The novel coronavirus SARS-CoV-2 has led to severe disruption across the globe. Case numbers rose significantly in the UK over the winter period of 2020 due to the emergence of a novel variant, the Alpha variant B.1.1.7. More recently, the Delta variant B.1.617.2 has accounted for the vast majority of COVID-19 cases in the current wave of infections. Asymptomatic and pre-symptomatic spread represent significant routes for COVID-19 spread, and a large number of non-pharmaceutical interventions have previously been put in place in the UK to help minimise spread (including the wearing of masks, regular access to hand sanitiser, social distancing policies, etc).

In response to the pandemic, the COVID-19 Genomics UK Consortium (COG-UK) was set up, providing a collaboration between academic institutes, NHS Trusts and Public Health Agencies to provide a systematic approach to understanding the spread of the virus throughout the UK. By using whole genome sequencing of the SARS-CoV-2 virus, viral subtypes and potential variants of concern (VOCs) such as Alpha and Delta can be rapidly identified. In addition, by observing small changes in the virus as it passes from person to person, genomic epidemiology can be used to help identify and mitigate potential issues with infection control.

Since the start of the pandemic, the University of Portsmouth have been at the forefront of the COG-UK network, acting as the South Coast Sequencing Hub for NHS Trusts across the region and Pillar 2 community testing sites across the UK, with over 10,000 samples processed and made publicly available. In this talk, I will discuss the University’s impact throughout the pandemic, as well as ongoing research projects looking at the role of nosocomial spread in healthcare settings, the efficacy of vaccination of healthcare workers on minimising viral spread, and the spread of the virus amongst University students.