Background: Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between on-going in-hospital transmission of virus and new introductions from the community and challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone. Methods: Real-time metagenomic sequencing during an on-going norovirus outbreak associated with a retrospective cohort study. Results: We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large tertiary pediatric hospital and was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping hospital-acquired norovirus cases were partitioned into three discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised hospital-acquired case patient. Analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host. Conclusions: This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.

Prospective real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters