Examination of SARS-CoV-2 severity, transmissibility and spread within Wales through the analysis of linked patient health records and genomic sequenc

Examination of SARS-CoV-2 severity, transmissibility and spread within Wales through the analysis of linked patient health records and genomic sequence data. As part of the COVID-19 response we have sequenced in excess of 5,000 SARS-CoV-2 genomes, representing approximately 40% of all Welsh COVID-19 cases. We have linked the viral genomic data we have generated to the linked, anonymised, patient health record dataset held by SAIL. Within our sequenced dataset, we have identified a set of variants that are present at varying frequencies across our dataset. We have already undertaken analyses to examine one of these - a mutation in the spike protein which may increase viral transmissibility. This project will focus on extending this work through the examination of the enormously rich and complex SAIL dataset to perform linked analyses of viral sequence data with the extensive linked medical records within SAIL in order to quantify the effect of viral variants on disease severity and transmission in Wales. This project makes use of a dataset of unprecedented size and scope, and will provide opportunities to extend the approaches developed and deployed to examine other pathogenic species for which whole genome sequence data is available in Wales.