Estimating prevalence from dried blood spots without using biological cut-offs: application of a novel approach to hepatitis C virus in drug users in France (ANRS-Coquelicot survey)

Abstract Seroprevalence estimation using cross-sectional serosurveys can be challenging due to inadequate or unknown biological cut-off limits of detection. In recent years, diagnostic assay cut-offs, fixed assay cut-offs and more flexible approaches as mixture modelling have been proposed to classify biological quantitative measurements into a positive or negative status. Our objective was to estimate the prevalence of anti-HCV antibodies among drug users (DU) in France in 2011 using a biological test performed on dried blood spots (DBS) collected during a cross-sectional serosurvey. However, in 2011, we did not have a cut-off value for DBS. We could not use the values for serum or plasma, knowing that the DBS value was not necessarily the same. Accordingly, we used a method which consisted of applying a two-component mixture model with age-dependent mixing proportions using penalised splines. The component densities were assumed to be log-normally distributed and were estimated in a Bayesian framework. Anti-HCV prevalence among DU was estimated at 43.3% in France and increased with age. Our method allowed us to provide estimates of age-dependent prevalence using DBS without having a specified biological cut-off value.

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Measuring the incidence, prevalence and genetic relatedness of hepatitis C infections among a community recruited sample of injecting drug users, using dried blood spots

Journal of Viral Hepatitis ◽

10.1111/j.1365-2893.2010.01297.x ◽

2010 ◽

Vol 18 (4) ◽

pp. 262-270 ◽

Cited By ~ 70

Author(s):

V. D. Hope ◽

M. Hickman ◽

S. L. Ngui ◽

S. Jones ◽

M. Telfer ◽

...

Keyword(s):

Hepatitis C ◽

Drug Users ◽

Genetic Relatedness ◽

Injecting Drug Users ◽

Dried Blood Spots ◽

Blood Spots ◽

Incidence Prevalence

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Comparison of cross-sectional HIV incidence assay results from dried blood spots and plasma

PLoS ONE ◽

10.1371/journal.pone.0172283 ◽

2017 ◽

Vol 12 (2) ◽

pp. e0172283 ◽

Cited By ~ 11

Author(s):

Katherine E. Schlusser ◽

Christopher Pilcher ◽

Esper G. Kallas ◽

Breno R. Santos ◽

Steven G. Deeks ◽

...

Keyword(s):

Dried Blood Spots ◽

Hiv Incidence ◽

Cross Sectional ◽

Blood Spots

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Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples

10.21203/rs.3.rs-69257/v2 ◽

2020 ◽

Author(s):

Noam Teyssier ◽

Anna Chen ◽

Elias Duarte ◽

Rene Sit ◽

Bryan Greenhouse ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Dropout Rate ◽

Dried Blood Spots ◽

Low Density ◽

Whole Genome ◽

Cross Sectional ◽

Modest Improvement ◽

Blood Spots ◽

Gates Foundation

Abstract Background: Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. We evaluated the effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification on the quality and fidelity of WGS data recovered from DBS. Results: At 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5X depth = 93% genome) than QIAamp extracted samples (5X depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published. Conclusions: Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys. Keywords: Malaria, P. falciparum, dried blood spots, Tween-Chelex, McrBC, selective whole genome amplification, whole genome sequencing This work was supported by the Bill & Melinda Gates Foundation, Grant Number OPP1132226 This work was supported by the Bill & Melinda Gates Foundation, Grant Number OPP1132226

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Novel biomarkers and age-related metabolite correlations in plasma and dried blood spots from patients with succinic semialdehyde dehydrogenase deficiency

Orphanet Journal of Rare Diseases ◽

10.1186/s13023-020-01522-5 ◽

2020 ◽

Vol 15 (1) ◽

Author(s):

Trevor Kirby ◽

Dana C. Walters ◽

Xutong Shi ◽

Coleman Turgeon ◽

Piero Rinaldo ◽

...

