Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak (preprint)

ABSTRACT

BackgroundWe have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK. MethodsFollowing multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests. ResultsThirty staff (25%) and 16 patients (62%) tested positive for COVID-19. Genomic sequencing data showed significant overlap of viral haplotypes in staff who had overlapping shift patterns. Patient haplotypes were more distinct from each other but had overlap with staff haplotypes. ConclusionsThis study includes clinical and genomic epidemiological detail that demonstrates the value of a combined approach. Viral genetic sequencing has identified that staff transmission of COVID-19 was important in this community hospital outbreak. Key pointsO_LIDetailed analysis of a large community hospital outbreak in older adults and staff with concurrent clinical and genomic data, including working patterns. C_LIO_LIStaff transmission was important in this community hospital outbreak. C_LIO_LIWe found plausible associations between staff and patient cases. C_LI