A5036289658- Herpesvirus Infections and Treatments
- Cytomegalovirus and herpesvirus research
- RNA modifications and cancer
- Virus-based gene therapy research
- Viral-associated cancers and disorders
- RNA and protein synthesis mechanisms
- Poxvirus research and outbreaks
- RNA Research and Splicing
- Vector-borne infectious diseases
- Toxin Mechanisms and Immunotoxins
- Viral Infections and Immunology Research
- Plant Virus Research Studies
- interferon and immune responses
- Cancer-related molecular mechanisms research
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Viral gastroenteritis research and epidemiology
- Research on Leishmaniasis Studies
- Trypanosoma species research and implications
- Animal Virus Infections Studies
- Insect and Pesticide Research
- Toxoplasma gondii Research Studies
- CRISPR and Genetic Engineering
- Mycobacterium research and diagnosis
- Neonatal Health and Biochemistry
University College London
2012-2025
Medizinische Hochschule Hannover
2021-2025
German Center for Infection Research
2022-2025
New York University
2018-2024
Institute of Virology of the Slovak Academy of Sciences
2023-2024
NYU Langone Health
2021
Institute of Infection and Immunity
2016-2020
Centre for Immunity, Infection and Evolution
2015-2016
MRC Laboratory for Molecular Cell Biology
2016
Wellcome Sanger Institute
2009-2011
TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research development needs. collaborative project, utilizing the GUS/WDK computational infrastructure developed Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) integrate genome annotation analyses from GeneDB elsewhere with wide functional genomics made available members global community,...
Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated reference genome for mexicana and refined the genomes major , infantum braziliensis . This has allowed identification remarkably low number genes or paralog groups (2, 14, 19, 67, respectively) unique one species. These were found be conserved additional isolates same predicted allelic variation find that these isolates, L....
ABSTRACT The rapid identification of antimicrobial resistance is essential for effective treatment highly resistant Mycobacterium tuberculosis . Whole-genome sequencing provides comprehensive data on mutations and strain typing monitoring transmission, but unlike conventional molecular tests, this has previously been achievable only from cultures M. Here we describe a method utilizing biotinylated RNA baits designed specifically DNA to capture full genomes directly infected sputum samples,...
Abstract Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated high gene density, overlapping reading frames, and splicing patterns. Direct (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding amplification biases inherent to other methodologies. Here we use direct RNA-seq profile herpes simplex virus type 1 (HSV-1) transcriptome during...
Modification of mRNA by N 6 -adenosine methylation (m A) on internal bases influences gene expression in eukaryotes. How the dynamic genome-wide landscape m A-modified mRNAs impacts virus infection and host immune responses remains poorly understood. Here, we show that type I interferon (IFN) production triggered dsDNA or human cytomegalovirus (HCMV) is controlled cellular A methyltrasferase subunit METTL14 ALKBH5 demethylase. While depletion reduced reproduction stimulated dsDNA-...
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral have been previously detected, location function this mark within infectious cycle unknown. Since complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we...
Members of the family Herpesviridae have enveloped, spherical virions with characteristic complex structures consisting symmetrical and non-symmetrical components. The linear, double-stranded DNA genomes 125-241 kbp contain 70-170 genes, which 43 been inherited from an ancestral herpesvirus. In general, herpesviruses coevolved are highly adapted to their hosts, comprise many mammalian, avian reptilian species. Following primary infection, they able establish lifelong latent during there is...
N 6 -methyladenosine (m A) is an abundant internal RNA modification, influencing transcript fate and function in uninfected virus-infected cells. Installation of m A by the nuclear methyltransferase METTL3 occurs cotranscriptionally; however, genomes some cytoplasmic viruses are also A-modified. How cellular modification machinery impacts coronavirus replication, which exclusively cytoplasm, unknown. Here we show that replication SARS-CoV-2, agent responsible for COVID-19 pandemic, a...
Abstract Aims/hypothesis The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of samples collected date. aim current work was examine presence enterovirus lymphoid without Methods We analysed pancreas, spleen, pancreatic lymph nodes duodenum following groups: (1) diabetes ( n =71) =35) or =36) insulin-containing islets; (2) single...