Keyword(s):

Dehydrogenase Deficiency ◽

Dried Blood Spots ◽

Succinic Semialdehyde ◽

Succinic Semialdehyde Dehydrogenase ◽

Blood Spots ◽

Semialdehyde Dehydrogenase ◽

Age Related ◽

Age Dependent ◽

Succinic Semialdehyde Dehydrogenase Deficiency ◽

Novel Biomarkers

Abstract Background Previous work has identified age-related negative correlations for γ-hydroxybutyric acid (GHB) and γ-aminobutyric acid (GABA) in plasma of patients with succinic semialdehyde dehydrogenase deficiency (SSADHD). Using plasma and dried blood spots (DBS) collected in an ongoing natural history study, we tested the hypothesis that other biomarkers would follow a similar age-related negative correlation as seen for GHB/GABA. Samples (mixed sex) included: patients (n = 21 unique samples, 1–39.5 yrs) and parallel controls (n = 9 unique samples, 8.4–34.8 yrs). Archival control data (DBS only; n = 171, 0.5–39.9 yrs) was also included. Results Metabolites assessed included amino acids (plasma, DBS) and acylcarnitines, creatine, creatinine, and guanidinoacetate (DBS only). Age-related negative correlations for glycine (plasma, DBS) and sarcosine (N-methylglycine, plasma) were detected, accompanied by elevated proline and decreased levels of succinylacetone, argininosuccinate, formaminoglutamate, and creatinine. Significantly low acylcarnitines were detected in patients across all chain lengths (short-, medium- and long-chain). Significant age-dependent positive correlations for selected acylcarnitines (C6-, C12DC(dicarboxylic)-, C16-, C16:1-, C18:1-, C18:2OH-carnitines) were detected in patients and absent in controls. Receiver operating characteristic (ROC) curves for all binary comparisons revealed argininosuccinate and succinylacetone to be the most discriminating biomarkers (area > 0.92). Conclusions Age-dependent acylcarnitine correlations may represent metabolic compensation responsive to age-related changes in GHB and GABA. Our study highlights novel biomarkers in SSADHD and expands the metabolic pathophysiology of this rare disorder of GABA metabolism.

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Population Based Prevalence of Myotonic Dystrophy Type 1 Using Genetic Analysis of State-wide Blood Screening Program

Neurology ◽

10.1212/wnl.0000000000011425 ◽

2021 ◽

pp. 10.1212/WNL.0000000000011425

Author(s):

Nicholas E Johnson ◽

Russell J Butterfield ◽

Katie Mayne ◽

Tara Newcomb ◽

Carina Imburgia ◽

...

Keyword(s):

New York ◽

Myotonic Dystrophy ◽

Screening Program ◽

Dried Blood Spots ◽

Population Based ◽

Repeat Expansion ◽

Cross Sectional ◽

Blood Spots ◽

Ctg Expansion ◽

Ctg Repeat

Objective:To determine whether the genetic prevalence of the CTG expansion in the DMPK gene associated with myotonic dystrophy (DM1) in an unbiased cohort is higher than previously reported population estimates, ranging from 5-20 per 100,000 individuals.Methods:This study used a cross-sectional cohort of de-identified dried blood spots (DBS) from the newborn screening program in the state of New York, taken from consecutive births from 2013-2014. Blood spots were screened for the CTG repeat expansion in the DMPK gene using triplet-repeat primed PCR and melt curve analysis. Melt curve morphology was assessed by four blinded reviewers to identify samples with possible CTG expansion. Expansion of the CTG repeat was validated by PCR fragment sizing using capillary electrophoresis for samples classified as positive or premutation to confirm the result. Prevalence was calculated as the number of samples with CTG repeat size ≥50 repeats compared to the overall cohort.Results:Out of 50,382 consecutive births, there were 24 with a CTG repeat expansion ≥50, consistent with a diagnosis of DM1. This represents a significantly higher DM1 prevalence of 4.76 per 10,000 births (95%CI 2.86, 6.67) or 1 in every 2,100 births. There were an additional 96 samples (19.1 per 10,000 or 1 in 525 births) with a CTG expansion in the DMPK gene in the premutation range (CTG)35-49.Conclusions:The prevalence of individuals with CTG repeat expansions in DMPK is up to five times higher than previous reported estimates. This suggests DM1, with multisystemic manifestations, is likely underdiagnosed in practice.

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Screening for Human Immunodeficiency Virus Infection by Use of a Fourth-Generation Antigen/Antibody Assay and Dried Blood Spots: In-Depth Analysis of Sensitivity and Performance Assessment in a Cross-Sectional Study

Journal of Clinical Microbiology ◽

10.1128/jcm.01645-19 ◽

2019 ◽

Vol 58 (1) ◽

Cited By ~ 1

Author(s):

Karl Stefic ◽

Jerome Guinard ◽

Gilles Peytavin ◽

Leïla Saboni ◽

Cécile Sommen ◽

...

