The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks

Francis, Rodric V; Billam, Harriet; Clarke, Mitch; Yates, Carl; Tsoleridis, Theocharis; Berry, Louise; Mahida, Nikunj; Irving, William L; Moore, Christopher; Holmes, Nadine; Ball, Jonathan; Loose, Matthew; McClure, C Patrick

Nosocomial SARS-CoV-2 infections have severely affected bed capacity and patient flow. We utilised whole genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the UK’s second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point of care testing and introduction of portable HEPA14 filters. Conversely WGS excluded nosocomial transmission in two instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.