Tracking the Virus
COVID-19 pandemic progress including hospital transmissions.
Sequencing the virus in real-time
The CVR is part of the COVID-19 Genomics UK Consortium (COG-UK), - comprised of the NHS, Public Health Agencies, Wellcome Sanger Institute, and numerous academic institutions - to deliver large scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the government.
Working in partnership with colleagues in COG-UK, NHS Greater Glasgow & Clyde (NHSGGC) and the West of Scotland Specialist Virology Centre (WoSSVC), CVR researchers have been rapidly sequencing SARS-CoV-2 from clinical samples since the first confirmed case of COVID-19 in Scotland.
More than 800 confirmed cases had been sequenced by 24 April 2020. And annotated genomes from more than 600 sequences deposited in public repositories.
An important aspect of this work focuses on samples from infected health care workers, where rapid sequencing and analyses can help to establish the likelihood of a nosocomial (hospital acquired) versus community acquired infection. These data are critical in determining whether hospital infection control measures have failed.
- Update report of COVID-19 in Scotland: multiple introductions - 10 March 2020
- First report of COVID-19 in Scotland - 4 March 2020
Developing software to analyse SARS-CoV-2 sequences
The CVR is leading the development of a software package known as CoV-GLUE.
This tool will help to monitor changes in the virus at a global scale and determine whether different strains are emerging.
CoV-GLUE obtains its data from GISAID and contains a database of all the substitutions and deletions which have been observed in the sequences sampled during the outbreak.
This data will be included within the COVID-19 Genomics UK Consortium (COG-UK) consortium pipeline. The functionality of this software will be expanded with time to include other aspects that support the prediction of functional change in the virus.
- CoV-GLUE - is developed and maintained by the CVR
- GISAID - Enabling Rapid and Open Access to Influenza Virus Data
Studying the seasonality of coronaviruses
CVR Research published in the Journal of Infectious Diseases, highlights when coronaviruses are most prevalent in different healthcare settings and how these viruses interact with other kinds of respiratory viruses. The work – one of the most detailed studies of coronaviruses in a patient population – could be important for understanding and predicting the behaviour of COVID-19.
Researchers used unique data from over 70,000 NHS Greater Glasgow and Clyde patients with respiratory illness between 2005 and 2017. Patients were tested for a panel of respiratory viruses, including common seasonal coronaviruses, to look for patterns related to age and seasonal frequency, and any variation between the different coronavirus types.
This analysis revealed that seasonal coronaviruses:
- were detected amongst all age groups,
- can coinfect with other respiratory viruses, and
- although different coronavirus types coexist in most winter seasons, they exhibit structured seasonal patterns.
- Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019 - 14 April 2020
- News Release: Patterns of common coronavirus infections could aid understanding of COVID-19 - 24 April 2020
Understanding SARS-CoV-2 evolution
There are outstanding evolutionary questions relating to the recent emergence of coronavirus SARS-CoV-2 in Hubei province, China that resulted in the COVID-19 pandemic.
- the relationship of this new virus to SARS-related coronaviruses,
- the role of bats as a reservoir species, and
- the role of recombination in viral emergence
The CVR is leading the development of CoV-GLUE to support an amino acid analysis of SARS_CoV-2 during the outbreak. SARS-CoV-2 will naturally accumulate nucleotide mutations (changes) in its RNA genome as the pandemic progresses. Many of the observed changes will have little or no impact on virus biology but some genetic variants may change or alter the virus phenotype. Tracking the emergence of these mutations will help us understand the evolution and spread of the virus at a global level. CoV-GLUE contains a database of replacements, insertions and deletions which have been observed in sequences sampled from the pandemic.
- CoV-GLUE - is developed and maintained by the CVR
CVR scientists have also published several studies that address these outstanding evolutionary questions.
- No evidence for distinct types in the evolution of SARS-CoV-2 -Virus Evolution, in press
- Multiple introductions and subsequent community transmission of SARS-CoV-2 highlight the role of international travel in the emergence of COVID-19 in Scotland - in preparation
The risk of zoonotic viruses spreading to humans found to be largely the same across diverse groups of animals.
- Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts - 13 April 2020
- ‘It’s kind of a numbers game' Researcher explains on Twitter - 14 April 2020
- News Release: Risk of viruses emerging in humans may not depend on their animal host -13 April 2020
Examination of sarbecoviruses – the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2.
- Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic - 30 March 2020
A preliminary analysis to characterise the evolutionary origins of SARS_CoV-2 helped counter the inaccurate reporting of a snake origin.
- Why snakes probably aren’t spreading the new China virus - 23 January 2020
- Virological nCoV’s relationship to bat coronaviruses & recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant - 22 January 2020
Genomic machine learning supports the suspected bat origin of SARS_CoV-2.
- Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes - 2 November 2018