Keyword(s):

Real Life ◽

Dried Blood Spots ◽

Cross Sectional Study ◽

Fourth Generation ◽

High Risk Population ◽

Sectional Study ◽

Cross Sectional ◽

Blood Spots ◽

Depth Analysis ◽

Antigen Antibody

ABSTRACT We evaluated the performance of a fourth-generation antigen/antibody (Ag/Ab) assay for detecting HIV-1 infection on dried blood spots (DBS) both in a conventional laboratory environment and in an epidemiological survey corresponding to a real-life situation. Although a 2-log loss of sensitivity compared to that with plasma was observed when using DBS in an analytical analysis, the median delay of positivity between DBS and crude serum during the early phase postacute infection was 7 days. The performance of the fourth-generation assay on DBS was approximately similar to that of a third-generation (antibody only) assay using crude serum samples. Among 2,646 participants of a cross-sectional study in a population of men having sex with men, 428 DBS were found reactive, but negative results were obtained from 5 DBS collected from individuals who self-reported a positive HIV status, confirmed by detection of antiretroviral (ARV) drugs in their DBS. The data generated allowed us to estimate a sensitivity of 98.8% of the fourth-generation assay/DBS strategy in a high-risk population, even including a broad majority of individuals on ARV treatment among those HIV positive. Our study brings additional proofs that DBS testing using a fourth-generation immunoassay is a reliable strategy able to provide alternative approaches for both individual HIV testing and surveillance of various populations.

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Age-dependent carriage of alleles and haplotypes of Plasmodium falciparum sera5, eba-175, and csp in a region of intense malaria transmission in Uganda

Malaria Journal ◽

10.1186/s12936-020-03432-0 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Constance Agwang ◽

Joseph Erume ◽

Brenda Okech ◽

Joseph Olobo ◽

Thomas G. Egwang

Keyword(s):

Plasmodium Falciparum ◽

Malaria Transmission ◽

Malaria Vaccine ◽

Dried Blood Spots ◽

P Value ◽

Cross Sectional ◽

Study Region ◽

P Values ◽

Vaccine Candidates ◽

Age Dependent

Abstract Background The development of malaria vaccines is constrained by genetic polymorphisms exhibited by Plasmodium falciparum antigens. The project the age-dependent distribution of alleles or haplotypes of three P. falciparum malaria vaccine candidates, Circumsporozoite Protein (csp), Erythrocyte Binding Antigen 175 (eba-175) and Serine Repeat Antigen 5 (sera5) in a region of intense malaria transmission in Uganda. Methods A cross-sectional study was carried out between August and November 2009 in which 250 study participants were selected from a population of 600. Finger prick blood samples were collected after informed consent from participants below 5 years, 5–10 years, and above 10 years of age. Blood was used for microscopy, RDT and dried blood spots. Plasmodium falciparum DNA was extracted by chelex method. Alleles of sera5 and eba-175 were determined by polymerase chain reaction (PCR) amplification followed by resolution of products by agarose gel electrophoresis. Allele calling was done using gel photographs from ethiduim bromide stained gels. Haplotypes of csp were identified by sequencing 63 PCR products using the P. falciparum 7G8 laboratory strain sequence as a reference. The data were analysed using SPSS 16, EQX for windows and Chi-square test was used to calculate associations (P-values), Excel was used to generate graphs. The BioEdit and NCBI blast software programs were used to analyse the sequences from which csp haplotypes map was constructed. Results Eba-175 FCR3 (48/178) and CAMP (16/178) alleles were observed, the FCR3 (24/67) allele being predominant among children aged below 5 years old while the CAMP (12/67) allele was predominant among older participants. Sera5 alleles ORI (6/204) and ORII (103/204) were observed in the population, ORII was more prevalent and was significantly associated with age (P values < 0.0001), parasite density (P-value < 0.0001) and clinical outcomes (P value = 0.018). There was marked csp diversity in the Th2/Th3 region. Out of 63 sequences, 16 conformed to the reference strain and one (1/16) was similar to a West African haplotype and the majority (14/16) of the haplotypes were unique to this study region. There was an age-dependent distribution of csp haplotypes with more haplotypes being harbored by children < 5-year of age, (10/16) compared to adults (2/16). Interestingly, the csp haplotype corresponding to 3D7 whose prototypical sequence is identical to the sequence of the leading malaria vaccine candidate RTS, S was not observed. Conclusion This data suggest that the eba-175 FCR3 allele, sera5 ORII allele, and csp haplotypes are targets of host immunity and under immune selection pressure in Apac District. These molecules could provide alternative malaria vaccine candidates as sub-unit vaccines.

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