The SARS-CoV-2 virus (COVID-19) is evolving and changing over time to form “new variants”. These variants are characterised by multiple changes (called mutations) in the genome of the virus. A genome is a word to describe all of the genetic information of an organism, in this case the virus. Vaccines may work less well against some new variants of the virus.

COG-UK is a pioneer in the use of large-scale, rapid sequencing of COVID-19 to understand virus transmission and evolution. This is used to inform public health responses and vaccine development. In order to monitor vaccine effectiveness in relation to virus genomic and patient clinical information, we will link multiple Scottish databases (hospital admission data, intensive care data, vaccine registry and deaths data) with the COG-UK database and with data generated through the Genotype2Phenotype (G2P) consortium within the Public Health Scotland National Safe Haven.

This will allow us to:

(1) Monitor changes in the genome of COVID-19 in the Scottish population and relate these to vaccine effectiveness

(2) Test new mutations found in the national dataset for evidence of reduced or no immunity from vaccines

Monitoring of mutations in the virus genome is really important to ensure:

(1) Public health interventions to prevent transmission of vaccine-resistant variants

(2) Development and roll-out of booster vaccines

We have already been involved in tracking the genomic evolution of COVID-19 since March 2020 with funding from the COG-UK consortium, the G2P consortium and the Scottish government.

Importantly, the use of linked data will now allow us to incorporate vaccine status, clinical information, and genetic data into the same analysis, which means we will be able to link key outcomes in people infected with different virus variants in Scotland.