Genomic epidemiology and transmission dynamics of SARS-CoV-2 in congregate healthcare facilities in Santa Clara County, California.

BACKGROUND: Outbreaks of SARS-CoV-2 in long term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between by combining genomic sequencing with epidemiologic investigations enables targeting infection control interventions.

METHODS: We conducted weekly surveillance of residents and staff in LTCFs in Santa Clara County, CA with at least one confirmed COVID-19 case between March and July 2020. Positive samples were referred for whole genome sequencing. Epidemiological investigations and phylogenetic analyses of the largest outbreaks (>30 cases) were carried out in six LTCFs (Facilities A through F).

RESULTS: Among the 61 LTCFs in the county, 41 had at least one confirmed case during the study period, triggering weekly SARS-CoV-2 testing. The six largest outbreaks accounted for 60% of cases and 90% of deaths in LTCFs, though the bed capacity of these facilities represents only 11% of the LTCF beds in the county. Phylogenetic analysis of 196 whole genome sequences recovered from those facilities showed that each outbreak was monophyletic, with staff and residents sharing a common viral lineage. Outbreak investigations revealed that infected staff members often worked at multiple facilities, and in one instance, a staff member infected while working in one facility was the likely index case in another.

CONCLUSIONS: We detected a pattern of rapid and sustained transmission after a single introduction of SARS-CoV-2 in six large LTCF outbreaks, with staff playing a key role in transmission within and between facilities. Infection control, testing, and occupational policies to reduce exposure and transmission risk for staff are essential components to keeping facility residents safe.