Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters

Abstract

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 ongoing in-hospital transmission of the virus and new introductions from the community, and it is 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 ongoing 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. The outbreak 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 3 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. An 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.

Keywords: hospital epidemiology; infection prevention; metagenomic next generation sequencing; norovirus; outbreak.

Figure 1.

A, Epidemiologic curve, including both hospital-acquired norovirus cases by hospital unit and staff cases of gastrointestinal symptoms. B, Diagram showing location of hospital-acquired norovirus cases within the hospital.

Figure 2.

Phylogenetic tree of hospital- and community-acquired norovirus sequences. Colored boxes represent hospital-acquired case clusters. Black lettering represents samples collected at SCH, while gray lettering represents samples collected at other facilities. All non-100% posterior probabilities are denoted. Abbreviations: SCH, Seattle Children’s Hospital; SNV, single-nucleotide variants.

Figure 3.

The 3 transmission clusters within the norovirus outbreak. Timelines of gastrointestinal symptoms (S), norovirus testing (N), hospitalizations, and outpatient visits for pediatric cluster members are shown on the top of each panel. The number of single-nucleotide variant differences between cluster members is shown on the bottom of each panel.