LABORATORY INFORMATICS GUIDE 2022
brightest innovators and the best manufacturers
“
and largely focuses on spike gene mutations of potential or known importance; providing information on cumulative frequency and data for the last 28 days, to give an approximate assessment of recent changes. COG-UK-ME draws UK genome
data from the MRC-CLIMB database. This data visualisation tool allows anyone to follow information over time on important changes in the Sars- CoV-2 genome.
Selecting the ‘Mutational Explorer’
tab takes you to three tables. Table 1 lists mutations in the spike gene that have led to an amino acid change (called a substitution, which is concentrated on because it may change the way that the virus interacts with humans). Mutations are ranked by frequency
in the MRC-CLIMB database (the most common mutations first). A search function allows individual mutations to be selected, and a file downloaded containing a list of COG-UK identifiers, dates and lineages. For example, selection of E484K provides links to information for each genome that carries this mutation, the date of the sample, and the lineage the isolate belongs to. Data can also be visualised for each mutation in a graph by clicking the visualiser tab. This shows the number of times the selected mutation has been detected over time. COG-UK-ME also displays mutations that could affect the way the virus interacts with the human immune
26
response based on laboratory studies (Antigenic information tab). Scientific evidence is graded. ‘High
confidence’ is applied when a mutation is found by multiple independent studies using multiple different approaches, including studies using polyclonal (convalescent or post- vaccine) antisera; ‘medium confidence’ means this has been found by multiple independent studies; and ‘lower confidence’ indicates this has been found by a single study only. Mutations with an antigenic role can also be filtered by domains of the spike protein. The Explorer will be updated with
new functions over time, based on scientific observations and ways of describing and thinking about variants. The current Covid-19 pandemic, caused by Sars-CoV-2, represents a major threat to health. The Covid-19 Genomics UK (COG-UK) consortium has been created to deliver large- scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. Led by Professor Sharon Peacock of
Cambridge University, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and 12 academic partners providing sequencing and analysis capacity. Professor Peacock is also on a part-time secondment to PHE as director of science, where she focuses on the development of pathogen sequencing through COG-UK. COG-UK was established in April 2020 supported by £20m funding from the Covid-19 rapid-research- response ‘fighting fund’ from the UK government, and administered by the National Institute for Health Research, UK Research and Innovation and the Wellcome Sanger Institute. The consortium was also backed
by the Department of Health and Social Care’s Testing Innovation Fund in November last year to facilitate the genome sequencing capacity needed to meet the increasing number of Covid-19 cases in the UK over the winter.l
www.scientific-computing.com
more of the supply chain onshore, sparing no effort to attract the
We’re increasing UK investment in research and development, bringing much
“
Lightspring/shutterstock
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38
