A summary of Thomas Christie Williams' presentation at the SARS-CoV-2/COVID-19 workshop. Real-time sequencing of SARS-CoV-2 could contribute in a number of ways. It can help to distinguish between cases which have been imported, and those which have been transmitted within the community, and help to characterise community-based clusters and spread throughout the UK. Within hospitals, it could help to identify chains of transmission and thus help to keep as many wards open as possible. On a wider scale, we could use it to track the impact of intervention measures, and to estimate the how many cases are going unreported, based on phylogeographic dynamics. Thomas and a team at NHS Lothian’s Royal Infirmary of Edinburgh have put into place a real-time sequencing protocol which uses Nanopore sequencing technology. The sequencing protocol, and associated data analysis methods, have been developed by the ARTIC Network (https://artic.network/ncov-2019). This includes the RAMPART data software developed by the University of Edinburgh’s Professor Andrew Rambaut and PhD student Áine O’Toole. The team is part of a UK-wide consortium, COG-UK, which will generate a geographically representative selection of SARS-CoV-2 genome sequences throughout the epidemic. Together with other Scottish teams, such as NHS Greater Glasgow and the MRC Centre for Virus Research, the NHS Lothian team aim to be able to sequence 200-400 SARS-CoV-2 samples per week. It is possible that, as we gain greater understanding of the virus, real-time sequencing could also be used to directly inform patient care. However, this will require careful thought and substantial investment of time, effort, and research expertise. Watch Thomas' talk This article was published on 2024-08-28
