ABSTRACT
Background. In Washington State, COVID-19 cases in long-term care facilities (LTCF) have accounted for less than 3% of all cases, yet 30% of all COVID-19 deaths. Understanding transmission patterns and outbreak epidemiology informs outbreak management. From April to October 2021, two large LTCFs experienced COVID-19 outbreaks. Whole genome sequencing and phylogenetic analysis were leveraged to explore transmission patterns and complement outbreak epidemiology. Methods. Epidemiologic data was exported from the Washington Disease Reporting System. Sequences, retrieved from GISAID, were aligned to the Wuhan-1 reference genome using Nextalign version 1.11.0. Pairwise single nucleotide polymorphism (SNP) distance matrices were calculated using SNP-Dists version 0.8.2. Phylogenetic trees for each outbreak were generated using IQ-Tree multicore version 2.2.0-beta COVID-edition using the GTR+F+G4 nucleotide substitution model with 1000 bootstrap replicates. MicrobeTrace was used to visualize the phylogeny, SNP heatmap, and identify clusters among sequences. Results. Weekly, LTCF A tested 162 residents and 800 staff, and LTCF B tested 60 residents and 144 staff. Of all cases in LTCF A (n= 119), 23% (n =27) were residents and 77% (n = 92) were staff, compared to 78% (n =28) residents and 22% (n =7) staff among total LTCF B cases (n=36). In LTCF A, 34% (n=40) of the cases had highquality sequences available. Seven clusters of two or more genetically related sequences and thirteen genetically unrelated sequences were identified. Five of the clusters involved resident and staff cases, linked by unit. Two clusters and remaining unrelated sequences were among staff. In LTCF B, 40% (n=14) of the cases had high-quality sequences available. One cluster of genetically related sequences was identified, all from residents of two floors. The SNP differences between sequences from LTCF A ranged from 0 to 70, whereas SNP differences between LTCF B sequences ranged from 0 to 6. Conclusion. Phylogenetic analysis of the two outbreaks confirms differences in disease transmission patterns. Multiple independent introductions of SARS-CoV-2 were identified in LTCF A, compared to a single introduction in LTCF B. Genomic epidemiology is a valuable resource for outbreak investigation and management.
ABSTRACT
Background. Large social gatherings during the COVID-19 pandemic have been linked to extensive community transmission. Healthcare workers (HCW) that engage in these social gatherings pose a risk to the vulnerable patients they serve. Public Health-Seattle & King County identified a COVID-19 outbreak associated with a wedding in July 2020 when the 14-day incidence rate was 105 cases per 100,000 residents. HCW who attended the wedding were subsequently linked to 45 outbreaks in healthcare settings across three counties in the next month. Methods. COVID-19 case interview data was used to identify HCW cases who reported the wedding as their exposure event. The Washington Disease Reporting System (WDRS), the state database in which COVID-19 cases and epi-linkages are tracked, was queried to identify healthcare outbreaks linked to the HCW wedding-attendee cases and the HCW that they infected. NodeXL was used to visualize the resulting chains of wedding-associated healthcare transmission using a Harel-Koren Fast Multiscale layout where the network visualization's directed arrows represent putative links and direction of transmission. Numbers of associated settings, cases, and deaths were calculated. Results. Seven HCW wedding attendees were linked to outbreaks in healthcare facilities that they worked at while infectious;HCWs linked to as many as six subsequent healthcare outbreaks. In total, the wedding was connected to 45 healthcare facilities: adult family homes (N=1), hospitals (N=1), supported living agencies (N=7) and associated group homes (N=38), assisted living (N=1), home health services (N=1), behavioral health (N=2), and rehab centers (N=1). Across the settings, 277 cases were identified, including 15 deaths. Conclusion. A series of COVID-19 healthcare outbreaks was traced back to a wedding. Cases worked in multiple homes, agencies, and other healthcare settings which likely facilitated rapid and wide transmission;the structure of these healthcare settings often do not facilitate a single job providing enough hours and income to support an individual. In terms of public health learnings, addressing these outbreaks require effective contact tracing, multijurisdictional coordination, and for supported living, interventions need to be applied across households sharing staff.