A flexible and high-throughput genotyping workflow tracked the emergence of SARS-CoV-2 variants in the UK in 2022

Abstract

AbstractIn late 2021, the Omicron SARS-CoV-2 variant spread rapidly worldwide. To track its emergence, and the continued evolution of SARS-CoV-2 while giving actionable epidemiological data that informs public health policy, we developed a high-throughput, automated, genotyping workflow that pairs flexible liquid handling with a re-configurable LIMS system. This workflow facilitated the real-time monitoring of the spread of BA.4 and BA.5, and by the time of its retirement, the system was responsible for typingc. 400,000 SARS-CoV-2 samples. When combined with a population-scale testing program, genotyping assays, can offer a rapid and cost-effective method of determining variants and horizon-scanning for changes in the pool of circulating mutations. Strategies to prepare diagnostics infrastructure for Pathogen X should consider the development of flexible systems with interchangeable components that can be rapidly re-configured to meet uncertain and changing requirements.