A5060455925- Bacteriophages and microbial interactions
- Respiratory viral infections research
- Plant Virus Research Studies
- Animal Virus Infections Studies
- Viral-associated cancers and disorders
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Polyomavirus and related diseases
- SARS-CoV-2 and COVID-19 Research
- Cytomegalovirus and herpesvirus research
- Epilepsy research and treatment
- HIV Research and Treatment
- Mosquito-borne diseases and control
- Parvovirus B19 Infection Studies
- Molecular Biology Techniques and Applications
- Inflammasome and immune disorders
- Gut microbiota and health
- Genetics and Neurodevelopmental Disorders
- SARS-CoV-2 detection and testing
- Immune Response and Inflammation
- COVID-19 Clinical Research Studies
- Virology and Viral Diseases
- Systemic Lupus Erythematosus Research
- Genomic variations and chromosomal abnormalities
Leiden University Medical Center
2018-2025
University Medical Center Utrecht
2016-2019
Utrecht University
2016-2018
Erasmus MC
2018
Hereditary recurrent fevers (HRFs) are rare inflammatory diseases sharing similar clinical symptoms and effectively treated with anti-inflammatory biological drugs. Accurate diagnosis of HRF relies heavily on genetic testing.This study aimed to obtain an experts' consensus the significance gene variants in four well-known genes: MEFV, TNFRSF1A, NLRP3 MVK.We configured a MOLGENIS web platform share analyse pathogenicity classifications manage consensus-based classification process. Four...
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety sample types from patients with infectious syndromes. mNGS still its early stages broader translation into clinical applications. To further support the development, implementation, optimization and standardization procedures virus diagnostics, European Society Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The...
Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous RNA DNA viruses is needed. Herein, were studied performance an in-house protocol for routine diagnostics infections with automated pan-pathogen detection. The bioinformatics analysis designed optimized, including exogenous internal controls. Subsequently, was retrospectively...
Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), respiratory bacterial viral infections an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has yet been applied COPD exacerbations.To study virome nasopharyngeal samples during exacerbations mNGS.88 swabs from 63 Bergen...
Summary Objective Phenotypes caused by de novo SCN 1A pathogenic variants are very variable, ranging from severely affected patients with Dravet syndrome to much milder genetic epilepsy febrile seizures plus cases. The most important determinant of disease severity is the type variant, that cause a complete loss function protein (α‐subunit neuronal sodium channel Nav1.1) being detected almost exclusively in patients. However, even within ranges greatly, and consequently other modifiers must...
Metagenomic sequencing is a powerful technique that enables detection of the full spectrum pathogens present in any specimen single test. Hence, metagenomics increasingly being applied for viruses clinical cases with suspected infections unknown etiology and large number relevant potential causes. This typically case patients presenting encephalitis, particular when immunity impaired by underlying disorders. In this study, viral has been to cohort hematological encephalitis origin. Because...
The SARS-CoV-2 pandemic of 2020 is a prime example the omnipresent threat emerging viruses that can infect humans. A protocol for identification novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to preparedness. aim this study validate virus discovery as tool coronavirus performance clinical setting was tested using samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, combination with databases generated contain only before dates these...
Rapid identification of the rise and spread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern remains critical for monitoring efficacy diagnostics, therapeutics, vaccines, control strategies. A wide range SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over last years, but cross-sequence technology benchmarking studies scarce. In current study, 26 clinical samples were sequenced using five protocols: AmpliSeq (Illumina), EasySeq RC-PCR...
Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares analytical performance two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap Roche (ViroCap) and (ii) Twist Comprehensive Research Panel workflow, for diagnostic use. Sensitivity, specificity, limit detection were analyzed using 25 synthetic sequences spiked in increasing proportions human background DNA, eight clinical...
ABSTRACT In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) conjunction human adenoviruses found. Five percent cases progressed acute liver failure, necessitating transplantation. The mechanism disease that accounts for fulminant failure these patients remains incompletely described. upsurge observed five total presented Dutch...
Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from SIMPLE studies evaluating RDV participants severe or moderate disease. The enrolled radiologic evidence pneumonia room-air oxygen saturation ≤94% >94%, respectively. Virology sample collection was optional study protocols. Sequencing...
Background: Diagnosis of infections in returning international travellers can be challenging because the broad spectrum potential infectious etiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has to detect any virus present a patient sample and is increasingly being used for difficult diagnose cases. The aim this study was analyze performance mNGS viral pathogen detection clinical setting with febrile illness. Methods: Thirty-eight serum samples from illness...
Background Dravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs substantial proportion of families (7%–13%) and has important implications for recurrence risks. However, can remain undetected methods regularly used diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), technique with high sensitivity detecting low-grade mosaic cost-effectiveness, to investigate the incidence SCN1A...
Immunocompromised patients are prone to reactivations and (re-)infections of multiple DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metagenomic next-generation sequencing (mNGS) approach was used identification transplantation-related viruses.Longitudinal plasma samples from six that were qPCR-positive cytomegalovirus (CMV), Epstein-Barr (EBV), BK polyomavirus (BKV), adenovirus (ADV),...
Viral metagenomics is increasingly applied in clinical diagnostic settings for detection of pathogenic viruses. While several benchmarking studies have been published on the use metagenomic classifiers abundance and diversity profiling bacterial populations, comparative performance virus pathogen are scarce. In this study, data sets (n = 88) from a cohort patients with respiratory complaints were used comparison five taxonomic classifiers: Centrifuge, Clark, Kaiju, Kraken2, Genome Detective....
Abstract Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares analytical performance two targeted metagenomic virus capture probe-based methods: i) SeqCap EZ HyperCap Roche (ViroCap) and ii) Twist Comprehensive Research Panel workflow, for diagnostic use. Sensitivity, specificity, limit detection, effect human background DNA were analysed, using synthetic sequences, clinical reference samples with known...
Abstract Introduction Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), respiratory bacterial viral infections an important trigger for the occurrence of such exacerbations. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis complete virome, but has yet been applied COPD Objectives To study virome nasopharyngeal...
Abstract Metagenomic sequencing is a powerful technique that enables detection of the full spectrum pathogens present in any specimen single test. Hence, metagenomics increasingly being applied for viruses clinical cases with suspected infections unknown etiology and large number relevant potential causes. This typically case patients presenting encephalitis, particular when immunity impaired by underlying disorders. In this study, viral has been to cohort hematological encephalitis origin....
Abstract Viral metagenomics is increasingly being applied in clinical diagnostic settings for detection of pathogenic viruses. While a number benchmarking studies have been published on the use metagenomic classifiers abundance and diversity profiling bacterial populations, comparative performance virus pathogen are scarce. In this study, data sets (N=88) from cohort patients with respiratory complaints were used comparison five taxonomic classifiers: Centrifuge, Clark, Kaiju, Kraken2,...
Introduction: Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection all potential pathogens in a clinical sample, including variants and even unknown pathogens. To apply mNGS viral diagnostics, there is need for sensitive simultaneous RNA DNA viruses. In this study, performance an in-house protocol routine diagnostics infections, with single tube sample-pre-treatment automated pan-pathogen was studied. Materials...
Abstract Background Diagnosis of infections in returning international travellers can be challenging because the broad spectrum potential infectious aetiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has to detect any virus present a patient sample and is increasingly being used for difficult diagnose cases. The aim this study was analyse performance mNGS viral pathogen detection clinical setting with febrile illness. Methods Thirty-eight serum samples from...