A pandemic in the age of next-generation sequencing

Since December 2019, the world has found itself rocked by the emergence of a highly contagious novel coronavirus disease, COVID-19, caused by the virus SARS-CoV-2. The global scientific community has rapidly come together to understand the virus and identify potential treatments and vaccine strategies to minimise the impact on public health. Key to this has been the use of cutting-edge technological advances in DNA and RNA sequencing, allowing identification of changes in the viral genome sequence as the infection spreads. This approach has allowed a widespread ‘genomic epidemiology’ approach to infection control, whereby viral transmission (e.g. in healthcare settings) can be detected not only by epidemiological assessment, but also by identifying similarities between viral sub-types among individuals. The UK has been at the forefront of this response, with researchers collaborating with public health agencies and NHS Trusts across the UK to form the COVID-19 Genomics UK (COG-UK) Consortium. Genomic surveillance at this scale has provided critical insight into the virulence and transmission of the virus, enabling near real-time monitoring of variants of concern and informing infection control measures on local, national and global scales. In the future, next-generation sequencing technologies, such as nanopore sequencing, are likely to become ubiquitous in diagnostic and healthcare settings, marking the transition to a new era of molecular medicine.