Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections

Early, Angela M.; Lievens, Marc; MacInnis, Bronwyn; Ockenhouse, Christian F.; Volkman, Sarah K.; Adjei, Samuel; Agbenyega, Tsiri; Ansong, Daniel; Gondi, Stacey M. O.; Greenwood, Brian; Hamel, Mary J.; Odero, Chris; Otieno, Kephas; Otieno, Walter; Owusu‐Agyei, Seth; Asante, Kwaku Poku; Sorgho, Hermann; Tina, Lucas; Tinto, Halidou; Valéa, Innocent; Wirth, Dyann F.; Neafsey, Daniel E.

doi:10.1038/s41467-018-03807-7

Cited by 29 publications

(32 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…F WS grades infections on a continuous scale of complexity where infections with an F WS >0.95 are considered clonal and DEploid estimates the number of haplotypes (K) present in sequence data by jointly estimating haplotypes and their abundances. In close agreement with contemporary estimates of within host diversity 20 , 22 of 49 infections (44.9%) were considered clonal by F WS . The within-host allele frequency (WHAF) captured from deep sequencing can be used to infer the presence of related parasites 21 .…”

Section: Infection Complexity In Bulk Sequenced Samplessupporting

confidence: 77%

Resolving within-host malaria parasite diversity using single-cell sequencing

Nkhoma

Trevino

Gorena

et al. 2018

Preprint

View full text Add to dashboard Cite

Malaria patients can carry one or more clonal lineage of the parasite, Plasmodium falciparum, but the composition of these infections cannot be directly inferred from bulk sequence data. Well-defined, complete haplotypes at single-cell resolution are ideal for describing within-host population structure and unambiguously determining parasite diversity, transmission dynamics and recent ancestry but have not been analyzed on a large scale. We generated 485 near-complete single-cell genome sequences isolated from fifteen P. falciparum patients from Chikhwawa, Malawi, an area of intense malaria transmission. Matched single-cell and bulk genomic analyses revealed patients harbored up to seventeen unique lineages. Estimation of parasite relatedness within patients suggests superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Our single-cell analysis indicates strong barriers to establishment of new infections in malaria-infected patients and allows high resolution dissection of intra-host variation in malaria parasites.

show abstract

Section: Infection Complexity In Bulk Sequenced Samplessupporting

confidence: 77%

Resolving within-host malaria parasite diversity using single-cell sequencing

Nkhoma

Trevino

Gorena

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…If two haplotypes within the same sample differed by only one nucleotide and had a read coverage ratio ≥8:1, they were merged, maintaining the identity of the more common haplotype. Previous implementations of this pipeline removed all potential chimeric reads and required samples to contain at least 200 reads for one of the two amplicons [1,8]. In this analysis, these metrics were analyzed, but hard filters were not applied to the samples before downstream analysis.…”

Section: Sample Analysis With Pasecmentioning

confidence: 99%

“…When targeting a highly polymorphic genomic region, a single amplicon can distinguish among hundreds of unique haplotypes [1], providing higher resolution than either SNP-based or length-based genotyping approaches. This improves estimates of the number of lineages within polyclonal infections (or complexity of infection; COI) [2][3][4], permits the discovery of unknown alleles [5][6][7], and provides increased information for haplotype-based analyses of epistasis and linkage disequilibrium [8].…”

Section: Introductionmentioning

confidence: 99%

“…Amplicon analysis in Plasmodium has been adapted to multiple sequencing platforms depending on the desired cost, sample size, and sequence length [3,[9][10][11]. Because of this high resolution and flexibility, amplicon-based methods have been utilized in a range of applications, including studies of allele-specific vaccine efficacy [1], disease severity [10], clearance rate [12], within-host competition [13], relapse rate [9], drug resistance [5][6][7], host selection [8], and population structure [8,14]. Amplicon sequencing has high sensitivity for the detection of minority parasite lineages within an infection, and is of particular interest in longitudinal studies that track intra-host dynamics [3,4].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

