SARS-CoV-2 outbreak investigation: from sample to response in a day
About Áine O'Toole
Áine is a researcher working in the Rambaut Group at The University of Edinburgh. Áine graduated with BA in Genetics and an MRes in Molecular Evolution from Trinity College Dublin. After completing an MSc in Hosts, Pathogens & Global Health at The University of Edinburgh, she joined the Rambaut Group & the ARTIC Network to complete her Ph.D. Prior to the COVID-19 pandemic, Áine developed software for viral surveillance & outbreak investigations. This year, Áine has worked in the phylogenetics core of COG-UK, and developed tools such as PANGOLIN and CIVET to help researchers around the world track the spread of SARS-CoV-2.
Since December 2019, SARS-CoV-2 has spread throughout the world and infected millions of individuals. In this genomic era, the spread has been accompanied by an unparalleled response, with now over 150K whole genomes shared online from over 100 countries. For this sequencing to inform local public health response, the data needs to be condensed and presented as actionable information within a useful time frame. With the use of GridION technology, protocols from the ARTIC Network, and our custom software PANGOLIN and CIVET, we have achieved real-time viral genomics, going from sample to informed response in a single day.