Identifying intra-hospital Norovirus GII transmission using whole-genome sequencing

Norovirus genogroup II (GII) is a common gastrointestinal pathogen that can cause spatially and temporally linked outbreaks due to its resistance to disinfectants and desiccation. Despite this threat, routine whole-genome sequencing has rarely been systematically applied to Norovirus. We performed whole-genome amplification of Norovirus GII from 665 clinical stool specimens collected between 2019 and 2025 at Children’s Hospital of Philadelphia (CHOP), and 47 samples from Children’s National Hospital, using a modified PCR protocol and Oxford Nanopore Technologies (ONT) sequencing. Viral genomes were assembled using long-read sequencing and paired with clinical metadata from the electronic medical record to identify suspected transmission events. Our assay improves on previous methods and achieved an 84% success rate in assembling CHOP samples into near-complete genomes. Genotyping analysis showed dominance of GII.4 Sydney [P16] from 2019 to 2024, with recent emergence of GII.17 [P17]. We identified multiple cliques (n = 44) of genetically indistinguishable or near-identical (≤ 5 SNP) strains. 32% (14/44) of these cliques were from patients on the same units and are considered “Likely” Norovirus GII transmission events. 20% (9/44) of the cliques are from different units or inpatient and emergency department and are “Possible” transmission events. All “Likely” Norovirus GII transmission events have a confirmed epidemiological link or occurred entirely within unit and 56% (5/9) of the “Possible” transmission events have an epidemiological link - either a shared clinician or shared off unit location or both. This study demonstrates that whole-genome sequencing of Norovirus GII is a powerful tool for high-resolution viral surveillance. Prospective genomic monitoring combined with informatics enables detection of nosocomial outbreaks and reveals hidden transmission chains. Routine implementation of this platform could facilitate earlier implementation of containment measures that may ultimately reduce healthcare-associated Norovirus transmission.