Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (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 facilities 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, California, with ≥1 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 6 LTCFs (Facilities A through F).

Results: Among the 61 LTCFs in the county, 41 had ≥1 confirmed case during the study period, triggering weekly SARS-CoV-2 testing. The 6 largest outbreaks accounted for 60% of cases and 90% of deaths in LTCFs, although 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 1 instance, a staff member infected while working in 1 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 6 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.

Keywords: elderly; epidemiology; genomics; healthcare; providers.

Figure 1.

Six major SARS-CoV-2 outbreaks in congregate senior healthcare facilities in Santa Clara County are monophyletic. Shown is a maximum-likelihood phylogenetic tree built from 706 viral genomes from Santa Clara County samples collected between February and July 2020. Resident and staff samples from each facility are drawn as dots colored by the facility at which the individual was tested or worked (n = 196). Dashed boxes contain all nodes descended from the index genotype of each facility, defined as the common ancestor of all genotypes sampled from residents at that facility (incoming branches are labeled with the defining SNV). NextStrain clades are labeled 19A–20C. All staff and resident genomes from each facility descend from the index genotype, consistent with a single introduction. Gray nodes (n = 16) indicate contextual samples which are also descended from facility index genotypes, representing potential onward transmission. Abbreviations: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SNV, single nucleotide variant.

Figure 2.

Genetic linkages between residents and staff within each facility. Insets of the tree in Figure 1 showing staff and residents from Facilities A (A) and B (B) together with samples from elsewhere descended from the index genotype. Instances where clusters of staff and residents share additional mutations beyond the index genotype of each outbreak indicate repeated transmission between those groups, and instances where external samples also share those mutations indicate likely onward transmission from the facility back into the community. Red boxes indicate clusters with epidemiological relationships discussed in the text. Abbreviation: SNF, skilled-nursing facility.

Figure 3.

Shared staff seed outbreak. The index case of the outbreak at Facility F (red arrow) was a staff member also working at Facility E. The genomic diversity of Facility F is nested entirely inside that of Facility E. Red asterisks indicate 2 additional CNAs who worked at both facilities and share a household. Abbreviation: CNA, certified nursing assistant.