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

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 large-scale 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 SARS-CoV-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 large-scale 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.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study

“…We identified one episode of likely transmission of SARS-CoV-2 from one resident to another, but there were no documented transmissions from residents to employees. Our findings are consistent with previous studies that identified nursing home employees as a primary source of transmission of SARS-CoV-2 to co-workers and residents [ 3 , 6 , 7 , 9 ]. Healthcare employees in hospital and outpatient settings have also been implicated as a frequent source of transmission to co-workers [ 14 ].…”

“…Preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in nursing home residents is a priority because factors such as age, frailty, and comorbid illnesses place them at high risk for adverse outcomes [2]. Pre-symptomatic and asymptomatic individuals may contribute substantially to transmission in long-term care facilities [3][4][5][6][7][8]. Therefore, in addition to other control measures, serial testing of asymptomatic employees and residents has been recommended in outbreak settings [9].…”

“…Whole genome sequencing is a valuable tool that can complement contact tracing investigations of suspected transmission events [14]. However, the use of whole genome sequencing has been reported in relatively few investigations of SARS-CoV-2 transmission in nursing homes, and most were conducted during early stages of the pandemic [3,[6][7][8][9]. In these previous studies, sequencing provided evidence of SARS-CoV-2 transmission from employees and visitors in nursing homes to residents [3,[6][7][8][9].…”

“…However, the use of whole genome sequencing has been reported in relatively few investigations of SARS-CoV-2 transmission in nursing homes, and most were conducted during early stages of the pandemic [3,[6][7][8][9]. In these previous studies, sequencing provided evidence of SARS-CoV-2 transmission from employees and visitors in nursing homes to residents [3,[6][7][8][9]. Additional investigations that include sequencing are needed to examine current routes of transmission in nursing homes, including the potential for nursing home residents to transmit SARS-CoV-2 to other residents or staff.…”