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

ABSTRACT:

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.

SUBMITTER: MacCannell T 

PROVIDER: S-EPMC8385848 | biostudies-literature |

REPOSITORIES: biostudies-literature