Joshua Quick
A5057587140- SARS-CoV-2 and COVID-19 Research
- Viral Infections and Vectors
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Mosquito-borne diseases and control
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- Animal Virus Infections Studies
- Viral gastroenteritis research and epidemiology
- Gut microbiota and health
- RNA modifications and cancer
- Viral Infections and Outbreaks Research
- COVID-19 Clinical Research Studies
- Nanopore and Nanochannel Transport Studies
- Virology and Viral Diseases
- Insect symbiosis and bacterial influences
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Bacterial Identification and Susceptibility Testing
- Virus-based gene therapy research
- Antibiotic Resistance in Bacteria
- Plant Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- Respiratory viral infections research
University of Birmingham
2016-2025
Indiana University
2023
University of Pretoria
2023
Imperial College London
2022
Quadram Institute
2022
Université Gustave Eiffel
2020
Czech Academy of Sciences, Institute of Microbiology
2015-2016
Queen Elizabeth Hospital Birmingham
2014-2015
NIHR Surgical Reconstruction and Microbiology Research Centre
2014-2015
National Institute for Health Research
2015
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost diversity. develop an experimental protocol computational tool, iVar, for using PrimalSeq measure diversity Illumina compare results Oxford Nanopore sequencing. utility by Zika...
Abstract Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded GISAID database. We published a method for ( https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w ) online on January 22, 2020. This approach rapidly become most popular due its simplicity and cost-effectiveness. Here we present improvements original protocol: i) an updated primer scheme 22 additional primers improve coverage, ii)...
HE OUTBREAK OF SHIGA-TOXIgenic Escherichia coli (STEC), which struck Germany in May-June 2011, illustrated the effects of a bacterial epidemic on wealthy, modern, industrialized society, with more than 3000 cases and 50 deaths. 1During an outbreak, rapid accurate pathogen identification characterization is essential for management individual entire outbreak.Traditionally, clinical bacteriology has relied primarily laboratory isolation bacteria pure culture as prerequisite to outbreak...
Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected large outbreak enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This was linked to community, national and European-wide cases. Hospital with are at high risk, require rapid response. initially investigated this by whole-genome sequencing using novel protocol on the Illumina MiSeq; we then integrated these data from surveillance sequencing, thereby...
Abstract Advances in nanopore sequencing technology have enabled investigation of the full catalogue covalent DNA modifications. We present first algorithm for identification modified nucleotides without need prior training data along with open source software implementation, nanoraw . Nanoraw accurately assigns contiguous raw signal to genomic positions, enabling novel visualization, and increasing power accuracy discovery covalently bases native DNA. Ground truth case studies utilizing...
Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, consequently have great potential for the study of microbial communities. However, best approaches analysis long-read metagenomic data unknown. Additionally, rigorous evaluation bioinformatics tools is hindered by a lack from validated samples with known composition.We sequenced 2 commercially available mock communities containing 10 species (ZymoBIOMICS Microbial Community Standards) Oxford Nanopore...
OBJECTIVES: Exploring associations between the gut microbiota and colonic inflammation assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into microbial origins of Crohn’s disease (CD). METHODS: Fecal samples (n=117) were collected from 23 CD 21 healthy children. From children fecal before, EEN, when patients returned to their habitual diets. Microbiota composition functional capacity characterized using sequencing 16SrRNAgene shotgun metagenomics. RESULTS:...
The MinION™ is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and powered from the USB 3.0 port of laptop computer. change current resulting DNA strands interacting with charged protein nanopore. These measurements can then be used to deduce underlying nucleotide sequence.We present read dataset whole-genome shotgun sequencing model organism Escherichia coli K-12 substr. MG1655 generated on device during early-access...
Abstract Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB’ relate to what we see today. Here describe 14 genome sequences M. tuberculosis , representing 12 distinct genotypes, obtained from human remains eighteenth-century Hungary using metagenomics. All our historic genotypes belong Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places most recent common ancestor this lineage...
Objectives Pseudomonas aeruginosa is a common nosocomial pathogen responsible for significant morbidity and mortality internationally. Patients may become colonised or infected with P. after exposure to contaminated sources within the hospital environment. The aim of this study was determine whether whole-genome sequencing (WGS) can be used source in cohort burns patients at high risk acquisition. Study design An observational prospective study. Setting Burns care ward critical UK....
We conducted the genome sequencing and analysis of first confirmed COVID-19 infections in Brazil. Rapid coupled with phylogenetic analyses context travel history corroborate multiple independent importations from Italy local spread during initial stage transmission
ABSTRACT High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short modifications not carried forward cDNA. We address limitations using a native poly(A) strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on from human cell line GM12878, generating 9.9 million aligned sequence reads....
<ns4:p>Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating is currently hampered by complex expensive methods. Untargeted, metagenomic nanopore can provide genomic information to identify pathogens, prepare or even prevent outbreaks.</ns4:p><ns4:p> SMART (Switching Mechanism at the 5′ end of RNA Template) popular RNA-Seq but most current methods rely on oligo-dT priming target polyadenylated mRNA molecules. We have...
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub Amazon region, little known about there, terms both transmission viral genetic diversity. Using portable genome sequencing, we generated 59 genomes Manaus. Phylogenetic analyses indicated multiple introductions from...
Monkeypox virus (MPXV), a zoonotic endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of first confirmed case MPXV Brazil. Shotgun metagenomic sequencing was completed 18 hours, from DNA extraction consensus sequence generation.
Metagenomics enables the reconstruction of microbial genomes in complex communities without need for culturing. Since assembly typically results fragmented grouping genome fragments (contigs) belonging to same genome, a process referred as binning, remains major informatics challenge. Here we present CONCOCT, computer program that combines three types information - sequence composition, coverage across multiple sample, and read-pair linkage automatically bin contigs into genomes. We...