COG-UK glossary

Definitions of COG-UK-related terms

Angiotensin-converting enzyme 2 (ACE2): Receptor found on the surface of many cell types, used by SARS-CoV-2 virus to enter lung epithelial cells.
Antimicrobial resistance (AMR): Umbrella term used to describe the diverse range of mechanisms that microbes, like bacteria, fungi, viruses and other parasites, use to survive the destructive effects of drugs like antibiotics, antivirals, antifungals and antimalarials.
Bayesian Evolutionary Analysis Sampling Trees (BEAST): Software used to carry out Bayesian analysis of molecular sequences related by an evolutionary tree.
Bioinformatics: Interdisciplinary field that harnesses computer tools to capture and analyse large, complex biological data sets.
cDNA: Short for complementary or copy DNA, cDNA is a double-stranded DNA that has been synthesised from an RNA template by reverse transcription.
Centers for Disease Control and Prevention (CDC): The national public health agency of the United States.
Centre for Genome Pathogen Surveillance (CGPS): Now based in Oxford, the Centre was established to inform pathogen control strategies on a local, national and international scale.
CL3 laboratory: Laboratory classified to have containment level 3. This is required for laboratories that work with high risk biological agents, including human pathogens that have the potential to be transmitted via inhalation.
Clone: A genetic replica of a cell or organism that has been created without sexual reproduction.
Cloud Infrastructure for Microbial Bioinformatics (CLIMB): UKs largest cloud-based system for the analysis of microbial genomes.
Cluster Investigation & Virus Epidemiology Tool (Civet): Software suite that works on CLIMB to generate a report for a set of genome sequences of interest, such as for an outbreak investigation.
COG-Train: International educational initiative providing open-access learning in SARS-CoV-2 genomics.
COVID Immunology Consortium (UK-CIC): Consortium of leading immunologists convened to understand the immunology of SARS-CoV-2 and COVID-19 to improve diagnostics, treatments and vaccines for the disease.
COVID-19 Genomics Consortium (COG-UK): COG-UK is a group of public health agencies and academic institutions set up in the UK in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response.
Department of Health and Social Care (DHSC): Department responsible for the UK government's policy on health and social care matters in England.
DNA polymerase: DNA polymerase is a type of enzyme that can be found in all living organisms. There are many types of DNA polymerase. Some help replicate DNA when a cell divides and others help in the day-to-day repair and maintenance of DNA.
Ebola virus: Also known as Zaire ebolavirus, the ebola virus can cause severe and often fatal haemorrhagic fever in humans and other mammals.
Enteric disease: Group of diseases that affect the stomach or intestine caused by microorganisms like bacteria, viruses and parasites frequently consumed through contaminated food or water. Symptoms are commonly nausea, vomiting, diarrhoea, abdominal cramps, fever, chills, and a loss of appetite.
Epidemic: Rapid spread of a disease above what is normally expected in an area or population.
Epidemiology: Branch of medical science that studies the determinants, occurrence and distribution of health and disease in a defined population.
Europe Nucleotide Archive (ENA): Repository for uploading and sharing annotated DNA and RNA sequences.
Food and Drug Administration (FDA): US Federal agency responsible for ensuring the safety, efficacy and security of human and veterinary drugs, biological products, and medical devices.
General Data Protection Regulation (GDPR): European Union regulation designed to protect personal data and privacy.
Genome: Complete set of genetic material within the single cell of an organism.
Genomics: A branch of genetics established in the 1980s directed towards studying the structure, function, evolution and mapping genomes in organisms.
Genotype: The set of genes in DNA which is responsible for a particular trait.
GitHub: GitHub is an internet platform that hosts open source software development projects.
Global Initiative on Sharing Avian Influenza Data (GISAID): Global repository for sharing the genomes of respiratory viruses, including influenza and SARS-CoV-2.
Graphics Processing Unit (GPU): Specialised electronic processor designed to accelerate graphics rendering.
GridION: Benchtop nanopore sequencing device designed to run multiple experiments simultaneously with 5 independent flow cells. Produced by Oxford Nanopore Technologies.
HighSeq 2500: High-though-put sequencing system developed by Illumina.
Hospital-onset COVID-19 infection study (HOCI): Study set up to evaluate the efficacy of rapid genome sequencing of SARS-CoV-2 for limiting the spread of COVID-19 in UK hospitals.
In vitro: Term comes from the Latin meaning 'in a glass' or 'in the glass'. It is used to describe studies carried out in an artificial, controlled environment outside the body, such as in a petri dish or test tube.
In vivo: Term comes from the Latin meaning 'within the living'. It is used to describe tests, experiments or procedures researchers perform in a whole living organism.
Infection Prevention and Control (IPC): A sub-discipline of epidemiology concerned with preventing the spread of healthcare-associated infections.
Intensive Care National Audit & Research Centre (ICNARC): Independent, not-for-profit, scientific organisation that oversees a broad programme of clinical audit and clinical/health services research. It hosts databases for multiple studies on the epidemiology of critical illness to help inform practice and policy.