Early

Daniels

Farrell

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Deep sequencing of targeted genomic regions is becoming a common tool for understanding the dynamics and complexity of Plasmodium infections, but its lower limit of detection is currently unknown. Here, a new amplicon analysis tool, the Parallel Amplicon Sequencing Error Correction (PASEC) pipeline, is used to evaluate the performance of amplicon sequencing on low-density Plasmodium DNA samples. Illumina-based sequencing of two P. falciparum genomic regions (CSP and SERA2) was performed on two types of samples: in vitro DNA mixtures mimicking low-density infections (1-200 genomes/μl) and extracted blood spots from a combination of symptomatic and asymptomatic individuals (44-653,080 parasites/μl). Three additional analysis tools-DADA2, HaplotypR, and SeekDeep-were applied to both datasets and the precision and sensitivity of each tool were evaluated.. Results:Amplicon sequencing can contend with low-density samples, showing reasonable detection accuracy down to a concentration of 5 Plasmodium genomes/μl. Due to increased stochasticity and background noise, however, all four tools showed reduced sensitivity and precision on samples with very low parasitemia (<5 copies/μl) or low read count (<100 reads per amplicon). PASEC could distinguish major from minor haplotypes with an accuracy of 90% in samples with at least 30 Plasmodium genomes/μl, but only 61% at low Plasmodium concentrations (<5 genomes/μl) and 46% at very low read counts (<25 reads per amplicon). The four tools were additionally used on a panel of extracted parasitepositive blood spots from natural malaria infections. While all four identified concordant patterns of complexity of infection (COI) across four sub-Saharan African countries, the COI values obtained for individual samples differed in some cases. Conclusions:Amplicon deep sequencing can be used to determine the complexity and diversity of low-density Plasmodium infections. Despite differences in their approach, four state-of-the-art tools resolved known haplotype mixtures with similar sensitivity and precision. Researchers can therefore choose from multiple robust approaches for analyzing amplicon data, however, error filtration approaches should not be uniformly applied across samples of varying parasitemia. Samples with very low parasitemia and very low read count have higher false positive rates and call for read count thresholds that are higher than current recommendations.

show abstract

“…Protective antibodies found in multigravidae may target conserved epitopes shared by multiple variants of a parasite or may represent the combined effect of specific reactivities against multiple parasite variants (24). The latter hypothesis has been recently demonstrated in a report showing that naturally acquired host immune defenses to different P. falciparum antigens act in an allele-specific manner to block specific parasite haplotypes from establishing blood-stage infections in infants and children, suggesting that vaccines targeting polymorphic parasite antigens must account for allele-specific immunity (25). Many studies have demonstrated that VAR2CSA displays extensive diversity between parasites/alleles, contains conserved interspersed regions shared between alleles (26)(27)(28), and is targeted by cross-reactive antibodies acquired during PM (29)(30)(31)(32).…”

mentioning

confidence: 97%

Functional Antibodies against Placental Malaria Parasites Are Variant Dependent and Differ by Geographic Region

et al. 2019

View full text Add to dashboard Cite

During pregnancy, Plasmodium falciparum-infected erythrocytes (IE) accumulate in the intervillous spaces of the placenta by binding to chondroitin sulfate A (CSA) and elicit inflammatory responses that are associated with poor pregnancy outcomes. Primigravidae lack immunity to IE that sequester in the placenta and thus are susceptible to placental malaria (PM). Women become resistant to PM over successive pregnancies as antibodies to placental IE are acquired. Here, we assayed plasma collected at delivery from Malian and Tanzanian women of different parities for total antibody levels against recombinant VAR2CSA antigens (FCR3 allele), and for surface reactivity and binding inhibition and opsonizing functional activities against IE using two CSA-binding laboratory isolates (FCR3 and NF54). Overall, antibody reactivity to VAR2CSA recombinant proteins and to CSA-binding IE was higher in multigravidae than in primigravidae. However, plasma from Malian gravid women reacted more strongly with FCR3 whereas Tanzanian plasma preferentially reacted with NF54. Further, acquisition of functional antibodies was variant dependent: binding inhibition of P. falciparum strain NF54 (P < 0.001) but not of the strain FCR3 increased significantly with parity, while only opsonizing activity against FCR3 (P < 0.001) increased significantly with parity. In addition, opsonizing and binding inhibition activities of plasma of multigravidae were significantly correlated in assays of FCR3 (r = 0.4, P = 0.01) but not of NF54 isolates; functional activities did not correlate in plasma from primigravidae. These data suggest that IE surface-expressed epitopes involved in each functional activity differ among P. falciparum strains. Consequently, geographic bias in circulating strains may impact antibody functions. Our study has implications for the development of PM vaccines aiming to achieve broad protection against various parasite strains.

show abstract

Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections

Cited by 29 publications

References 65 publications

Resolving within-host malaria parasite diversity using single-cell sequencing

Resolving within-host malaria parasite diversity using single-cell sequencing

Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

Functional Antibodies against Placental Malaria Parasites Are Variant Dependent and Differ by Geographic Region

Contact Info

Product

Resources

About