Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria

Shah, Zalak; Naung, Myo; Moser, Kara A; Adams, Matthew; Buchwald, Andrea G; Dwivedi, Ankit; Ouattara, Amed; Seydel, Karl B.; Mathanga, Don P.; Barry, Alyssa E.; Serre, David; Laufer, Miriam K.; Silva, Joana C.; Takala-Harrison, Shannon

doi:10.1371/journal.pgen.1009576

Cited by 6 publications

(4 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This study presents a detailed analysis of the genetic diversity and immune selection of 23 candidate vaccine antigens and a framework for analysis of further antigens which has already contributed critical information about the diversity of novel vaccine candidates [96][97][98]. In addition, the incorporation of sequence-based metrics such as Tajima's D into protein structures enhances biological understanding, as evidenced by the finding of unique patterns of immune selection in different geographic areas.…”

Section: Plos Computational Biologymentioning

confidence: 99%

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

et al. 2022

Self Cite

View full text Add to dashboard Cite

Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene ‘haplotypes’ from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.

show abstract

Section: Plos Computational Biologymentioning

confidence: 99%

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…Based on > 3800 global P. falciparum isolates, the three microhaplotype regions comprising the genotyping marker all had an expected heterozygosity > 50% and 9, 8, and 2 SNPs detected in each 200 bp region, respectively (Additional file 1 : Table S1). To evaluate potential haplotype resolution of the candidate genotyping marker, the number of SNPs and unique haplotypes was estimated at the marker locus from whole genome sequence (WGS) data generated from 95 Malawian P. falciparum field isolates [ 24 , 25 ] (average read depth = ~ 150x). For comparison, the number of unique haplotypes at two loci widely used for blood stage amplicon sequencing ( ama-1 and sera-2 ) [ 26 , 27 ] was also estimated from the same data set.…”

Section: Methodsmentioning

confidence: 99%

Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing

Vareta,

Horstman,

Adams

et al. 2024

Malar J

Self Cite

View full text Add to dashboard Cite

Background Understanding the dynamics of gametocyte production in polyclonal Plasmodium falciparum infections requires a genotyping method that detects distinct gametocyte clones and estimates their relative frequencies. Here, a marker was identified and evaluated to genotype P. falciparum mature gametocytes using amplicon deep sequencing. Methods A data set of polymorphic regions of the P. falciparum genome was mined to identify a gametocyte genotyping marker. To assess marker resolution, the number of unique haplotypes in the marker region was estimated from 95 Malawian P. falciparum whole genome sequences. Specificity of the marker for detection of mature gametocytes was evaluated using reverse transcription-polymerase chain reaction of RNA extracted from NF54 mature gametocytes and rings from a non-gametocyte-producing strain of P. falciparum. Amplicon deep sequencing was performed on experimental mixtures of mature gametocytes from two distinct parasite clones, as well as gametocyte-positive P. falciparum field isolates to evaluate the quantitative ability and determine the limit of detection of the genotyping approach. Results A 400 bp region of the pfs230 gene was identified as a gametocyte genotyping marker. A larger number of unique haplotypes was observed at the pfs230 marker (34) compared to the sera-2 (18) and ama-1 (14) markers in field isolates from Malawi. RNA and DNA genotyping accurately estimated gametocyte and total parasite clone frequencies when evaluating agreement between expected and observed haplotype frequencies in gametocyte mixtures, with concordance correlation coefficients of 0.97 [95% CI: 0.92–0.99] and 0.92 [95% CI: 0.83–0.97], respectively. The detection limit of the genotyping method for male gametocytes was 0.41 pfmget transcripts/µl [95% CI: 0.28–0.72] and for female gametocytes was 1.98 ccp4 transcripts/µl [95% CI: 1.35–3.68]. Conclusions A region of the pfs230 gene was identified as a marker to genotype P. falciparum gametocytes. Amplicon deep sequencing of this marker can be used to estimate the number and relative frequency of parasite clones among mature gametocytes within P. falciparum infections. This gametocyte genotyping marker will be an important tool for studies aimed at understanding dynamics of gametocyte production in polyclonal P. falciparum infections.

show abstract

“…Using whole genome sequence data generated from 140 P. falciparum isolates, we identified 25 genes that encode possible targets of allele-specific acquired immunity to clinical malaria. 35 As part of future studies, we will further characterize these parasite proteins for their potential as vaccine candidates through immunological epitope mapping and functional studies of antibodies elicited to these proteins.…”

Section: Characterizing the Host And Parasite Determinants Of The Out...mentioning

confidence: 99%

Understanding the Intransigence of Malaria in Malawi

Cohee

Goupeyou-Youmsi

Seydel

et al. 2022

The American Journal of Tropical Medicine and Hygiene

Self Cite

View full text Add to dashboard Cite

ABSTRACT. Despite the scale-up of interventions against malaria over the past decade, this disease remains a leading threat to health in Malawi. To evaluate the epidemiology of both Plasmodium falciparum infection and malaria disease, the Malawi International Center of Excellence for Malaria Research (ICEMR) has developed and implemented diverse and robust surveillance and research projects. Descriptive studies in ICEMR Phase 1 increased our understanding of the declining effectiveness of long-lasting insecticidal nets (LLINs), the role of school-age children in malaria parasite transmission, and the complexity of host–parasite interactions leading to disease. These findings informed the design of ICEMR Phase 2 to test hypotheses about LLIN use and effectiveness, vector resistance to insecticides, demographic targets of malaria control, patterns and causes of asymptomatic to life-threatening disease, and the impacts of RTS,S vaccination plus piperonyl butoxide-treated LLINs on infection and disease in young children. These investigations are helping us to understand mosquito-to-human and human-to-mosquito transmission in the context of Malawi's intransigent malaria problem.

show abstract

Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria

Cited by 6 publications

References 72 publications

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing

Understanding the Intransigence of Malaria in Malawi

Contact Info

Product

Resources

About