The Irish National SARS-CoV-2 Whole Genome Sequencing Surveillance Programme

Abstract

Abstract Issue In response to the COVID-19 pandemic in Ireland, a national SARS-CoV-2 Whole Genome Sequencing (WGS) Surveillance Programme was set up in 2021 to track the molecular epidemiology of SARS-CoV-2 in Ireland to inform and enhance the urgent public health response to the COVID-19 pandemic. Description The Programme is a ‘hub and spoke’ model, led by the Health Protection Surveillance Centre with the National Virus Reference Laboratory (hub) and seven acute hospital laboratories (spokes), representing Ireland's six Regional Health Areas and Children's Health Ireland Hospitals. The two streams within the Programme's surveillance strategy are: 1. National surveillance of SARS-CoV-2 variants, including samples from GP sentinel sites and severe acute respiratory infection (SARI) surveillance, vaccine effectiveness studies, hospital in-patient, intensive care cases and deaths. 2. Targeted surveillance of risk groups e.g. outbreak cases, cases with unusual epidemiological/clinical characteristics. Results As of 30/03/2023, 103,258 COVID-19 cases (6% all notified cases in Ireland) have been sequenced since week 51, 2020. Data produced contribute to: public health policy in Ireland; local/national clinical and public health action; tracking variants nationally and variant shifts over time; the global community through reporting of WGS data to ECDC, WHO and global repository (GISAID). Lessons The hub and spoke model is an efficient and sustainable design for a laboratory public health programme. It is scalable, allowing addition of new spokes where needed. It ensures regional equity and builds capacity both nationally and regionally, increasing resilience and expertise throughout the country. Key messages • WGS will be key component of future epidemic/pandemic preparedness. • Programme successfully implements sustainable nationwide WGS surveillance and will expand to include other pathogens.