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.