Genomic epidemiology of key viral and bacterial pathogens in the UK

The UK is a world leader in SARS-CoV-2 genome sequencing thanks to the COVID-19 Genomics UK Consortium (COG-UK). The Quadram Institute, in particular the Page group, have been at the forefront of sequencing SARS-CoV-2 genomes with over 60,000 sequenced in 18 months making Norfolk the most densely sequenced region of England.

This project focuses on looking more deeply at how the pandemic unfolded within this region to gain a deep understanding of the genomic epidemiology which will help to inform future management of infectious diseases. Using genomics, the aim is to seek answers to questions like: how did the Alpha variant spread within the region, what happened during hospital outbreaks, did different aged people spread the virus in different ways, were samples from closed environments like prisons linked to the local community, did trends from random community surveillance match up with trends seen in hospitals? This builds upon existing research which looked at the early days of the pandemic (https://dx.doi.org/10.1099%2Fmgen.0.000589).