaria from Mozambique

BACKGROUND

The effectiveness of artemisinin-based combination therapies (ACT) in treating Plasmodium falciparum, is vital for global malaria control efforts, particularly in sub-Saharan Africa. The examination of imported cases from endemic areas holds implications for malaria chemotherapy on a global scale.

METHOD

A 45-year-old male presented with high fever, dry cough, diarrhoea and generalized muscle pain, following a two-week trip to Mozambique. P. falciparum infection with hiperparasitemia was confirmed and the patient was treated initially with quinine and doxycycline, then intravenous artesunate. To assess drug susceptibility, ex vivo half-maximal inhibitory concentration assays were conducted, and the isolated P. falciparum genome was deep sequenced.

RESULTS

The clinical isolate exhibited elevated ex vivo half-maximal inhibitory concentration values to dihydroartemisinin, lumefantrine, mefloquine and piperaquine. Genomic analysis identified a I416V mutation in the P. falciparum Kelch13 (PF3D7_1343700) gene, and several mutations at the Kelch13 interaction candidate genes, pfkics (PF3D7_0813000, PF3D7_1138700, PF3D7_1246300), including the ubiquitin carboxyl-terminal hydrolase 1, pfubp1 (PF3D7_0104300). Mutations at the drug transporters and genes linked to next-generation antimalarial drug resistance were also present.

CONCLUSIONS

This case highlights the emergence of P. falciparum strains carrying mutations in artemisinin resistance-associated genes in Mozambique, couple with a reduction in ex vivo susceptibility to ACT drugs. Continuous surveillance of mutations linked to drug resistance and regular monitoring of drug susceptibility are imperative to anticipate the spread of potential resistant strains emerging in Mozambique and to maintain effective malaria control strategies.