A pandemic in the age of next-generation sequencing

Abstract

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 scientificcommunity has rapidly come together to understand the virus and identify potential treatments andvaccine strategies to minimise the impact on public health. Key to this has been the use of cutting-edgetechnological advances in DNA and RNA sequencing, allowing identification of changes in theviral genome sequence as the infection spreads. This approach has allowed a widespread ‘genomicepidemiology’ 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 betweenviral sub-typesamong individuals. The UK has been at the forefront of this response, with researcherscollaborating with public health agencies and NHS Trusts across the UK to form the COVID-19GenomicsUK (COG-UK)Consortium. Genomic surveillance at this scale has provided critical insight into thevirulence and transmission of the virus, enabling near real-timemonitoring of variants of concernand informing infection control measures on local, national and global scales. In the future, next-generationsequencing technologies, such as nanopore sequencing, are likely to become ubiquitousin diagnostic and healthcare settings, marking the transition to a new era of molecular medicine