International Committee of Taxonomy of Viruses (ICTV): Set up in 1966, ICTV authorises and organises the classification and naming of viruses.
International Severe Acute Respiratory and emerging Infection Consortium (ISARIC): Global federation of clinical research networks set up to coordinate response to outbreak-prone infectious diseases.
LamPORE: Diagnostic platform for the detection of the SARS-CoV-2 virus.
Ligation: Term used to describe the joining of 2 DNA strands or other molecules together.
Lighthouse labs: UK network of diagnostic labs set up to carry out community testing for COVID-19.
Lineage: Used to describe a group of closely related viruses with a common ancestor.
Lockdown: Policy used in emergency situations to restrict the movement of people to prevent the spread of disease.
Long-Covid: Used to describe the effects of COVID-19 that last for several weeks or months beyond the initial illness.
lower middle income countries (LMICs): Term used for countries with low-income or middle-income economies listed by the Organisation for Economic Co-operation and Development.
Malaria Genomic Epidemiology Network (MalariaGEN): A network of researchers building large-scale human, malaria parasite and mosquito data resources to better understand the evolution and epidemiology of malaria to help control the disease.
Messenger RNA (mRNA): A molecule in cells that conveys genetic information from DNA to the ribosome, the site of protein synthesis.
Metadata: In genomics, metadata provides information on the time and origin of the sample that the genetic material was taken from, as well as certain characteristics, such as a person’s age, which is essential to correctly interpret the genomic data and understand its context..
Metagenomics: A broad discipline that studies genetic material collected from environmental or clinical samples.
Microbiology: A discipline that investigates the biology of microscopic organisms like viruses, bacteria, algae, fungi, slime moulds and protozoa.
MicroReact: An open source web tool for visualising and sharing genomic epidemiology, phylogenetic trees and metadata.
Middle East Respiratory Syndrome (MERS): A rare but severe type of respiratory illness caused by a novel coronavirus first identified in Saudi Arabia in 2012.
MinION: A portable nanopore sequencing device produced by Oxford Nanopore Technologies.
MiSeq: Benchtop genome sequencer produced by Illumina.
Monoclonal antibody: Laboratory produced antibody designed to recognise and bind to specific receptors found on the surface of cells. Derived from natural antibodies, monoclonal antibodies are produced by creating a hybrid cell line, known as a hybridoma, by fusing a short-lived antibody-producing B cell, a type of white blood cell, collected from the spleen of an immunised animal with an immortal cancer cell line. Maintained in a medium, the hybridoma will secrete endless quantities of antibodies. Each of these antibodies are identical and clones of a unique parent cell - hence the term 'monoclonal'.
Mutation: A term used to signify a single change in the genetic code of a virus or other pathogens. Mutations frequently happen in viruses and other pathogens as they evolve but only sometimes change their characteristics.
Nanopore sequencing: Technique that reads the sequence of a single strand of DNA as it passes through extremely tiny pores embedded in a membrane.
National Health Service (NHS): Publicly funded healthcare system in England, Wales, Scotland and Northern Ireland.
NextEra: DNA library preparation kit provided by Illumina.
NextStrain: International collaborative project which provides open-source tools for visualising the genetics behind the spread of viral outbreaks.
NimaGen: Dutch based company that manufactures and supplies pre-designed and customised tests, reagents and workflow solutions for DNA sequencing.
NovaSeq: Whole genome sequencing platform produced by Illumina.
Nucleic acid: Long molecule made up of smaller molecules called nucleotides which are chemically linked together in a chain. Nucleotides are instrumental in transferring genetic information from one generation to another. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Nucleotides: Nucleotides are molecules present in all cells of the body. They serve many purposes, including acting as cellular messengers between the outside and the inside of a cell's nucleus, storing energy and as physiological mediators. Nucleotides are also necessary to the construction of the nucleic acids DNA and RNA. DNA is made up of four base nucleotides: adenine (A), cytosine (C), guanine (G) and thymine (T). RNA is made up of A, G, and C, plus uracil.
Office for National Statistics (ONS): UK's largest independent producer of official statistics.
Oligonucleotide: Commonly made in the laboratory, an oligonucleotide is a short sequence of DNA (usually 2-50 bases). Oligonucleotides are important in artificial gene synthesis, polymerase chain reactions, DNA sequencing, library construction and can be used as molecular probes.
Oxford Nanopore Technologies (ONT): UK based company that develops and sells nanopore sequencing products.
Pandemic: An outbreak of an infectious disease that spreads across a large region, for example multiple continents or worldwide.
Pango system: A dynamic nomenclature system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern.
Pathogen genomics: Approach using genomic sequencing to understand the evolution and spread of pathogens to help control the spread of an infectious disease .
Pathogen Genomics Unit, Public Health Wales (PenGU): Body established in 2018 to provide an accredited sequencing environment for a range of clinical pathogen genomics services for the whole of Wales.
