• Characterization of PfCRT F145I in piperaquine-resistant Plasmodium falciparum isolates from Cambodia through zinc-finger nuclease-mediated gene editing

      Shrestha, Biraj; Takala-Harrison, Shannon (2019)
      ACTs are the first-line treatment for clinical malaria in the malaria-endemic world and have reduced malaria-associated mortality and morbidity. However, the recent emergence of Plasmodium falciparum that is resistant to both the artemisinins and key partner drugs, piperaquine, in Cambodia and nearby countries in GMS poses a threat to the control and elimination of malaria. Identification and validation of molecular markers of antimalarial drug resistance provide surveillance tools to monitor resistance and inform drug policy decisions and insights into the molecular mechanisms underlying resistance. Previous studies have found that F145I mutation within the PfCRT and plasmepsin2/3 gene copy number are associated with resistance to piperaquine. When PfCRT F145I is introduced into Dd2 of P. falciparum, it confers piperaquine resistance. In this study, we will use gene-editing approaches to remove F145I from field isolates that contain both this mutation and amplified plasmepsin2/3, to quantify the effect on malaria parasite susceptibility to piperaquine.
    • The Effect of Drug Pressure and Transmission Setting on Sulfadoxine-Pyrimethamine Resistant Plasmodium falciparum Haplotype Prevalence and Selective Sweep Characteristics, in Malawi

      Artimovich, Elena M.; Takala-Harrison, Shannon (2014)
      Background: The continued expansion of resistance to anti-malarial chemotherapies is a threat to public health, and to malaria control and elimination. The reexpansion of drug sensitive parasites after the removal of drug pressure has renewed interest in epidemiological factors affecting resistance haplotype dynamics, in the hopes that previously abandoned drugs might once again find clinical utility. Objectives: Estimate the effect of changes in drug pressure and different malaria transmission settings on sulfadoxine-pyrimethamine (SP)-resistant haplotype prevalence and characteristics of selective sweeps. Methods: DNA was extracted from dried blood spots representing malaria infections from three time periods (high-SP use 1999-2001, transition-period 2007-2008, low-SP use 2012) of drug pressure in Malawi and three transmission settings (urban-low, rural-moderate, rural-high). Pyrosequencing and microsatellite genotyping were performed on all samples to determine haplotype prevalence and sweep characteristics. Changes in haplotype prevalence were assessed via Chi-squared tests and changes in sweep characteristics via permutation. Results: We observed the persistence of the DHFR 51I/59R/108N and DHPS 437G/540E haplotypes, five years after reduction in SP pressure as well as an increase in the prevalence of DHPS 437G/540E/581G haplotype. Selective sweeps indicated little to no fitness cost to the DHFR 51I/59R/108N and DHPS 437G/540E haplotypes in the absence of strong SP pressure. A decline in polyclonal infections was found across the three time periods. No significant difference in haplotype prevalence was found between transmission settings. Sweep characteristics could suggest divergent evolutionary history in the rural-moderate transmission setting. Conclusions: There is little to no fitness cost of SP-resistance in the absence of strong SP pressure in these three transmission settings within Malawi. The reexpansion of SP sensitive parasites in the region is not expected under current epidemiological conditions. Reduction in the amount of malaria in the region could further reduce the likelihood of reexpansion through the elimination of rare haplotypes due to genetic drift.
    • Whole-genome analysis of Plasmodium falciparum isolates to understand allele-specific immunity to malaria

      Shah, Zalak; Takala-Harrison, Shannon (2020)
      After repeated P. falciparum infections, individuals in high-transmission areas acquire clinical immunity to malaria. However, the genes important in determining allele-specific immunity are not entirely known. Previous genome-wide approaches explored signatures of selection in the parasite genome to identify targets of clinical immunity; however, these approaches did not account for individual level allele-specific immunity. Here we take a whole-genome approach to identify genes that may be involved in acquisition of allele-specific immunity to malaria by analyzing parasite genomes collected from infected individuals in Malawi. However, obtaining whole genome sequence data from clinical samples is one of the major hurdles in the field of malaria genomics. In order to obtain whole genome sequence data from non-leukocyte depleted, low parasitemia samples, we optimized a selective-whole genome amplification (sWGA) by filtering the DNA prior to sWGA, to generate high coverage, whole genome sequence data from P. falciparum clinical samples with low amounts of parasite DNA. Using this optimized approach, we successfully performed whole-genome sequencing on 202 parasite isolates. We compared parasite genomes from individuals with varying levels of clinical immunity, defined using an individual’s proportion of symptomatic infections during the course of the study, hypothesizing that individuals with higher immunity become symptomatically ill due to infection with parasites with less common alleles. Using FST, we identified 161 SNPs to be genetically differentiated between the two groups and the median allele frequency was significantly lower at these sites in individuals in higher immunity group compared to the lower immunity group. We also examined pairs of parasites collected at different time points from the same individuals and identified 225 loci in 174 genes that vary within same individuals more often than expected by chance. Using both of these approaches, we identified 25 genes that encode likely targets of immunity, including a known antigen, CLAG8. Further analysis of clag8 global diversity showed evidence of immune selection in the C-terminal region, supporting the use of this approach in identification of new vaccine targets. Identifying and further analyzing these genomic regions will provide insights into mechanisms involved in allele-specific acquired immunity.