SARS‑CoV‑2 entry into and evolution within a skilled nursing facility

Authors

• Nicole R. Sexton, Colorado State University, University of Nebraska-LincolnFollow
• Parker Parker Cline, Colorado State University
• Emily N. Gallichotte, Colorado State University
• Emily Fitzmeyer, Colorado State University
• Michael C. Young, Colorado State University
• Ashley J. Janich, Colorado State University
• Kristy L. Pabilonia, Colorado State University
• Nicole Ehrhart, Colorado State University
• Gregory D. Ebel, Colorado State University

Document Type

Article

Date of this Version

7-19-2023

Citation

Scientific Reports | (2023) 13:11657 | https://doi.org/10.1038/s41598-023-38544-5

Comments

Open access.

Abstract

SARS-CoV-2 belongs to the family Coronaviridae which includes multiple human pathogens that have an outsized impact on aging populations. As a novel human pathogen, SARS-CoV-2 is undergoing continuous adaptation to this new host species and there is evidence of this throughout the scientific and public literature. However, most investigations of SARS-CoV-2 evolution have focused on largescale collections of data across diverse populations and/or living environments. Here we investigate SARS-CoV-2 evolution in epidemiologically linked individuals within a single outbreak at a skilled nursing facility beginning with initial introduction of the pathogen. The data demonstrate that SARSCoV- 2 was introduced to the facility multiple times without establishing an interfacility transmission chain, followed by a single introduction that infected many individuals within a week. This largescale introduction by a single genotype then persisted in the facility. SARS-CoV-2 sequences were investigated at both the consensus and intra-host variation levels. Understanding the variability in SARS-CoV-2 during transmission chains will assist in understanding the spread of this disease and can ultimately inform best practices for mitigation strategies.