A5036864905- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Antibiotic Resistance in Bacteria
- Virus-based gene therapy research
- Plant Virus Research Studies
- Metabolism and Genetic Disorders
- Genomics and Rare Diseases
- Pharmaceutical and Antibiotic Environmental Impacts
- Cytomegalovirus and herpesvirus research
- Respiratory viral infections research
- Evolution and Genetic Dynamics
- COVID-19 epidemiological studies
- Bacterial Identification and Susceptibility Testing
- Plant and Fungal Interactions Research
- Geriatric Care and Nursing Homes
- COVID-19 and healthcare impacts
- Infectious Diseases and Mycology
- Inflammasome and immune disorders
- Immune responses and vaccinations
Great Ormond Street Hospital for Children NHS Foundation Trust
2021-2025
Great Ormond Street Hospital
2022-2024
University College London
1998-2024
Goshen College
2023
London Cancer
2022
Animal and Plant Health Agency
2021-2022
University of Reading
2020
Abstract Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis children have been reported worldwide, including 278 the UK 1 . Here we report an investigation 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination genomic, transcriptomic, proteomic immunohistochemical methods. We detected high levels adeno-associated virus 2 (AAV2) DNA liver, blood, plasma or stool from 27 28 cases....
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA quantities, measured by reverse transcription quantitative PCR (RT-qPCR), have been proposed to stratify clinical risk or determine analytical performance targets. We investigated reproducibility and how setting diagnostic cutoffs altered the sensitivity of disease 2019 (COVID-19) testing.Quantitative SARS-CoV-2 distributions [quantification cycle (Cq) copies/mL] from more than 6000 patients 3 laboratories in United Kingdom,...
Abstract The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is public health concern in case vaccine escape. Described are 3 patients with advanced human immunodeficiency virus (HIV)-1 and chronic SARS-CoV-2 infection whom there evidence selection persistence novel mutations that associated increased transmissibility immune
Mycobacterium abscessus complex is responsible for 2.6-13.0% of all non-tuberculous mycobacterial pulmonary infections and these are notoriously difficult to treat due the regimens required, drug resistance adverse effects. Hence, bacteriophages have been considered in clinical practice as an additional treatment option. Here, we evaluated antibiotic phage susceptibility profiles M. isolates. Whole-genome sequencing (WGS) revealed phylogenetic relationships, dominant circulating clones...
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society Clinical Virology (ESCV) Network on NGS (ENNGS). A mock reference panel was designed mimic low biomass specimens. The assess performance twelve...
Adeno-associated viruses (AAVs) are the most used vectors in gene therapy but can frequently cause liver complications patients. The mechanisms underlying AAV-related toxicity remain poorly understood, posing challenges for effective prevention and intervention. We undertook long short read metagenomic sequencing of tissue from a child with Spinal Muscular Atrophy type 1 experiencing significant hepatitis after receiving onasemnogene abeparvovec. identified manufacturing plasmid sequences,...
Summary Since the first reports of hepatitis unknown aetiology occurring in UK children, over 1000 cases have been reported worldwide, including 268 UK, with majority younger than 6 years old. Using genomic, proteomic and immunohistochemical methods, we undertook extensive investigation 28 136 control subjects. In five who underwent liver transplantation, detected high levels adeno-associated virus 2 (AAV2) explanted livers. AAV2 was also at blood from 10/11 non-transplanted cases. Low...
Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials low or absent. We monitored antimicrobial-resistant Escherichia coli over 1 year a UK outdoor pig farm with usage (AMU) compared to conventional farms United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed identify genes, phylogeny mobile elements 385 E. isolates...
Metagenomic next-generation sequencing (mNGS) is an untargeted technique capable of detecting all microbial nucleic acid within a sample. This protocol outlines our wet laboratory method for mNGS cerebrospinal fluid (CSF) specimens and tissues from sterile sites. We use this routinely in clinical service, processing 178 over the past 2.5 years that adheres to ISO:15189 standards. have successfully used diagnose multiple cases encephalitis hepatitis.
Abstract Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, detection antimicrobial resistance (AMR). Numerous published methods protocols exist, but lack harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital global genomic diagnostics surveillance. As an exemplar, this study evaluated the sensitivity specificity five well-established...
Abstract Background Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, barriers to broader take-up include need high depths, long turnaround times, limited sensitivity. Newer metagenomics protocols Oxford Nanopore Technologies (ONT) allow acquisition analysis data real time, potentially reducing high-volume enabling point-of-care testing....
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery effective infection prevention and control. The increased resolution pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, often remains limited by lack genomic variation between source case contacts. Although within-host genetic diversity common among a wide variety pathogens, conventional phylogenetic approaches exclusively use...
ABSTRACT The emergence of new SARS-COV-2 variants is public health concern in case vaccine escape. Described are three patients with advanced HIV-1 and chronic SARS-CoV-2 infection whom there evidence selection persistence novel mutations which associated increased transmissibility immune
Reverse transcriptase quantitative PCR (RT-qPCR) is the main diagnostic assay used to detect SARS-CoV-2 RNA in respiratory samples. RT-qPCR performed by specifically targeting viral genome using complementary oligonucleotides called primers and probes. This approach relies on prior knowledge of genetic sequence target. Viral variants with changes primer/probe binding region may reduce performance assays have potential cause failure. In this work we demonstrate how two single nucleotide...
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery effective infection prevention and control. The increased resolution pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, often remains limited by lack genomic variation between source case contacts. Although within-host genetic diversity common among a wide variety pathogens, conventional phylogenetic approaches reconstruct...
Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting considerable economic loss. We examined bacterial pathogens mushrooms and bacteriophages that target them to understand disease opportunities for control. The Pseudomonastolaasii genome encoded single type III protein secretion system (T3SS), but contained largest number non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes can play...
Abstract Since the first reports of hepatitis unknown aetiology occurring in UK children, over 1000 cases have been reported worldwide, including 268 UK, with majority younger than 6 years old. Using genomic, proteomic and immunohistochemical methods, we undertook extensive investigation 28 136 control subjects. In five who underwent liver transplantation, detected high levels adeno-associated virus 2 (AAV2) explanted livers. AAV2 was also at blood from 10/11 non-transplanted cases. Low...
Abstract Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society Clinical Virology (ESCV) Network on NGS (ENNGS). A mock reference panel was designed mimic low biomass specimens. The assess...