A5077249581- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Animal Virus Infections Studies
- Genomics and Phylogenetic Studies
- COVID-19 epidemiological studies
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Rabies epidemiology and control
- Microbial infections and disease research
- vaccines and immunoinformatics approaches
- Monoclonal and Polyclonal Antibodies Research
- Viral Infections and Vectors
- Gene expression and cancer classification
- Immune responses and vaccinations
- Inflammasome and immune disorders
- COVID-19 and Mental Health
- Poxvirus research and outbreaks
- Geriatric Care and Nursing Homes
- Genomics and Rare Diseases
- Viral gastroenteritis research and epidemiology
- Viral Infections and Immunology Research
University of Birmingham
2016-2024
Czech Academy of Sciences, Institute of Microbiology
2024
Genomics England
2021
COVID-19 Genomics UK Consortium
2021
The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access relevant computational resources appropriate bioinformatics infrastructure. Here, we present Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility,...
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but understudied. Many case studies have been published which describe one or a small number long-term infected individuals no study has combined these sequences into cohesive dataset. This work aims to rectify this and genomics patient group through combination literature searches as well identifying new series directly from...
Abstract The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access relevant computational resources appropriate bioinformatics infrastructure. Here, we present Cloud Infrastructure for Microbial Bioinformatics (CLIMB)...
<ns4:p>Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely monitor endemic transmission and control in low- middle-income countries. Rabies almost invariably fatal viral that causes a large public health economic burden Asia Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving global goal zero dog-mediated human rabies deaths by 2030, establishing effective tools critical. Genomic...
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely monitor endemic transmission and control in low- middle-income countries. Rabies almost invariably fatal viral that causes a large public health economic burden Asia Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving global goal zero dog-mediated human rabies deaths by 2030, establishing effective tools critical. data can provide...
The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at time writing. This wealth sequence provides important context for interpreting local outbreaks. However, placing interest into national and international is difficult given size global dataset. Often outbreak investigations genomic surveillance efforts require running similar analyses again on latest dataset producing reports. We developed civet (cluster...
Abstract Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough inform outbreak response, and cheaply justify dense sampling of even large epidemics. With increased availability sequencing is agile networks facilities collaborate on the analysis genomic data. In response ongoing SARS-CoV-2 pandemic in United Kingdom, COVID-19 Genomics UK (COG-UK) consortium was formed with aim...
Abstract Long-term SARS-CoV-2 infections in immunodeficient patients are an important source of variation for the virus but understudied. Many case studies have been published which describe one or a small number long-term infected individuals no study has combined these sequences into cohesive dataset. This work aims to rectify this and genomics patient group through combination literature searches as well identifying new series directly from COG-UK The spike gene receptor binding domain...
Summary We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single nucleotide polymorphisms deletions that are characteristic B.1.1.7 variant concern, but lack full complement lineage-defining mutations. Instead, remainder their share contiguous genetic variation with non-B.1.1.7 circulating same geographic area at time as recombinants. In four instances there was onward...
Abstract The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at time writing. This wealth sequence provides important context for interpreting local outbreaks. However, placing interest into national and international is difficult given size global dataset. Often outbreak investigations genomic surveillance efforts require running similar analyses again on latest dataset producing reports. We developed civet...
In response to the escalating SARS-CoV-2 pandemic, in March 2020 COVID-19 Genomics UK (COG-UK) consortium was established enable national-scale genomic surveillance UK. By end of 2020, 49% all genome sequences globally had been generated as part COG-UK programme, and date, this system has >3 million genomes. Rapidly reliably analysing unprecedented number genomes an enormous challenge. To fulfil need inform public health decision-making, we developed a centralized pipeline that performs...