NCM 2021: Highlights of a regional sequencing surveillance hub during a global pandemic

Hannah presented how her team’s work in a sequencing hub ‘aided the fight’ against SARS-CoV-2 in the UK, via their partnership with the COVID-19 Genomics UK Consortium (COG-UK) sequencing network. As Hannah started her PhD during lockdown, ‘like many other people, my PhD took a little bit of a back seat’; she was therefore seconded to COG-UK as a sequencing technician, based at the University of Liverpool. The team used the ARTIC protocol for SARS-CoV-2 genome sequencing of samples received from hospital laboratories. With their rapid 48-hour workflow, data could be produced for epidemiologists to analyse in a ‘time relevant manner’. Hannah emphasised that similar processes were being established across the UK. Such data contributed to the understanding of viral transmission, and Hannah highlighted the potential demonstrated for using real-time surveillance to support infection control decision making in hospital settings. Hannah also discussed their work investigating COVID-19 monitoring via wastewater sampling of viral RNA, suggesting that this method has the potential to be used as an ‘early warning sign of which viral variants are circulating’. Lastly, Hannah demonstrated the local impact of real-time SARS-CoV-2 sequencing, presenting her team’s work uncovering local variants, which caused concern due to their potential for increased immune evasion. As the delta variant increased prevalence however, that lineage disappeared. Hannah emphasised that real-time genome sequencing enabled quick response in characterising positive samples and identifying infection control measures. Hannah highlighted her blogs on COVID-19 research, which have even been used by the British embassy in Stockholm!