Pathogenwatch: Computer platform that makes it possible to compare pathogen genome sequences from around the world.
Phenotype: The physical characteristics of an organism that result from the interactions between genes, environment, disease, molecular mechanisms, and chance.
Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN): Computational tool able to assign the most likely lineage to a given SARS-CoV-2 genome sequence based on the Pango dynamic lineage nomenclature scheme.
Phylogenetic tree: Also known as phylogeny, a phylogenetic tree is a branching diagram used to show the evolutionary relationships between a particular set of organisms.
Phylogenetics: Study of the evolutionary relationships among a particular group of organisms sharing a common ancestor.
Pillar 1 testing: COVID-19 testing of hospitalised patients.
Pillar 2 testing: COVID-19 testing undertaken in the community through drive-through test centres, mobile testing units and satellite test centres.
Pipeline: Term used to describe end to end process all the way from receipt of a sample through to getting validated data at the end.
Polymerase chain reaction (PCR): A technique that is used to copy a specific DNA sequence. The technique provides the means to make one billion exact copies of an original target DNA within a couple of hours.
Primer: Template strand of DNA used to generate a new double-strand of DNA.
Principal Investigator (PI): Person responsible for the conduct of a research study at a site.
Public Health Agency (PHA): Body responsible for public health protection.
Public Health England (PHE): Executive agency of the Department of Health and Social Care in England established in 2013. In 2021 it was replaced by the UK Health Security Agency.
Public Health Scotland (PSA): Scotland's national public health body.
Public Health Wales (PHW): Wales' national public health body.
QIAcube HT: Instrument used to perform nucleic acid purification.
REal-time Assessment of Community Transmission trial (REACT): Research study led by Imperial College in partnership with Ipsos MORI and Imperial College Healthcare NHS Trust to examine the prevalence of SARS-CoV-2 virus in the general population. It involves over 150,000 participants each month using home testing to improve our understanding of how the COVID-19 pandemic is progressing across England.
Respiratory syncytial virus (RSV ): Common respiratory virus that can cause mild, cold-like symptoms, but can be serious for infants and older adults.
Reverse complement PCR (RC-PCR): Modification of polymerase chain reaction used to generate amplicon libraries for DNA sequencing.
Reverse transcriptase: An multifunctional enzyme able to catalyse the creation of a double-stranded DNA from an RNA template
Ribonucleic acid (RNA): A type of molecule that plays a role in the coding, decoding, regulation and expression of genes. There are two types of RNA: 1) messenger RNA (mRNA), responsible for carrying the genetic code to the ribosome to build a protein; and 2) transfer RNA (tRNA).
RNASeq: Technique that provides a means to examine the quantity and sequences of RNA in a sample using next-generation sequencing.
SARS-CoV-2 variants of concern: Term used to describe a SARS-CoV-2 variant with genetic changes observed to be more infectious and more likely to cause breakthrough infections or reinfections in people already vaccinated and previously infected. Five variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) had been identified by February 2023.
Scientific Advisory Group for Emergencies (SAGE): Independent advisory group convened to support the UK government in the event of a national emergency. The group does not make decisions or set policy, it only provides advice.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus): A strain of coronavirus first identified in China in late 2019 that is highly contagious and responsible for the COVID-19 pandemic which by October 2022 had caused more than 6 million deaths.
Staphylococcus aureus (S. aureus): Most common staphylococcal bacteria. They are responsible for many different health problems in humans, including carbuncles, food-poisoning, and infections around medical devices and wounds.
Taqman assay: Genotyping assay used to amplify and detect specific alleles in genomic DNA.
Tuberculosis (TB): A highly infectious disease caused by the bacterium Mycobacterium tuberculosis. The bacterium most commonly attacks the lungs but it can also attack other parts of the body, including the abdomen, glands, bone and nervous system. Tiny droplets from coughs and sneezes of infected patients spread the disease. Most common symptoms are a persistent cough which can be bloody, night sweats, fever, neck swelling, fatigue and loss of appetite. The disease can be cured with the right antibiotics.
UK Health Security Agency (UKHSA): A UK government agency set up in April 2021 to oversee England-wide public health protection.
Variant of concern (VOC): Term used to describe a SARS-CoV-2 variant with genetic changes observed to be more infectious and more likely to cause breakthrough infections or reinfections in people already vaccinated and previously infected. Five variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) had been identified by February 2023.
Variant of interest (VOI): Term used to describe a SARS-CoV-2 variant with genetic changes that have the potential to be more transmissible, able to evade immunity or cause more severe disease.
Virological: Online forum for the analysis and interpretation of virus molecular evolution and epidemiology.
World Health Organization (WHO): United Nations agency set up in 1948 to oversee international public health.
Zika virus: First isolated in the Zika Forest of Uganda in 1947, the virus is transmitted between humans and animals by mosquitoes. In most cases it causes a very mild infection with no long-term harm. But it can be dangerous in pregnancy as it can lead to birth defects, in particular causing babies to have abnormally small heads (microcephaly).