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

Masoli, J.; Jeffries, A.; Temperton, B.; Auckland, C.; Michelsen, M.; Warwick-Dugdale, J.; Manley, R.; Farbos, A.; Ellard, S.; Knight, B.; Bewshea, C.; Sambles, C.; Harrison, J. W.; Bunce, B.; Carr, A.; Hattersley, A. T.; Michell, S. L.; Studholme, D.

Background Whole-genome sequencing has been used successfully 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. Methods Following multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests. Findings Thirty 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. Interpretation This 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.