Whole genome sequencing of viruses directly from clinical samples is integral for understanding the genetics host-virus interactions. Here, we report use sample sparing target enrichment (by hybridisation) viral nucleic acid separation and deep-sequencing herpesvirus genomes a range including saliva, blood, virus vesicles, cerebrospinal fluid, tumour cell lines. We demonstrate effectiveness method by 13 highly cell-associated human generating full length alignments at high read depth....
RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution this population, frequency and/or occurrence individual viral variants can show marked or subtle fluctuations. Since development massively parallel sequencing platforms, such populations now be investigated unprecedented resolution. A critical problem with analyses is presence sequencing-related errors that obscure identification true...
Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV) genome-wide intrahost diversity that rival those persistent RNA viruses [Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF (2011) PLoS Pathog 7:e1001344]. Here, we deep sequence HCMV genomes recovered from single and longitudinally collected blood samples immunocompromised children show the observations high within-host nucleotide are explained by frequent occurrence mixed infections caused genetically...
Immunization with the vOka vaccine prevents varicella (chickenpox) in children and susceptible adults.The strain comprises a mixture of genotypes and, despite attenuation, causes rashes small numbers recipients.Like wildtype virus, establishes latency neuronal tissue can later reactivate to cause Herpes zoster (shingles).Using hybridization-based methodologies, we have purified sequenced directly from skin lesions.We show that alleles present be recovered lesions demonstrate presence severe...
Varicella-zoster virus (VZV), an alphaherpesvirus, establishes lifelong latent infection in the neurons of >90% humans worldwide, reactivating one-third to cause shingles, debilitating pain and stroke. How VZV maintains latency remains unclear. Here, using ultra-deep virus-enriched RNA sequencing latently infected human trigeminal ganglia (TG), we demonstrate consistent expression a spliced mRNA, antisense open reading frame 61 (ORF61). The latency-associated transcript (VLT) is expressed TG...
-methyladenosine (m
The chemical modification of ribonucleotides regulates the structure, stability and interactions RNAs. Profiling these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. cannot be assigned to specific transcript isoforms in regions sequence overlap. An alternative strategy uses current fluctuations nanopore-based long read direct RNA (DRS) infer location identity nucleotides that differ between two experimental...
Chlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases sexually transmitted infections annually. Whole-genome sequencing powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The objective this study was perform whole-genome enrichment C. directly from clinical samples.C. positive samples comprising seven vaginal swabs three...
ABSTRACT Varicella-zoster virus (VZV) is a human herpesvirus, which during primary infection typically causes varicella (chicken pox) and establishes lifelong latency in sensory autonomic ganglia. Later life, the may reactivate to cause herpes zoster (HZ; also known as shingles). To prevent these diseases, live-attenuated heterogeneous vaccine preparation, vOka, used routinely many countries worldwide. Recent studies of another alphaherpesvirus, infectious laryngotracheitis virus,...
Background. Noroviruses are a highly transmissible and major cause of nosocomial gastroenteritis resulting in bed hospital-ward closures. Where hospital outbreaks suspected, it is important to determine the routes spread so that appropriate infection-control procedures can be implemented. To investigate cluster norovirus cases occurring children undergoing bone marrow transplant, we undertook genome sequencing by next-generation methods. Detailed comparison sequence data from 2 linked...
Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout host's life in a latent state with periodic episodes reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by emergence antiviral resistance absence an effective vaccine, development which is likely complicated numerous immune evasins encoded to counter adaptive responses,...
Human cytomegalovirus (HCMV) is a significant pathogen in immunocompromised individuals, with the potential to cause fatal pneumonitis and colitis, as well increasing risk of organ rejection transplant patients. With advent new anti-HCMV drugs there therefore considerable interest using virus sequence data monitor emerging resistance antiviral HCMV viraemia disease, including identification putative mutations. We used target-enrichment deep DNA from 11 immunosuppressed pediatric patients...
Varicella-zoster virus (VZV) establishes latency in human sensory and cranial nerve ganglia during primary infection (varicella), the can reactivate cause zoster after infection. The mechanism of how maintains it reactivates is poorly understood, largely due to lack robust models. We found that axonal neurons derived from hESCs a microfluidic device with cell-free parental Oka (POka) VZV resulted latent inability detect several viral mRNAs by reverse transcriptase-quantitative PCR, no...