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.

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.

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.

Examination of sarbecoviruses – the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2.

A preliminary analysis to characterise the evolutionary origins of SARS_CoV-2 helped counter the inaccurate reporting of a snake origin.

Genomic machine learning supports the suspected bat origin of SARS_CoV-2.