Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona

Abstract

Individuals living in congregate settings, including those in group homes, have been disproportionately impacted by COVID-19 and may be at increased risk of exposure or infection due to underlying illness. In mid-May 2020, local public health officials responded to an outbreak of COVID-19 among staff and residents associated with a multi-residential group home that provides care for adults with intellectual and developmental disabilities. Samples were collected at 16 of the homes. In four of the homes all the residents tested positive, and in the remaining 12 houses where samples were collected, all residents tested negative. Of the 152 individuals tested, 15/58 (25.9%) residents and 27/94 (28.7%) staff were positive for SARS-CoV-2, including eight hospitalizations and four deaths. Phylogenetic analysis of genomes from this outbreak in the context of genomes from Northern Arizona shows that very few mutations separate the samples from this outbreak. A potential transmission network was developed to illustrate person-place epidemiologic linkages and further demonstrates the dynamic connections between staff and residents with respect to each group home location. Epidemiologic and genomic evidence correlate, and suggest that asymptomatic infected staff likely introduced and spread COVID-19 in this setting. Implementation of public health prevention measures alongside rapid genomic analysis can help guide policy development and guide management efforts to prevent and mitigate future outbreaks.

HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations

“…MicrobeTrace was originally developed as a browser-based web application for secure, local HIV surveillance data analysis for cluster detection and outbreak response [40]. Its use has expanded for the study of other pathogen outbreaks [38,[46][47][48][49]. During the 2022-2023 global mpox outbreak, the MicrobeTrace team at the CDC built a local Nextstrain [65] and MicrobeTrace pipeline for continued US mpox genomic surveillance and to support secure cluster analysis of HIV-mpox coinfections [66].…”

“…MicrobeTrace is a secure web browser tool developed at the CDC [38] that remains operational without an internet connection and facilitates data integration and analysis with a suite of customizable views, including networks, phylogenetic trees, world maps, tables and charts that could be tailored as a dashboard view for real-time data analytics and reporting. MicrobeTrace has been widely used to integrate, visualize and analyze data from several pathogens, including HIV [39][40][41][42][43], hepatitis [44,45], tuberculosis [46] and SARS-CoV-2 [47][48][49]. We describe the expansion of MicrobeTrace as a pathogen-specific tool for genomic surveillance and variant classification.…”

Incidence, Hospitalization, Mortality and Risk Factors of COVID-19 in Long-Term Care Residential Homes for Patients with Chronic Mental Illness

“…Private ownership as a risk factor is indicated in studies of long-term care homes considering the high occupancy, the inadequate facilities, and regarding older design standards than the public ownership centers [31,32]. The COVID-19 incidence in the staff have been found to be associated with COVID-19 outbreaks in these centers [33,34]. The severe disability was found in nursing homes, and it is well known risk factor [35][36][37].…”