Identification of a conserved var gene in different Plasmodium falciparum strains

Dimonte, Sandra; Bruske, Ellen; Enderes, Corinna; Otto, Thomas D.; Turner, Louise; Kremsner, Peter G.; Frank, Matthias

doi:10.1186/s12936-020-03257-x

Cited by 8 publications

(12 citation statements)

References 41 publications

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“…Whilst extensive studies have compared microscopy and RDT based on standard 18S rRNA PCR results, this study is the first in Ghana to make comparisons using var ATS qPCR as reference in a clinical setting. Most P. falciparum strains possess relatively fewer 18S ribosomal subunits (5–8 copies/genome) [ 44 ] than the multi-copy var gene family which has approximately 59–60 copies/genome [ 45 , 46 ]. var ATS qPCR therefore has a very low limit of detection (~ 0.03–0.15 parasites/µL) and has been proven to be tenfold more sensitive than traditional 18S rRNA PCR methods [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT and a highly sensitive quantitative PCR looking at the implications for submicroscopic infections

Afriyie

Addison

Gebre

et al. 2023

Malar J

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Background The World Health Organization recommends parasitological confirmation of all suspected malaria cases by microscopy or rapid diagnostic tests (RDTs) before treatment. These conventional tools are widely used for point-of-care diagnosis in spite of their poor sensitivity at low parasite density. Previous studies in Ghana have compared microscopy and RDT using standard 18S rRNA PCR as reference with varying outcomes. However, how these conventional tools compare with ultrasensitive varATS qPCR has not been studied. This study, therefore, sought to investigate the clinical performance of microscopy and RDT assuming highly sensitive varATS qPCR as gold standard. Methods 1040 suspected malaria patients were recruited from two primary health care centers in the Ashanti Region of Ghana and tested for malaria by microscopy, RDT, and varATS qPCR. The sensitivity, specificity, and predictive values were assessed using varATS qPCR as gold standard. Results Parasite prevalence was 17.5%, 24.5%, and 42.1% by microscopy, RDT, and varATS qPCR respectively. Using varATS qPCR as the standard, RDT was more sensitive (55.7% vs 39.3%), equally specific (98.2% vs 98.3%), and reported higher positive (95.7% vs 94.5%) and negative predictive values (75.3% vs 69.0%) than microscopy. Consequently, RDT recorded better diagnostic agreement (kappa = 0.571) with varATS qPCR than microscopy (kappa = 0.409) for clinical detection of malaria. Conclusions RDT outperformed microscopy for the diagnosis of Plasmodium falciparum malaria in the study. However, both tests missed over 40% of infections that were detected by varATS qPCR. Novel tools are needed to ensure prompt diagnosis of all clinical malaria cases.

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Section: Discussionmentioning

confidence: 99%

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT and a highly sensitive quantitative PCR looking at the implications for submicroscopic infections

Afriyie

Addison

Gebre

et al. 2023

Malar J

View full text Add to dashboard Cite

show abstract

“…Whiles extensive studies have compared microscopy and RDT based on standard 18S rRNA PCR results, this study is the rst in Ghana to make comparisons using varATS qPCR as reference in a clinical setting. Most P. falciparum strains possess relatively fewer 18S ribosomal subunits (5-8 copies/genome) (42) than the multi-copy var gene family which has approximately 59-60 copies/genome (43,44). varATS qPCR therefore has a very low limit of detection (~0.03 -0.15 parasites/µL) and has been proven to be 10-fold more sensitive than traditional 18S rRNA PCR methods (28).…”

Section: Discussionmentioning

confidence: 99%

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT, and a highly sensitive quantitative PCR and the implication of submicroscopic infections

Afriyie

Addison

Gebre

et al. 2022

Preprint

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Background: The World Health Organization recommends parasitological confirmation of all suspected malaria cases by microscopy or rapid diagnostic tests (RDTs) before treatment. These conventional tools are widely used for point-of-care diagnosis in spite of their poor sensitivity at low parasite density. Several studies have compared the diagnostic accuracy of microscopy and RDT using standard 18S rRNA PCR as reference with varying outcomes. Here, we present for the first time in Ghana, the accuracy of diagnosis of microscopy and RDT using highly sensitive varATS qPCR as reference in a clinical setting.Methods: 1,040 febrile patients were recruited from two primary health care centers in the Ashanti Region of Ghana and tested for malaria by microscopy, RDT, and varATS qPCR. The sensitivity, specificity, and predictive values were assessed using qPCR as gold standard.Results: Parasite prevalence was 17.5%, 24.5%, and 42.1% by microscopy, RDT, and varATS qPCR respectively. Using qPCR as the standard, RDT was more sensitive (55.7% vs 39.3%), marginally less specific (98.2% vs 98.3%), and had higher positive (95.7% vs 94.5%) and negative predictive values (75.3% vs 69.0%) than microscopy. Parasite prevalence and density was higher among the 5-14 age group than the <5, 15-30, and >30 age groups across all the tests.Conclusions: RDT outperformed microscopy for the diagnosis of P. falciparum malaria in the study area. However, both diagnostic methods missed over 40% of infections that were detected by varATS qPCR. Novel tools are needed to ensure prompt diagnosis of all clinical malaria cases.

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“…Gabonese parasite isolate and characterised (34). The homolog to the DBLα tag of this var gene was found to occur at high frequencies (ranging from 7.0% to 20.2% in different locations) and present in all locations except, strangely, in Gabon itself.…”

Section: A Conserved P Falciparum Var Gene (Pf3d7_0617400) Was Also R...mentioning

confidence: 94%

“…With the exception of one specific var gene involved in pregnancy-associated malaria (i.e., var2csa), all other var genes encode for a DBLα domain, which is one of the most diverse domains and has been shown to be immunogenic to variant-specific epitopes, recognised serologically in an age-dependent manner (30). Multiple studies have noted that there exists a minority of DBLα types that are highly conserved over various spatial scales (16,(31)(32)(33)(34)(35).…”

Section: Introductionmentioning

confidence: 99%

A paradoxical population structure ofvarDBLα types in Africa

Tan,

Tiedje,

Feng

et al. 2023

Preprint

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Thevarmultigene family encodes theP. falciparumerythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology ofP. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBLα-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBLα types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm,cUps, we performed anin silicoexploration of DBLα conservation through time and space in Africa. In all three ups groups, the population structure of DBLα types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBLα types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBLα types within each isolate DBLα repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBLα types in Africa.

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Identification of a conserved var gene in different Plasmodium falciparum strains

Cited by 8 publications

References 41 publications

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT and a highly sensitive quantitative PCR looking at the implications for submicroscopic infections

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT and a highly sensitive quantitative PCR looking at the implications for submicroscopic infections

Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT, and a highly sensitive quantitative PCR and the implication of submicroscopic infections

A paradoxical population structure ofvarDBLα types in Africa

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